| Abeliophyllum distichum | Chloroplast | 1 | ndhD | 1 |
| Abelmoschus esculentus | Chloroplast | 1 | ndhD | 1 |
| Abies sibirica | Chloroplast | 2 | psbZ, trnI-CAU | 3 |
| Acacia dealbata | Chloroplast | 2 | ndhD, psbL | 3 |
| Acacia ligulata | Chloroplast | 2 | ndhD, psbL | 3 |
| Acnistus arborescens | Chloroplast | 2 | ndhD, psbL | 2 |
| Acnistus arborescens x Iochroma cyaneum | Chloroplast | 4 | clpP, ndhD, petB, psbL | 5 |
| Acoelorraphe wrightii | Plastid | 3 | ndhD, rpl2, rps19 | 7 |
| Aconitum austrokoreense | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Aconitum carmichaelii | Chloroplast | 1 | rpl2 | 4 |
| Aconitum chiisanense | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Aconitum ciliare | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Aconitum coreanum | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Aconitum kusnezoffii | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Aconitum longecassidatum | Chloroplast | 3 | ndhB, ndhD, rpl2 | 6 |
| Aconitum monanthum | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Aconitum pseudolaeve | Chloroplast | 3 | ndhB, ndhD, rpl2 | 6 |
| Acorus americanus | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Acorus gramineus | Plastid | 2 | ndhD, rpl2 | 5 |
| Actinidia arguta | Chloroplast | 1 | ndhD | 1 |
| Actinidia chinensis | Chloroplast | 1 | ndhD | 1 |
| Actinidia deliciosa | Chloroplast | 1 | ndhD | 1 |
| Actinidia eriantha | Chloroplast | 1 | ndhD | 1 |
| Actinidia kolomikta | Chloroplast | 1 | ndhD | 1 |
| Actinidia polygama | Chloroplast | 1 | ndhD | 1 |
| Actinidia tetramera | Chloroplast | 1 | ndhD | 1 |
| Adenanthera microsperma | Chloroplast | 2 | ndhD, psbL | 2 |
| Adenolobus garipensis | Chloroplast | 2 | ndhD, psbL | 2 |
| Adenophora divaricata | Chloroplast | 1 | psbL | 1 |
| Adenophora erecta | Chloroplast | 1 | psbL | 1 |
| Adenophora remotiflora | Chloroplast | 1 | psbL | 1 |
| Adenophora stricta | Chloroplast | 2 | ndhD, psbL | 2 |
| Adiantum capillus-veneris | Chloroplast | 56 | accD, atpA, atpB, atpE, atpF, atpH, atpI, ccsA, cemA, chlB, chlL, chlN, clpP, infA, ndhA, ndhB, ndhC, ndhD, ndhF, ndhG, ndhH, ndhJ, ndhK, petA, petB, petD, petN, psaA, psaB, psbB, psbE, psbF, psbJ, psbL, psbM, psbT, rpl14, rpl2, rpl20, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3 | 71 |
| Adinandra angustifolia | Plastid | 1 | ndhD | 1 |
| Adinandra millettii | Plastid | 1 | ndhD | 1 |
| Adoxa moschatellina | Chloroplast | 1 | ndhD | 1 |
| Aegilops speltoides | Chloroplast | 1 | rpl2 | 4 |
| Aegilops tauschii subsp. tauschii | Chloroplast | 1 | rpl2 | 2 |
| Aethionema cordifolium | Chloroplast | 1 | ndhD | 1 |
| Aethionema grandiflorum | Chloroplast | 1 | ndhD | 1 |
| Agapanthus coddii | Chloroplast | 1 | rpl2 | 4 |
| Agathis dammara | Chloroplast | 1 | trnR | 1 |
| Agave americana | Chloroplast | 1 | rpl2 | 4 |
| Agave attenuata | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Agrostemma githago | Chloroplast | 1 | ndhD | 1 |
| Agrostis stolonifera | Chloroplast | 1 | rpl2 | 4 |
| Ajuga reptans | Mitochondrion
Plastid | 3 | nad4L, ndhD, rps12 | 6 |
| Akebia quinata | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Akebia trifoliata | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Albizia odoratissima | Chloroplast | 1 | ndhD | 2 |
| Albuca kirkii | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Aletris fauriei | Chloroplast | 1 | rpl2 | 2 |
| Aletris spicata | Chloroplast | 1 | rpl2 | 4 |
| Allium cepa | Mitochondrion | 2 | nad1, nad4L | 6 |
| Alloeochaete namuliensis | Chloroplast | 2 | psbC, rpl2 | 5 |
| Alloeochaete oreogena | Chloroplast | 2 | psbC, rpl2 | 5 |
| Alloeochaete uluguruensis | Chloroplast | 2 | psbC, rpl2 | 5 |
| Allomaieta villosa | Chloroplast | 1 | ndhD | 1 |
| Allosyncarpia ternata | Chloroplast | 1 | ndhD | 1 |
| Alniphyllum eberhardtii | Plastid | 1 | ndhD | 1 |
| Aloe maculata | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Aloe vera | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Alsophila spinulosa | Chloroplast | 44 | accD, atpA, atpH, atpI, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhE, ndhF, ndhG, ndhH, petA, petB, petD, petN, psaB, psbE, psbM, psbN, rpl2, rpl20, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3 | 54 |
| Amana anhuiensis | Chloroplast | 1 | rpl2 | 2 |
| Amana edulis | Chloroplast | 1 | rpl2 | 2 |
| Amana erythronioides | Chloroplast | 1 | rpl2 | 2 |
| Amana kuocangshanica | Chloroplast | 1 | rpl2 | 2 |
| Amborella trichopoda | Chloroplast | 3 | ndhD, psbL, rpl2 | 6 |
| Ambrosia artemisiifolia | Chloroplast | 2 | ndhD, psbL | 2 |
| Ammophila breviligulata | Plastid | 1 | rpl2 | 4 |
| Ammopiptanthus mongolicus | Chloroplast | 2 | ndhD, psbL | 2 |
| Ammopiptanthus nanus | Chloroplast | 2 | ndhD, psbL | 2 |
| Ampelocalamus calcareus | Plastid | 1 | rpl2 | 4 |
| Ampelodesmos mauritanicus | Plastid | 1 | rpl2 | 4 |
| Ampelopteris prolifera | Chloroplast | 59 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbL, psbM, rpl14, rpl16, rpl2, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps16, rps18, rps19, rps2, rps3, rps4, rps7, ycf1, ycf2, ycf3 | 141 |
| Amphicarpum muhlenbergianum | Chloroplast | 1 | rpl2 | 4 |
| Amphipogon caricinus | Chloroplast | 2 | psbC, rpl2 | 5 |
| Amphipogon turbinatus | Chloroplast | 2 | psbC, rpl2 | 5 |
| Anacardium occidentale | Chloroplast | 1 | ndhD | 1 |
| Ananas comosus | Chloroplast | 1 | rpl2 | 4 |
| Anaphalis sinica | Chloroplast | 1 | ndhD | 1 |
| Andropogon abyssinicus | Chloroplast | 2 | rpl2, rps19 | 6 |
| Andropogon burmanicus | Chloroplast | 2 | rpl2, rps19 | 6 |
| Andropogon chinensis | Chloroplast | 2 | rpl2, rps19 | 5 |
| Andropogon distachyos | Chloroplast | 2 | rpl2, rps19 | 6 |
| Andropogon fastigiatus | Chloroplast | 1 | rpl2 | 4 |
| Anemarrhena asphodeloides | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Aneura pinguis | Mitochondrion | 1 | trnI | 1 |
| Angelica acutiloba | Chloroplast | 1 | ndhD | 1 |
| Angelica dahurica | Chloroplast | 1 | ndhD | 1 |
| Angelica gigas | Chloroplast | 1 | ndhD | 1 |
| Angophora costata | Chloroplast | 1 | ndhD | 1 |
| Angophora floribunda | Chloroplast | 1 | ndhD | 1 |
| Anneslea fragrans | Plastid | 1 | ndhD | 1 |
| Annona cherimola | Plastid | 3 | ndhD, psbL, rpl2 | 7 |
| Anomochloa marantoidea | Chloroplast | 1 | rpl2 | 2 |
| Anomodon attenuatus | Mitochondrion | 5 | atp1, ccmFN, cox3, tatC, trnI | 6 |
| Anomodon rugelii | Mitochondrion | 6 | atp1, ccmC, ccmFN, cox3, tatC, trnI | 7 |
| Anthericum ramosum | Chloroplast | 1 | rpl2 | 4 |
| Anthoceros angustus | Chloroplast | 78 | accD, atpA, atpB, atpE, atpF, atpH, atpI, ccsA, cemA, chlB, chlL, chlN, clpP, cysA, cysT, infA, ndhA, ndhB, ndhC, ndhD, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK, Novel, ORF1031, ORF473, ORF51, petA, petB, petD, petG, petL, psaA, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbJ, psbK, psbM, psbT, rbcL, rpl14, rpl16, rpl2, rpl20, rpl21, rpl22, rpl23, rpl32, rpl33, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps12, rps14, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, trnK, ycf2, ycf3, ycf4 | 1018 |
| Anthoxanthum nitens | Plastid | 1 | rpl2 | 4 |
| Anthoxanthum odoratum | Plastid | 1 | rpl2 | 4 |
| Aphyllanthes monspeliensis | Chloroplast | 1 | rpl2 | 4 |
| Apluda mutica | Plastid | 1 | rpl2 | 4 |
| Apopellia endiviifolia | Chloroplast | 25 | atpB, atpF, atpH, atpI, ccsA, clpP, ndhB, ndhD, ndhE, ndhF, ndhG, ndhK, petA, petB, petG, petL, petN, psaB, psbB, psbC, psbM, rpl23, rpoB, rpoC2, ycf3 | 55 |
| Apostasia odorata | Chloroplast | 1 | matK | 1 |
| Apterosperma oblata | Plastid | 1 | ndhD | 1 |
| Arabidopsis halleri | Chloroplast | 1 | ndhD | 1 |
| Arabidopsis lyrata | Chloroplast | 1 | ndhD | 1 |
| Arabidopsis lyrata subsp. lyrata MN47 | Chloroplast | 19 | accD, atpF, clpP, matK, ndhB, ndhD, ndhF, ndhG, Novel, petL, psbE, psbF, psbJ, psbZ, rpoA, rpoB, rpoC1, rps14, rps16 | 37 |
| Arabidopsis thaliana | Chloroplast
Mitochondrion | 49 | accD, ArthMp062, ArthMp086, ArthMp087, ArthMp104, atp1, atp6, atp9, atpF, ccb203, ccb206, ccb256, ccb382, ccb452, clpP, cob, cox2, cox3, matK, matR, nad1, nad2, nad4, nad4L, nad5, nad6, nad7, nad9, ndhB, ndhD, ndhF, ndhG, orf25, orfX, petL, psbE, psbF, psbZ, rpl16, rpl2, rpl23, rpl5, rpoA, rpoB, rpoC1, rps12, rps14, rps3, rps4 | 1020 |
| Arabis hirsuta JO23 | Chloroplast | 1 | ndhD | 1 |
| Archibaccharis asperifolia | Chloroplast | 2 | ndhD, psbL | 2 |
| Archidendron lucyi | Chloroplast | 2 | ndhD, psbL | 3 |
| Areca vestiaria | Plastid | 2 | ndhD, rpl2 | 3 |
| Arenga caudata | Plastid | 3 | ndhD, rpl2, rps19 | 7 |
| Aristida purpurea | Plastid | 1 | rpl2 | 4 |
| Aristida rufescens | Chloroplast | 1 | rpl2 | 4 |
| Artemisia annua | Plastid | 1 | psbL | 1 |
| Artemisia argyi | Chloroplast | 2 | ndhD, psbL | 2 |
| Artemisia capillaris | Chloroplast | 2 | ndhD, psbL | 2 |
| Artemisia frigida | Chloroplast | 2 | ndhD, psbL | 2 |
| Artemisia gmelinii | Chloroplast | 2 | ndhD, psbL | 2 |
| Artemisia montana | Chloroplast | 2 | ndhD, psbL | 2 |
| Arthraxon hispidus | Chloroplast | 2 | rpl2, rps19 | 6 |
| Arthraxon lanceolatus | Chloroplast | 2 | rpl2, rps19 | 5 |
| Arthraxon microphyllus | Chloroplast | 2 | rpl2, rps19 | 6 |
| Arthraxon prionodes | Chloroplast | 1 | rpl2 | 4 |
| Arundinaria appalachiana | Chloroplast | 1 | rpl2 | 4 |
| Arundinaria fargesii | Chloroplast | 1 | rpl2 | 4 |
| Arundinaria gigantea | Chloroplast | 1 | rpl2 | 4 |
| Arundinaria tecta | Chloroplast | 1 | rpl2 | 4 |
| Arundinella deppeana | Chloroplast | 1 | rpl2 | 4 |
| Asclepias nivea | Chloroplast | 1 | ndhD | 1 |
| Asclepias syriaca | Chloroplast
Mitochondrion | 33 | atp1, atp4, atp9, ccmB, ccmC, ccmFc, ccmFN, cob, cox1, cox2, cox3, matR, mttB, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, ndhD, rpl10, rpl5, rps10, rps12, rps13, rps19, rps3, rps4, rps7, sdh3, sdh4 | 114 |
| Asparagus officinalis | Chloroplast | 1 | rpl2 | 4 |
| Asparagus schoberioides | Chloroplast | 1 | rpl2 | 4 |
| Asplenium pekinense | Chloroplast | 57 | accD, atpA, atpB, atpF, atpH, atpI, cemA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbM, rpl14, rpl2, rpl20, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, ycf1, ycf2, ycf3 | 131 |
| Asplenium prolongatum | Chloroplast | 58 | accD, atpA, atpB, atpF, atpH, atpI, cemA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbL, psbM, rpl14, rpl16, rpl2, rpl22, rpl23, rpoA, rpoB, rpoC1, rpoC2, rps11, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, ycf1, ycf2, ycf3, ycf4 | 130 |
| Aster altaicus | Chloroplast | 2 | ndhD, psbL | 2 |
| Aster spathulifolius | Chloroplast | 2 | ndhD, psbL | 2 |
| Astrebla pectinata | Plastid | 1 | rpl2 | 4 |
| Athyrium anisopterum | Chloroplast | 50 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhC, ndhF, ndhG, petA, petB, petN, psaB, psbB, psbC, psbD, psbE, psbH, psbI, psbM, rpl14, rpl16, rpl2, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps14, rps15, rps16, rps18, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3 | 130 |
| Athyrium opacum | Chloroplast | 62 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbE, psbF, psbH, psbI, psbM, psbT, rpl14, rpl16, rpl2, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3, ycf4 | 139 |
| Athyrium sheareri | Chloroplast | 64 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbM, psbT, rpl14, rpl16, rpl2, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps12, rps14, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3 | 144 |
| Athyrium sinense | Chloroplast | 63 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbM, rpl14, rpl16, rpl2, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps12, rps14, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3 | 146 |
| Atrichum angustatum | Mitochondrion | 3 | atp9, tatC, trnI | 3 |
| Atropa belladonna Ab5p(kan) | Chloroplast | 2 | ndhD, psbL | 4 |
| Austroblechnum melanocaulon | Chloroplast | 64 | accD, atpA, atpB, atpF, atpH, atpI, chlB, chlL, chlN, infA, matK, ndhA, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, petA, petB, petD, petG, petN, psaA, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbL, psbM, psbT, pseudo-ndhB, rpl14, rpl16, rpl2, rpl20, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3, ycf4 | 137 |
| Avena sativa | Plastid | 1 | rpl2 | 4 |
| Avena sterilis | Chloroplast | 1 | rpl2 | 4 |
| Averrhoa carambola | Chloroplast | 3 | ndhD, psbL, trnI-CAU | 4 |
| Axonopus fissifolius | Chloroplast | 1 | rpl2 | 4 |
| Axonopus ramosus | Chloroplast | 1 | rpl2 | 4 |
| Aztecaster matudae | Chloroplast | 2 | ndhD, psbL | 2 |
| Baccharis genistelloides | Chloroplast | 2 | ndhD, psbL | 2 |
| Baccharis tricuneata | Chloroplast | 2 | ndhD, psbL | 2 |
| Bambusa arnhemica | Plastid | 1 | rpl2 | 4 |
| Bambusa bambos | Plastid | 1 | rpl2 | 4 |
| Bambusa oldhamii | Chloroplast | 2 | BaolC_p061, BaolC_p081 | 4 |
| Barbarea verna | Chloroplast | 1 | ndhD | 1 |
| Barclaya longifolia | Chloroplast | 1 | psbL | 1 |
| Barnardia japonica | Chloroplast | 1 | rpl2 | 4 |
| Barringtonia fusicarpa | Plastid | 1 | ndhD | 1 |
| Barringtonia racemosa | Plastid | 1 | ndhD | 1 |
| Barthea barthei | Chloroplast | 1 | ndhD | 1 |
| Bartramia pomiformis | Mitochondrion | 2 | tatC, trnI | 2 |
| Batis maritima | Mitochondrion | 7 | atp6, atp9, ccmC, ccmFC, nad1, rps10, sdh4 | 13 |
| Baxteria australis | Plastid | 1 | rpl2 | 4 |
| Berberis amurensis | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Berberis koreana | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Bergenia scopulosa | Chloroplast | 1 | ndhD | 1 |
| Bertolonia acuminata | Chloroplast | 1 | ndhD | 1 |
| Beschorneria septentrionalis | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Beta macrocarpa | Mitochondrion | 27 | atp1, atp6, atp8, atp9, ccmB, ccmFC, ccmFN, cob, cox2, cox3, mat-r, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, nad9, Novel, rpl5, rps12, rps13, rps3, rps4, rps7 | 293 |
| Beta vulgaris subsp. maritima | Mitochondrion | 27 | atp1, atp6, atp8, atp9, ccmB, ccmFC, ccmFN, cob, cox2, cox3, mat-r, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, nad9, orf25, rpl5, rps12, rps13, rps3, rps4, rps7 | 303 |
| Beta vulgaris subsp. vulgaris | Mitochondrion | 40 | atp1, atp6, atp8, atp9, ccb206, ccb438, ccb577, cob, cox2, cox3, mat-r, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, nad9, Novel, orf112a, orf115b, orf116, orf117, orf155b, orf189, orf25, orf288, orf290, orf300, orf399, orf518, orfX, rpl5, rps12, rps13, rps3, rps4, rps7 | 363 |
| Bismarckia nobilis | Plastid | 1 | rpl2 | 4 |
| Blakea schlimii | Chloroplast | 1 | ndhD | 1 |
| Blakiella bartsiifolia | Chloroplast | 2 | ndhD, psbL | 2 |
| Bomarea edulis | Plastid | 2 | ndhD, rpl2 | 5 |
| Borassodendron machadonis | Plastid | 3 | ndhD, rpl2, rps19 | 7 |
| Bothriochloa alta | Chloroplast | 1 | rpl2 | 4 |
| Botryococcus braunii | Chloroplast | 1 | trnI | 1 |
| Boulardia latisquama | Plastid | 2 | rps15, rps2 | 2 |
| Bouteloua curtipendula | Plastid | 1 | rpl2 | 4 |
| Bouteloua gracilis | Plastid | 1 | rpl2 | 4 |
| Bowenia serrulata | Chloroplast | 4 | petL, psbZ, rps8, trnI | 4 |
| Brachiaria fragrans | Chloroplast | 1 | rpl2 | 4 |
| Brachyelytrum aristosum | Plastid | 1 | rpl2 | 4 |
| Brachypodium distachyon | Chloroplast | 2 | ndhB, rpl2 | 6 |
| Brachythecium rivulare | Mitochondrion | 5 | atp1, ccmC, ccmFN, tatC, trnI | 5 |
| Bracteacoccus giganteus | Chloroplast | 1 | trnI | 1 |
| Brahea brandegeei | Plastid | 3 | ndhD, rpl2, rps19 | 7 |
| Brasenia schreberi | Chloroplast | 2 | ndhD, psbL | 2 |
| Brassica carinata | Mitochondrion | 4 | ccmFN2, matR, nad1, tatC | 8 |
| Brassica juncea | Mitochondrion | 4 | CcmFN2, matR, nad1, tatC | 8 |
| Brassica napus | Mitochondrion | 33 | atp1, atp6, atp9, ccmB, ccmC, ccmFC, ccmFN1, ccmFN2, cob, cox1, cox2-1, cox2-2, cox3, matR, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, nad9, orf25, orfB, orfX, rpl16, rpl2, rpl5, rps12, rps3, rps4, rps7 | 852 |
| Brassica nigra | Chloroplast
Mitochondrion | 2 | nad1, ndhD | 12 |
| Brassica oleracea var. oleracea | Mitochondrion | 4 | ccmFN2, matR, nad1, tatC | 8 |
| Brassica rapa subsp. oleifera | Mitochondrion | 4 | ccmFN2, matR, nad1, tatC | 8 |
| Brighamia insignis | Plastid | 1 | ndhD | 1 |
| Briza maxima | Plastid | 1 | rpl2 | 4 |
| Bromus vulgaris | Plastid | 1 | rpl2 | 4 |
| Broussonetia papyrifera | Plastid | 2 | psbL, trnI-CAU | 2 |
| Bruinsmia polysperma | Chloroplast | 1 | ndhD | 1 |
| Bucklandiella orthotrichacea | Mitochondrion | 1 | trnI | 1 |
| Buergersiochloa bambusoides | Plastid | 1 | rpl2 | 4 |
| Bupleurum falcatum | Chloroplast
Mitochondrion | 3 | nad1, ndhD, rps10 | 16 |
| Bupleurum latissimum | Chloroplast | 1 | ndhD | 1 |
| Burmannia championii | Chloroplast | 2 | rpl2, trnI-CAU | 6 |
| Burmannia coelestis | Chloroplast | 2 | rpl2, trnI-CAU | 6 |
| Burmannia cryptopetala | Chloroplast | 2 | rpl2, trnI-CAU | 4 |
| Burmannia disticha | Chloroplast | 2 | rpl2, trnI-CAU | 6 |
| Burmannia nepalensis | Chloroplast | 2 | rpl2, trnI-CAU | 4 |
| Burmannia oblonga | Chloroplast | 1 | trnI-CAU | 2 |
| Burmeistera auriculata | Chloroplast | 1 | ndhD | 1 |
| Burmeistera borjensis | Chloroplast | 1 | ndhD | 1 |
| Burmeistera ceratocarpa | Chloroplast | 1 | ndhD | 1 |
| Burmeistera crispiloba | Chloroplast | 1 | ndhD | 1 |
| Burmeistera cyclostigmata | Chloroplast | 1 | ndhD | 1 |
| Burmeistera cylindrocarpa | Chloroplast | 1 | ndhD | 1 |
| Burmeistera domingensis | Chloroplast | 1 | ndhD | 1 |
| Burmeistera fuscoapicata | Chloroplast | 1 | ndhD | 1 |
| Burmeistera loejtnantii | Chloroplast | 1 | ndhD | 1 |
| Burmeistera lutosa | Chloroplast | 1 | ndhD | 1 |
| Burmeistera oyacachensis | Chloroplast | 1 | ndhD | 1 |
| Burmeistera parviflora | Chloroplast | 1 | ndhD | 1 |
| Burmeistera pirrensis | Chloroplast | 1 | ndhD | 1 |
| Burmeistera resupinata | Chloroplast | 1 | ndhD | 1 |
| Burmeistera rubrosepala | Chloroplast | 1 | ndhD | 1 |
| Burmeistera smaragdi | Chloroplast | 1 | ndhD | 1 |
| Burmeistera sodiroana | Chloroplast | 1 | ndhD | 1 |
| Butomus umbellatus | Mitochondrion | 3 | ccmFc, nad1, nad4L | 8 |
| Buxbaumia aphylla | Mitochondrion | 3 | cox2, tatC, trnI | 4 |
| Buxus microphylla | Chloroplast | 2 | ndhD, psbL | 2 |
| Cabomba caroliniana | Chloroplast | 2 | ndhD, psbL | 2 |
| Calamus caryotoides | Plastid | 1 | rpl2 | 4 |
| Calanthe triplicata | Chloroplast | 1 | rpl2 | 2 |
| Callitropsis nootkatensis | Plastid | 1 | clpP | 1 |
| Callitropsis vietnamensis | Plastid | 1 | clpP | 1 |
| Calycanthus floridus var. glaucus | Chloroplast | 1 | psbL | 1 |
| Calypogeia arguta | Mitochondrion | 3 | nad2, rpl16, trnI | 4 |
| Calypogeia integristipula | Mitochondrion | 3 | nad2, rpl16, trnI | 4 |
| Calypogeia neogaea | Mitochondrion | 3 | nad2, rpl16, trnI | 4 |
| Calypogeia suecica | Mitochondrion | 3 | nad2, rpl16, trnI | 4 |
| Camassia scilloides | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Camellia crapnelliana | Chloroplast | 1 | ndhD | 1 |
| Camellia cuspidata | Chloroplast | 1 | ndhD | 1 |
| Camellia danzaiensis | Chloroplast | 1 | ndhD | 1 |
| Camellia elongata | Plastid | 1 | ndhD | 1 |
| Camellia impressinervis | Chloroplast | 1 | ndhD | 1 |
| Camellia mairei | Plastid | 1 | ndhD | 1 |
| Camellia oleifera | Plastid | 1 | ndhD | 1 |
| Camellia pitardii | Chloroplast | 1 | ndhD | 1 |
| Camellia sinensis | Chloroplast | 1 | ndhD | 1 |
| Camellia szechuanensis | Plastid | 1 | ndhD | 1 |
| Camellia taliensis | Chloroplast | 1 | ndhD | 1 |
| Camellia yunnanensis | Chloroplast | 1 | ndhD | 1 |
| Campanula punctata | Plastid | 1 | psbL | 1 |
| Campanula takesimana | Chloroplast | 1 | psbL | 1 |
| Camptotheca acuminata | Chloroplast | 1 | psbL | 1 |
| Campynema lineare | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Cannabis sativa | Chloroplast
Mitochondrion | 8 | nad1, nad5, psbL, rpl16, rps10, rps19, rps4, sdh4 | 34 |
| Capillipedium venustum | Chloroplast | 1 | rpl2 | 4 |
| Capsicum annuum | Chloroplast
Mitochondrion | 3 | ndhD, psbL, rps10 | 8 |
| Capsicum chacoense | Chloroplast | 2 | ndhD, psbL | 2 |
| Capsicum chinense | Chloroplast | 2 | ndhD, psbL | 2 |
| Capsicum eximium | Chloroplast | 2 | ndhD, psbL | 2 |
| Capsicum frutescens | Chloroplast | 2 | ndhD, psbL | 2 |
| Capsicum galapagoense | Chloroplast | 2 | ndhD, psbL | 2 |
| Capsicum lycianthoides | Chloroplast | 1 | psbL | 1 |
| Capsicum tovarii | Chloroplast | 2 | ndhD, psbL | 2 |
| Caragana korshinskii | Chloroplast | 1 | trnI-CAU | 1 |
| Caragana kozlowii | Chloroplast | 1 | trnI-CAU | 1 |
| Caragana microphylla | Chloroplast | 1 | trnI-CAU | 1 |
| Cardamine impatiens | Plastid | 1 | ndhD | 1 |
| Cardamine resedifolia | Plastid | 1 | ndhD | 1 |
| Carex neurocarpa | Chloroplast | 1 | trnI-CAU | 2 |
| Carica papaya | Mitochondrion | 8 | atp6, atp9, ccmFC, cox1, nad3, nad4L, rps1, rps10 | 9 |
| Carissa macrocarpa | Chloroplast | 2 | ndhD, trnI-CAU | 3 |
| Carludovica palmata | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Carnegiea gigantea | Chloroplast | 1 | psbL | 1 |
| Carteria cerasiformis | Chloroplast | 1 | trnI | 1 |
| Carthamus tinctorius | Chloroplast | 2 | ndhD, psbL | 2 |
| Caryota mitis | Plastid | 1 | rpl2 | 4 |
| Cassytha filiformis | Chloroplast | 2 | psbL, rpl2 | 3 |
| Castanea henryi | Chloroplast | 1 | ndhD | 1 |
| Castanea mollissima | Chloroplast | 1 | ndhD | 1 |
| Castilleja paramensis | Mitochondrion | 2 | rpl16, rps10 | 3 |
| Catapodium rigidum | Chloroplast | 1 | rpl2 | 4 |
| Cathaya argyrophylla | Chloroplast | 2 | petL, trnI | 4 |
| Cattleya crispata | Chloroplast | 1 | rpl2 | 2 |
| Cedrus deodara | Chloroplast | 1 | trnI | 2 |
| Cenchrus purpureus | Chloroplast | 1 | rpl2 | 4 |
| Centaurea diffusa | Chloroplast | 1 | psbL | 1 |
| Centotheca lappacea | Plastid | 1 | rpl2 | 4 |
| Centropodia glauca | Plastid | 1 | rpl2 | 4 |
| Centropogon nigricans | Chloroplast | 1 | ndhD | 1 |
| Cephalotaxus wilsoniana | Chloroplast | 1 | trnI | 3 |
| Ceratophyllum demersum | Chloroplast | 3 | ndhD, psbL, rpl2 | 6 |
| Ceratozamia hildae | Chloroplast | 4 | petL, psbZ, rps8, trnI | 4 |
| Cercis glabra | Chloroplast | 2 | ndhD, psbL | 2 |
| Chaetium bromoides | Chloroplast | 1 | rpl2 | 4 |
| Chamaerops humilis | Plastid | 3 | ndhD, rpl2, rps19 | 7 |
| Chamaetrichon basiliensis | Chloroplast | 1 | trnI | 1 |
| Champereia manillana | Plastid | 1 | psbL | 1 |
| Characiochloris acuminata | Chloroplast | 1 | trnI | 1 |
| Chasechloa egregia | Chloroplast | 1 | rpl2 | 4 |
| Chasechloa madagascariensis | Chloroplast | 1 | rpl2 | 4 |
| Chasmanthium laxum | Chloroplast | 2 | psbC, rpl2 | 5 |
| Chenopodium album | Chloroplast | 2 | ndhD, psbL | 2 |
| Chenopodium quinoa | Chloroplast | 2 | ndhD, psbL | 2 |
| Chikusichloa aquatica | Chloroplast | 1 | rpl2 | 4 |
| Chimonocalamus longiusculus | Chloroplast | 1 | rpl2 | 4 |
| Chionanthus retusus | Chloroplast | 1 | ndhD | 1 |
| Chionochloa macra | Plastid | 1 | rpl2 | 4 |
| Chloranthus spicatus | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Chloris barbata | Plastid | 1 | rpl2 | 4 |
| Chloris truncata | Chloroplast | 1 | rpl2 | 4 |
| Chloris virgata | Chloroplast | 1 | rpl2 | 4 |
| Chlorogalum pomeridianum | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Choricystis parasitica | Chloroplast | 1 | trnI | 1 |
| Christella appendiculata | Chloroplast | 52 | accD, atpA, atpF, atpH, atpI, ccsA, chlB, chlL, infA, matK, ndhB, ndhC, ndhE, ndhF, ndhG, ndhH, ndhI, Novel, petA, petB, petN, psaB, psbB, psbC, psbD, psbE, psbH, psbL, psbM, rpl14, rpl16, rpl2, rpl20, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3 | 134 |
| Chrysanthemum indicum | Chloroplast | 1 | psbL | 1 |
| Chrysanthemum x morifolium | Chloroplast | 1 | psbL | 1 |
| Chrysobalanus icaco | Chloroplast | 1 | ndhD | 1 |
| Chrysopogon gryllus | Chloroplast | 2 | rpl2, rps19 | 6 |
| Chrysopogon orientalis | Chloroplast | 2 | rpl2, rps19 | 6 |
| Chrysopogon serrulatus | Chloroplast | 1 | rpl2 | 4 |
| Chrysopogon zizanioides | Chloroplast | 2 | rpl2, rps19 | 6 |
| Chuniophoenix nana | Plastid | 1 | rpl2 | 4 |
| Chusquea liebmannii | Plastid | 1 | rpl2 | 4 |
| Chusquea spectabilis | Plastid | 1 | rpl2 | 4 |
| Cicer arietinum | Chloroplast | 4 | ndhB, ndhD, psbL, rps8 | 5 |
| Cinnamomum camphora | Chloroplast | 3 | ndhD, psbL, rpl2 | 4 |
| Cinnamomum micranthum | Chloroplast | 1 | ndhD | 1 |
| Cinnamomum verum | Chloroplast | 3 | ndhD, psbL, rpl2 | 4 |
| Circaeaster agrestis | Chloroplast | 1 | rpl2 | 4 |
| Cistanche phelypaea | Plastid | 1 | matK | 2 |
| Cistanthe longiscapa | Chloroplast | 1 | psbL | 1 |
| Citrullus lanatus | Mitochondrion | 37 | atp1, atp4, atp6, atp8, atp9, ccmB, ccmC, ccmFc, ccmFn, cob, cox1, cox2, cox3, matR, mttB, nad1, nad2, nad3, nad4, nad4L, nad5, nad7, nad9, Novel, rpl16, rpl2, rpl5, rps1, rps10, rps12, rps13, rps19-2, rps3, rps4, rps7, sdh3-1, sdh3-2 | 463 |
| Citrus aurantiifolia | Chloroplast | 1 | ndhD | 1 |
| Citrus depressa | Chloroplast | 1 | ndhD | 2 |
| Citrus platymamma | Chloroplast | 1 | ndhD | 1 |
| Clematis terniflora | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Climacium americanum | Mitochondrion | 4 | atp1, ccmFN, tatC, trnI | 4 |
| Closterium baillyanum | Chloroplast
Mitochondrion | 2 | trnI, trnR | 8 |
| Coccomyxa subellipsoidea C-169 | Mitochondrion | 1 | trnI | 1 |
| Cocos nucifera | Chloroplast
Mitochondrion | 29 | accD, atpA, atpB, atpF, atpI, clpP, matK, nad1, ndhA, ndhB, ndhD, ndhF, ndhG, ndhH, ndhK, petB, psaI, rpl2, rpl23, rpoA, rpoB, rpoC1, rpoC2, rps14, rps2, rps3, rps8, ycf3, ycf4 | 162 |
| Codonopsis minima | Chloroplast | 1 | psbL | 1 |
| Codriophorus aciculare | Mitochondrion | 1 | trnI | 1 |
| Codriophorus laevigatus | Mitochondrion | 1 | trnI | 1 |
| Codriophorus varius | Mitochondrion | 1 | trnI | 1 |
| Coelachne africana | Chloroplast | 2 | psbC, rpl2 | 5 |
| Coffea arabica | Chloroplast | 1 | ndhD | 1 |
| Coffea canephora | Chloroplast | 1 | ndhD | 1 |
| Coix lacryma-jobi | Chloroplast | 3 | rpl2, rps16, rps19 | 10 |
| Colchicum autumnale | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Coleataenia prionitis | Plastid | 1 | rpl2 | 4 |
| Coleochaete scutata | Chloroplast | 1 | trnI | 1 |
| Colobanthus quitensis | Chloroplast | 1 | trnI-CAU | 2 |
| Colocasia esculenta | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Colpothrinax cookii | Plastid | 1 | rpl2 | 4 |
| Conopholis americana | Plastid | 3 | matK, rpl20, rps18 | 3 |
| Conyza bonariensis | Chloroplast | 2 | ndhD, psbL | 2 |
| Corallorhiza bulbosa | Plastid | 1 | rpl2 | 4 |
| Corallorhiza macrantha | Plastid | 1 | rpl2 | 4 |
| Corallorhiza mertensiana | Plastid | 2 | cemA, rpl2 | 5 |
| Corallorhiza odontorhiza | Plastid | 2 | cemA, rpl2 | 5 |
| Corallorhiza trifida | Plastid | 1 | rpl2 | 4 |
| Corallorhiza wisteriana | Plastid | 2 | cemA, rpl2 | 5 |
| Cordyline indivisa | Chloroplast | 1 | rpl2 | 4 |
| Coreanomecon hylomeconoides | Chloroplast | 1 | rpl2 | 4 |
| Coriandrum sativum | Chloroplast | 1 | ndhD | 1 |
| Cortaderia selloana | Plastid | 1 | rpl2 | 4 |
| Corymbia eximia | Chloroplast | 1 | ndhD | 1 |
| Corymbia gummifera | Chloroplast | 1 | ndhD | 1 |
| Corymbia henryi | Chloroplast | 1 | ndhD | 1 |
| Corymbia maculata | Chloroplast | 1 | ndhD | 1 |
| Corymbia torelliana | Chloroplast | 1 | ndhD | 1 |
| Corynocarpus laevigatus | Chloroplast | 1 | psbL | 1 |
| Corypha lecomtei | Plastid | 2 | rpl2, rps19 | 5 |
| Cosmarium botrytis | Chloroplast | 1 | trnI | 1 |
| Couepia guianensis | Chloroplast | 1 | ndhD | 1 |
| Crinipes abyssinicus | Chloroplast | 2 | psbC, rpl2 | 5 |
| Crinipes longifolius | Chloroplast | 2 | psbC, rpl2 | 5 |
| Crucihimalaya wallichii JS5 | Chloroplast | 1 | ndhD | 1 |
| Cryptocarya chinensis | Chloroplast | 3 | ndhD, petL, psbL | 3 |
| Cucumis hystrix | Plastid | 1 | ndhD | 1 |
| Cucumis sativus | Mitochondrion | 10 | atp6, atp9, ccmFn, cox1, nad1, nad4L, rpl16, rps10, rps4, trnI-CAU | 16 |
| Cucurbita pepo | Mitochondrion | 37 | atp1, atp4, atp6, atp8, atp9, ccmB, ccmC, ccmFc, ccmFn, cob, cox1, cox2, cox3, matR, mttB, nad1, nad2, nad3, nad4, nad4L, nad5, nad7, nad9, rpl16, rpl2, rpl5, rps1, rps10, rps12, rps13, rps19-1, rps19-2, rps3, rps4, rps7, sdh3, sdh4 | 448 |
| Cupressus sempervirens | Plastid | 1 | clpP | 1 |
| Curcuma flaviflora | Chloroplast | 1 | rpoB | 1 |
| Curcuma roscoeana | Plastid | 1 | rpl2 | 4 |
| Cuscuta exaltata | Chloroplast | 2 | matK, psbL | 2 |
| Cuscuta gronovii | Chloroplast | 3 | psbL, rps14, rps2 | 4 |
| Cuscuta reflexa | Chloroplast | 9 | accD, atpF, petB, psbE, psbL, rpoB, rpoC1, rps14, rps2 | 15 |
| Cycas taitungensis | Chloroplast
Mitochondrion | 19 | atp1, atp4, atp6, atp8, atp9, ccmFC, cox1, matR, nad1, nad4, nad4L, nad6, petL, rpl2, rps10, rps11, rps12, rps7, sdh3 | 40 |
| Cylindrocystis brebissonii | Chloroplast | 1 | trnI | 1 |
| Cymbidium aloifolium | Chloroplast | 1 | rpl2 | 2 |
| Cymbidium faberi | Chloroplast | 1 | rpl2 | 2 |
| Cymbidium kanran | Chloroplast | 1 | rpl2 | 4 |
| Cymbidium lancifolium | Chloroplast | 1 | rpl2 | 4 |
| Cymbidium macrorhizon | Chloroplast | 1 | rpl2 | 4 |
| Cymbidium mannii | Chloroplast | 1 | rpl2 | 2 |
| Cymbidium sinense | Chloroplast | 1 | rpl2 | 2 |
| Cymbidium tortisepalum | Chloroplast | 1 | rpl2 | 2 |
| Cymbidium tracyanum | Chloroplast | 1 | rpl2 | 2 |
| Cymbopogon flexuosus | Chloroplast | 2 | rpl2, rps19 | 6 |
| Cynanchum wilfordii | Chloroplast | 1 | ndhD | 1 |
| Cynara baetica | Chloroplast | 3 | ndhD, ndhE, psbL | 3 |
| Cynara cornigera | Chloroplast | 3 | ndhD, ndhE, psbL | 3 |
| Cynara humilis | Chloroplast | 2 | ndhD, psbL | 2 |
| Cynodon dactylon | Chloroplast | 1 | rpl2 | 4 |
| Cynosurus cristatus | Chloroplast | 1 | rpl2 | 4 |
| Cypripedium formosanum | Chloroplast | 3 | petN, rpl2, rps19 | 7 |
| Cypripedium japonicum | Plastid | 2 | ndhD, rpl2 | 5 |
| Cypripedium macranthos | Chloroplast | 20 | accD, atpA, atpF, ccsA, clpP, matK, ndhB, ndhD, ndhJ, petB, psbF, rpl2, rpl20, rpoA, rpoB, rpoC1, rpoC2, rps14, rps8, ycf3 | 53 |
| Cyrtomium devexiscapulae | Chloroplast | 47 | accD, atpA, atpH, atpI, chlB, chlL, infA, matK, ndhB, ndhC, ndhF, ndhG, Novel, petA, petD, petN, psaB, psbB, psbC, psbD, psbJ, psbL, psbM, psbN, rpl14, rpl16, rpl2, rpl21, rpl22, rpl32, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps12, rps15, rps16, rps18, rps2, rps3, rps4, rps7, ycf1, ycf2, ycf3 | 120 |
| Cyrtomium falcatum | Chloroplast | 38 | accD, atpA, atpH, atpI, chlB, chlL, infA, matK, ndhF, ndhG, petA, petD, petN, psaB, psbB, psbC, psbD, psbL, psbM, rpl14, rpl16, rpl2, rpl21, rpl22, rpl36, rpoB, rpoC1, rpoC2, rps11, rps15, rps18, rps2, rps3, rps4, rps7, ycf1, ycf2, ycf3 | 103 |
| Cystopteris chinensis | Chloroplast | 60 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbL, psbT, rpl14, rpl16, rpl2, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, ycf1, ycf2, ycf3, ycf4 | 139 |
| Dactylis glomerata | Plastid | 1 | rpl2 | 4 |
| Dactyloctenium aegyptium | Chloroplast | 1 | rpl2 | 4 |
| Daiswa dunniana | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Daiswa fargesii | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Daiswa yunnanensis | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Danthonia californica | Plastid | 1 | rpl2 | 4 |
| Danthoniopsis dinteri | Chloroplast | 1 | rpl2 | 4 |
| Dasypogon bromeliifolius | Plastid | 1 | rpl2 | 4 |
| Davidia involucrata | Chloroplast | 1 | psbL | 1 |
| Decaisnea insignis | Chloroplast | 2 | ndhD, rpl2 | 3 |
| Dendrobium candidum | Plastid | 1 | rpl2 | 4 |
| Dendrobium chrysotoxum | Chloroplast | 2 | ndhD, ndhJ | 2 |
| Dendrobium huoshanense | Chloroplast | 2 | ndhD, ndhJ | 2 |
| Dendrobium nobile | Chloroplast | 2 | ndhD, ndhJ | 2 |
| Dendrobium officinale | Chloroplast | 22 | accD, atpA, atpB, atpF, atpI, ccsA, clpP, matK, ndhB, ndhD, ndhJ, petB, psaB, psaI, psbF, rpl2, rpl20, rpoA, rpoB, rpoC1, rps14, ycf3 | 54 |
| Dendrobium pendulum | Chloroplast | 2 | ndhD, ndhJ | 2 |
| Dendrobium strongylanthum | Chloroplast | 3 | ndhD, ndhJ, rpl2 | 6 |
| Dendrocalamus latiflorus | Chloroplast | 2 | rpl2, rps15 | 6 |
| Dendropanax morbifer | Chloroplast | 1 | ndhD | 1 |
| Deparia lancea | Chloroplast | 60 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbL, psbM, rpl14, rpl16, rpl2, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3 | 148 |
| Deparia pycnosora | Chloroplast | 63 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbL, psbM, psbT, rpl14, rpl16, rpl2, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps14, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3 | 152 |
| Deparia viridifrons | Chloroplast | 61 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbL, psbM, rpl14, rpl16, rpl2, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3 | 147 |
| Deschampsia antarctica | Plastid | 15 | atpA, atpB, matK, ndhA, ndhB, ndhD, ndhF, petB, rpl2, rpl20, rpoA, rpoB, rpoC2, rps8, ycf3 | 38 |
| Diandrolyra sp. Clark 1301 | Plastid | 1 | rpl2 | 4 |
| Diarrhena obovata | Plastid | 1 | rpl2 | 4 |
| Dichaetaria wightii | Chloroplast | 2 | psbC, rpl2 | 5 |
| Dichanthelium acuminatum | Chloroplast | 1 | rpl2 | 4 |
| Dichanthium sericeum | Chloroplast | 2 | rpl2, rps19 | 5 |
| Dichrostachys cinerea | Chloroplast | 2 | ndhD, psbL | 2 |
| Dicloster acuatus | Chloroplast | 1 | trnI | 2 |
| Digitalis lanata | Plastid | 1 | ndhD | 1 |
| Dimeria ornithopoda | Chloroplast | 2 | rpl2, rps19 | 6 |
| Dioon spinulosum | Chloroplast | 2 | petL, rps8 | 2 |
| Dioscorea elephantipes | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Dioscorea villosa | Plastid | 1 | ndhD | 1 |
| Diospyros blancoi | Chloroplast | 2 | ndhD, trnI-CAU | 3 |
| Diospyros dumetorum | Plastid | 1 | ndhD | 1 |
| Diospyros glaucifolia | Chloroplast | 1 | ndhD | 1 |
| Diospyros kaki | Chloroplast | 1 | ndhD | 1 |
| Diospyros lotus | Chloroplast | 1 | ndhD | 1 |
| Diospyros oleifera | Chloroplast | 1 | ndhD | 1 |
| Diospyros strigosa | Plastid | 1 | ndhD | 1 |
| Diplaziopsis cavaleriana | Chloroplast | 58 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhI, ndhK, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbL, psbM, rpl14, rpl2, rpl21, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3, ycf4 | 135 |
| Diplaziopsis javanica | Chloroplast | 62 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbL, psbM, psbT, rpl14, rpl16, rpl2, rpl21, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps14, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3 | 145 |
| Diplazium bellum | Chloroplast | 59 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbM, rpl14, rpl16, rpl2, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps15, rps18, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3 | 136 |
| Diplazium dilatatum | Chloroplast | 58 | accD, atpA, atpB, atpF, atpH, atpI, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbM, psbT, rpl14, rpl16, rpl2, rpl21, rpl22, rpl23, rpoA, rpoB, rpoC1, rpoC2, rps11, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, ycf1, ycf2, ycf3 | 134 |
| Diplazium dushanense | Chloroplast | 62 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, clpP, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbM, rpl14, rpl16, rpl2, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps14, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3 | 149 |
| Diplazium striatum | Chloroplast | 57 | accD, atpA, atpB, atpF, atpH, atpI, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbE, psbF, psbH, psbM, psbT, rpl14, rpl16, rpl2, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, ycf1, ycf2, ycf3 | 138 |
| Diplazium unilobum | Chloroplast | 58 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, clpP, infA, matK, ndhA, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbM, rpl14, rpl16, rpl2, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps15, rps16, rps18, rps19, rps2, rps3, rps7, rps8, ycf1, ycf2, ycf3 | 130 |
| Diplopanax stachyanthus | Chloroplast | 1 | psbL | 1 |
| Diplopterygium glaucum | Chloroplast | 45 | accD, atpA, atpB, atpH, atpI, cemA, chlB, chlL, chlN, clpP, infA, matK, ndhA, ndhE, ndhF, ndhG, petA, petB, petG, psaA, psaB, psaC, psaI, psbB, psbE, psbJ, rpl2, rpl20, rpl21, rpl23, rpoA, rpoB, rpoC1, rpoC2, rps11, rps15, rps18, rps19, rps2, rps3, rps4, rps7, ycf1, ycf2, ycf3 | 53 |
| Diplostephium alveolatum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium antioquense | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium apiculatum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium azureum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium barclayanum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium cajamarquillense | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium callilepis | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium camargoanum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium cayambense | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium cinerascens | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium cinereum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium colombianum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium coriaceum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium costaricense | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium crypteriophyllum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium empetrifolium | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium ericoides | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium eriophorum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium espinosae | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium floribundum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium foliosissimum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium frontinense | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium glandulosum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium glutinosum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium gnidioides | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium goodspeedii | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium gynoxyoides | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium haenkei | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium hartwegii | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium heterophyllum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium hippophae | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium huertasii | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium inesianum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium jaramilloi | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium jelskii | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium jenesanum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium juajibioyi | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium juniperinum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium lacunosum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium lechleri | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium meyenii | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium mutiscuanum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium oblanceolatum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium oblongifolium | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium obtusum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium ochraceum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium oxapampanum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium phylicoides | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium pulchrum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium revolutum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium rhododendroides | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium rhomboidale | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium romeroi | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium rosmarinifolium | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium rupestre | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium sagasteguii | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium schultzii | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium serratifolium | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium spinulosum | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium tachirense | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium tenuifolium | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium venezuelense | Chloroplast | 2 | ndhD, psbL | 2 |
| Diplostephium violaceum | Chloroplast | 2 | ndhD, psbL | 2 |
| Distichlis bajaensis | Plastid | 1 | rpl2 | 4 |
| Distichlis spicata | Plastid | 1 | rpl2 | 4 |
| Dodonaea viscosa | Chloroplast | 1 | ndhD | 1 |
| Draba nemorosa JO21 | Chloroplast | 1 | ndhD | 1 |
| Dregeochloa pumilla | Chloroplast | 1 | rpl2 | 4 |
| Drimys granadensis | Chloroplast | 1 | psbL | 1 |
| Dryopteris decipiens | Chloroplast | 58 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbF, psbL, psbM, psbN, rpl14, rpl2, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3 | 135 |
| Dunalia brachyacantha | Chloroplast | 2 | ndhD, psbL | 2 |
| Dunalia obovata | Chloroplast | 3 | ndhD, psbL, rpl20 | 3 |
| Dunalia solanacea | Chloroplast | 2 | ndhD, psbL | 2 |
| Echinacea angustifolia | Plastid | 2 | ndhD, psbL | 2 |
| Echinacea atrorubens | Plastid | 2 | ndhD, psbL | 2 |
| Echinacea laevigata | Plastid | 2 | ndhD, psbL | 2 |
| Echinacea pallida | Plastid | 2 | ndhD, psbL | 2 |
| Echinacea paradoxa | Plastid | 2 | ndhD, psbL | 2 |
| Echinacea purpurea | Plastid | 2 | ndhD, psbL | 2 |
| Echinacea sanguinea | Plastid | 2 | ndhD, psbL | 2 |
| Echinacea speciosa | Plastid | 2 | ndhD, psbL | 2 |
| Echinacea tennesseensis | Plastid | 2 | ndhD, psbL | 2 |
| Echinochloa esculenta | Chloroplast | 1 | rpl2 | 4 |
| Echinochloa stagnina | Chloroplast | 1 | rpl2 | 4 |
| Echinochloa ugandensis | Chloroplast | 1 | rpl2 | 4 |
| Echites umbellatus | Plastid | 1 | ndhD | 1 |
| Eclipta prostrata | Chloroplast | 2 | ndhD, psbL | 2 |
| Edaphochlorella mirabilis | Chloroplast | 1 | trnI | 1 |
| Ehrharta bulbosa | Chloroplast | 1 | rpl2 | 4 |
| Elaeagnus macrophylla | Chloroplast | 1 | ndhD | 1 |
| Elaeis guineensis | Chloroplast | 18 | atpB, atpF, clpP, ndhB, ndhH, ndhK, petB, rpl2, rpl22, rpl23, rps12, rps16, rps3, rps7, rps8, ycf1, ycf2, ycf4 | 33 |
| Eleusine indica | Chloroplast | 1 | rpl2 | 4 |
| Eleutherococcus senticosus | Chloroplast | 1 | ndhD | 1 |
| Elleanthus sodiroi | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Elliptochloris bilobata | Chloroplast | 1 | trnI | 1 |
| Elodea canadensis | Chloroplast | 1 | ndhD | 1 |
| Elytrophorus globularis | Chloroplast | 2 | psbC, rpl2 | 5 |
| Elytrophorus spicatus | Plastid | 1 | rpl2 | 4 |
| Emmenopterys henryi | Chloroplast | 1 | ndhD | 1 |
| Encephalartos lehmannii | Chloroplast | 2 | petL, rps8 | 2 |
| Enneapogon oblongus | Chloroplast | 1 | rpl2 | 4 |
| Entolasia imbricata | Chloroplast | 1 | rpl2 | 4 |
| Entransia fimbriata | Chloroplast
Mitochondrion | 1 | trnI | 4 |
| Ephedra equisetina | Chloroplast | 2 | trnI, trnR | 9 |
| Epimedium acuminatum | Chloroplast | 2 | ndhD, rpl2 | 3 |
| Epimedium dolichostemon | Chloroplast | 2 | ndhD, rpl2 | 2 |
| Epimedium koreanum | Chloroplast | 2 | ndhD, rpl2 | 2 |
| Epimedium lishihchenii | Chloroplast | 2 | ndhD, rpl2 | 2 |
| Epimedium pseudowushanense | Chloroplast | 2 | ndhD, rpl2 | 2 |
| Epimedium sagittatum | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Epipogium aphyllum | Plastid | 1 | rpl2 | 2 |
| Epipogium roseum | Plastid | 1 | rpl2 | 1 |
| Epipremnum aureum | Chloroplast | 1 | ndhD | 1 |
| Equisetum arvense | Chloroplast | 3 | accD, rps11, trnA-UGC | 3 |
| Equisetum hyemale | Chloroplast | 1 | accD | 1 |
| Eragrostis minor | Plastid | 1 | rpl2 | 4 |
| Eragrostis tef | Plastid | 1 | rpl2 | 4 |
| Eragrostis walteri | Chloroplast | 2 | psbC, rpl2 | 5 |
| Eremochloa ciliaris | Chloroplast | 2 | rpl2, rps19 | 6 |
| Eremochloa eriopoda | Chloroplast | 2 | rpl2, rps19 | 6 |
| Eremochloa ophiuroides | Chloroplast | 1 | rpl2 | 4 |
| Eremospatha macrocarpa | Plastid | 4 | accD, ndhD, rpl2, rps19 | 8 |
| Eriachne armittii | Chloroplast | 1 | rpl2 | 4 |
| Eriachne mucronata | Chloroplast | 2 | psbC, rpl2 | 5 |
| Eriachne stipacea | Plastid | 1 | rpl2 | 4 |
| Eriochloa meyeriana | Chloroplast | 1 | rpl2 | 4 |
| Eriochrysis cf. cayennensis 365-2 | Chloroplast | 1 | rpl2 | 4 |
| Eriochrysis laxa | Chloroplast | 1 | rpl2 | 4 |
| Eriocnema fulva | Chloroplast | 1 | ndhD | 1 |
| Eriolarynx fasciculata | Chloroplast | 1 | psbL | 1 |
| Erodium absinthoides | Chloroplast | 1 | psbL | 1 |
| Erodium carvifolium | Chloroplast | 2 | ndhD, psbL | 2 |
| Erodium chrysanthum | Chloroplast | 2 | accD, psbL | 2 |
| Erodium crassifolium | Plastid | 1 | psbL | 1 |
| Erodium gruinum | Plastid | 1 | psbL | 1 |
| Erodium manescavi | Plastid | 1 | psbL | 1 |
| Erodium reichardii | Plastid | 1 | psbL | 1 |
| Erodium rupestre | Plastid | 1 | psbL | 1 |
| Erodium texanum | Plastid | 1 | psbL | 1 |
| Erodium trifolium | Plastid | 2 | ndhD, psbL | 2 |
| Erythranthe guttata | Mitochondrion | 4 | atp6, ND4L, rps10, rps4 | 5 |
| Erythranthe lutea | Chloroplast | 1 | ndhD | 1 |
| Erythroxylum novogranatense | Chloroplast | 1 | ndhD | 1 |
| Ettlia pseudoalveolaris | Chloroplast | 1 | trnI | 1 |
| Eucalyptus aromaphloia | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus baxteri | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus camaldulensis | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus cladocalyx | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus cloeziana | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus curtisii | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus deglupta | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus delegatensis | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus diversicolor | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus diversifolia | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus elata | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus erythrocorys | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus globulus subsp. globulus | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus guilfoylei | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus marginata | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus melliodora | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus microcorys | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus nitens | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus obliqua | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus patens | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus polybractea | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus radiata | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus regnans | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus saligna | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus salmonophloia | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus sieberi | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus spathulata | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus torquata | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus umbra | Chloroplast | 1 | ndhD | 1 |
| Eucalyptus verrucata | Chloroplast | 1 | ndhD | 1 |
| Eugeissona tristis | Plastid | 3 | ndhD, rpl2, rps19 | 7 |
| Eugenia uniflora | Plastid | 2 | ndhD, psbL | 2 |
| Eulalia aurea | Chloroplast | 1 | rpl2 | 4 |
| Eulalia contorta | Chloroplast | 2 | rpl2, rps19 | 6 |
| Eulalia siamensis | Chloroplast | 2 | rpl2, rps19 | 6 |
| Eulaliopsis binata | Chloroplast | 2 | rpl2, rps19 | 6 |
| Euphorbia esula | Chloroplast | 1 | ndhD | 1 |
| Euptelea pleiosperma | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Eustachys glauca | Chloroplast | 1 | rpl2 | 4 |
| Eustrephus latifolius | Plastid | 2 | ndhD, rpl2 | 5 |
| Eutrema halophilum | Chloroplast | 1 | ndhD | 1 |
| Eutrema heterophyllum | Chloroplast | 1 | ndhD | 1 |
| Eutrema yunnanense | Chloroplast | 1 | ndhD | 1 |
| Exostigma notobellidiastrum | Chloroplast | 2 | ndhD, psbL | 2 |
| Fagopyrum esculentum subsp. ancestrale | Chloroplast | 2 | ndhD, psbL | 2 |
| Fagopyrum tataricum Daegwan3-3 | Chloroplast | 2 | ndhD, psbL | 2 |
| Faidherbia albida | Chloroplast | 2 | ndhD, psbL | 3 |
| Fargesia denudata | Chloroplast | 1 | rpl2 | 4 |
| Fargesia nitida | Chloroplast | 1 | rpl2 | 4 |
| Fargesia spathacea | Chloroplast | 1 | rpl2 | 4 |
| Fargesia yunnanensis | Chloroplast | 1 | rpl2 | 4 |
| Festuca altissima | Plastid | 1 | rpl2 | 4 |
| Festuca arundinacea | Chloroplast | 5 | atpF, ccsA, ndhD, ndhK, rpoB | 6 |
| Festuca ovina | Plastid | 1 | rpl2 | 4 |
| Festuca pratensis | Plastid | 1 | rpl2 | 4 |
| Ficus carica | Chloroplast | 1 | ndhD | 1 |
| Floscaldasia hypsophila | Chloroplast | 2 | ndhD, psbL | 2 |
| Floydiella terrestris | Chloroplast | 1 | trnI | 1 |
| Forsythia suspensa | Chloroplast | 21 | accD, atpA, atpF, atpI, ccsA, matK, ndhA, ndhB, ndhD, ndhF, ndhG, petB, petG, psbE, rpl2, rpl20, rpoA, rpoB, rpoC2, rps14, rps2 | 52 |
| Francoa sonchifolia | Plastid | 2 | ndhD, psbL | 2 |
| Franklinia alatamaha | Plastid | 1 | ndhD | 1 |
| Fritillaria taipaiensis | Chloroplast | 1 | rpl2 | 4 |
| Fritillaria thunbergii | Chloroplast | 3 | ndhD, psbT, rpl2 | 6 |
| Fritillaria ussuriensis | Chloroplast | 3 | ndhD, psbT, rpl2 | 6 |
| Funaria hygrometrica | Mitochondrion | 1 | trnI | 1 |
| Fusochloris perforata | Chloroplast | 1 | trnI | 1 |
| Galinsoga quadriradiata | Chloroplast | 2 | ndhD, psbL | 2 |
| Gaoligongshania megalothyrsa | Chloroplast | 1 | rpl2 | 4 |
| Garcinia mangostana | Chloroplast | 2 | ndhD, trnI-CAU | 3 |
| Garnotia tenella | Chloroplast | 2 | rpl2, rps19 | 5 |
| Garnotia thailandica | Chloroplast | 2 | rpl2, rps19 | 6 |
| Gastridium ventricosum | Chloroplast | 1 | rpl2 | 4 |
| Gastrochilus fuscopunctatus | Chloroplast | 1 | trnI-CAU | 2 |
| Gastrochilus japonicus | Chloroplast | 1 | trnI-CAU | 2 |
| Gelidocalamus tessellatus | Chloroplast | 1 | rpl2 | 4 |
| Geminella minor | Chloroplast | 1 | trnI | 1 |
| Genlisea margaretae | Chloroplast | 1 | psbL | 1 |
| Geranium incanum | Plastid | 1 | psbL | 1 |
| Geranium maderense | Mitochondrion
Plastid | 3 | nad1, psbL, trnI-CAU | 8 |
| Geranium palmatum | Plastid | 2 | psbL, rps18 | 2 |
| Germainia capitata | Chloroplast | 2 | rpl2, rps19 | 6 |
| Ginkgo biloba | Mitochondrion | 33 | atp1, atp4, atp6, atp8, atp9, ccmC, ccmFc, ccmFn, cox1, cox2, cox3, matR, mttB, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, nad9, rpl16, rpl2, rps10, rps11, rps12, rps13, rps19, rps2, rps3, rps4, sdh4 | 634 |
| Glehnia littoralis | Chloroplast | 1 | ndhD | 1 |
| Gloeotilopsis sterilis | Chloroplast | 1 | trnI | 1 |
| Gloriosa superba | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Glycine canescens | Chloroplast | 3 | ndhB, ndhD, psbL | 6 |
| Glycine cyrtoloba | Chloroplast | 3 | ndhB, ndhD, psbL | 6 |
| Glycine dolichocarpa | Chloroplast | 3 | ndhB, ndhD, psbL | 6 |
| Glycine falcata | Chloroplast | 3 | ndhB, ndhD, psbL | 6 |
| Glycine gracilis | Chloroplast | 1 | psbL | 1 |
| Glycine max | Chloroplast
Mitochondrion | 8 | ccmFc, mttB, nad1, nad4L-1, nad4L-2, ndhD, psbL, rps10 | 28 |
| Glycine stenophita | Chloroplast | 3 | ndhB, ndhD, psbL | 6 |
| Glycine syndetika | Chloroplast | 3 | ndhB, ndhD, psbL | 6 |
| Glycine tomentella | Chloroplast | 3 | ndhB, ndhD, psbL | 6 |
| Glycyrrhiza glabra | Chloroplast | 1 | psbL | 1 |
| Glycyrrhiza lepidota | Chloroplast | 2 | ndhD, psbL | 2 |
| Gnetum parvifolium | Chloroplast | 1 | trnI | 2 |
| Gonium pectorale | Chloroplast | 1 | trnI | 1 |
| Goodyera fumata | Chloroplast | 4 | ndhD, petN, rpl2, rps19 | 8 |
| Gordonia brandegeei | Plastid | 1 | ndhD | 1 |
| Gordonia fruticosa | Plastid | 1 | ndhD | 1 |
| Gordonia lasianthus | Plastid | 1 | ndhD | 1 |
| Gossypium anomalum | Chloroplast | 1 | ndhD | 1 |
| Gossypium arboreum | Chloroplast
Mitochondrion | 4 | nad1, nad4L, ndhD, rps10 | 18 |
| Gossypium areysianum | Chloroplast | 1 | ndhD | 1 |
| Gossypium aridum | Chloroplast | 1 | ndhD | 1 |
| Gossypium armourianum | Chloroplast | 1 | ndhD | 1 |
| Gossypium australe | Chloroplast | 1 | ndhD | 1 |
| Gossypium barbadense | Chloroplast
Mitochondrion | 4 | nad1, nad4L, ndhD, rps10 | 18 |
| Gossypium bickii | Chloroplast | 1 | ndhD | 1 |
| Gossypium capitis-viridis | Chloroplast | 1 | ndhD | 1 |
| Gossypium darwinii | Chloroplast | 1 | ndhD | 1 |
| Gossypium davidsonii | Chloroplast
Mitochondrion | 4 | nad1, nad4L, ndhD, rps10 | 18 |
| Gossypium gossypioides | Chloroplast | 1 | ndhD | 1 |
| Gossypium harknessii | Chloroplast
Mitochondrion | 3 | nad4L, ndhD, rps10 | 8 |
| Gossypium herbaceum | Chloroplast | 1 | ndhD | 1 |
| Gossypium herbaceum subsp. africanum | Chloroplast | 1 | ndhD | 1 |
| Gossypium hirsutum | Chloroplast
Mitochondrion | 3 | nad4L, ndhD, rps10 | 8 |
| Gossypium incanum | Chloroplast | 1 | ndhD | 1 |
| Gossypium klotzschianum | Chloroplast | 1 | ndhD | 1 |
| Gossypium longicalyx | Chloroplast | 1 | ndhD | 1 |
| Gossypium mustelinum | Chloroplast | 1 | ndhD | 1 |
| Gossypium nelsonii | Chloroplast | 1 | ndhD | 1 |
| Gossypium populifolium | Chloroplast | 1 | ndhD | 1 |
| Gossypium raimondii | Chloroplast
Mitochondrion | 4 | nad1, nad4L, ndhD, rps10 | 18 |
| Gossypium robinsonii | Chloroplast | 1 | ndhD | 1 |
| Gossypium somalense | Chloroplast | 1 | ndhD | 1 |
| Gossypium stocksii | Chloroplast | 1 | ndhD | 1 |
| Gossypium sturtianum | Chloroplast | 1 | ndhD | 1 |
| Gossypium thurberi | Chloroplast
Mitochondrion | 4 | nad1, nad4L, ndhD, rps10 | 18 |
| Gossypium tomentosum | Chloroplast | 1 | ndhD | 1 |
| Gossypium trilobum | Chloroplast
Mitochondrion | 3 | nad1, ndhD, rps10 | 16 |
| Graffenrieda moritziana | Chloroplast | 1 | ndhD | 1 |
| Greslania sp. McPherson 19217 | Plastid | 1 | rpl2 | 4 |
| Guadua angustifolia | Chloroplast | 1 | rpl16 | 2 |
| Guadua weberbaueri | Plastid | 1 | rpl2 | 4 |
| Guibourtia leonensis | Chloroplast | 2 | ndhD, psbL | 2 |
| Guizotia abyssinica | Chloroplast | 2 | ndhD, psbL | 2 |
| Gymnospermium microrrhynchum | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Gynerium sagittatum | Chloroplast | 1 | rpl2 | 4 |
| Habenaria pantlingiana | Chloroplast | 5 | ndhD, petN, psbT, rpl2, rps19 | 9 |
| Habenaria radiata | Chloroplast | 1 | trnI-CAU | 2 |
| Hafniomonas laevis | Chloroplast | 1 | trnI | 1 |
| Hakonechloa macra | Plastid | 1 | rpl2 | 4 |
| Halopyrum mucronatum | Chloroplast | 1 | rpl2 | 4 |
| Haloxylon ammodendron | Chloroplast | 2 | ndhD, psbL | 2 |
| Haloxylon persicum | Chloroplast | 2 | ndhD, psbL | 2 |
| Hanabusaya asiatica | Chloroplast | 1 | psbL | 1 |
| Hanguana malayana | Plastid | 3 | ndhD, rpl2, rps19 | 7 |
| Helianthus annuus | Chloroplast
Mitochondrion | 3 | cob, ndhD, psbL | 6 |
| Helianthus argophyllus | Chloroplast | 3 | ndhD, petB, psbL | 3 |
| Helianthus debilis | Chloroplast | 2 | ndhD, psbL | 2 |
| Helianthus decapetalus | Plastid | 2 | ndhD, psbL | 2 |
| Helianthus divaricatus | Plastid | 2 | ndhD, psbL | 2 |
| Helianthus giganteus | Plastid | 2 | ndhD, psbL | 2 |
| Helianthus grosseserratus | Plastid | 2 | ndhD, psbL | 2 |
| Helianthus hirsutus | Plastid | 2 | ndhD, psbL | 2 |
| Helianthus maximiliani | Plastid | 2 | ndhD, psbL | 2 |
| Helianthus strumosus | Plastid | 2 | ndhD, psbL | 2 |
| Helianthus tuberosus | Plastid | 2 | ndhD, psbL | 2 |
| Heliconia collinsiana | Plastid | 1 | rpl2 | 2 |
| Helicosporidium sp. ex Simulium jonesi ATCC 50920 | Mitochondrion | 1 | trnI | 2 |
| Helictochloa hookeri | Plastid | 1 | rpl2 | 4 |
| Heloniopsis tubiflora | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Helwingia himalaica | Chloroplast | 1 | ndhD | 1 |
| Hemisorghum mekongense | Chloroplast | 2 | rpl2, rps19 | 6 |
| Henriettea barkeri | Chloroplast | 1 | ndhD | 1 |
| Hesperaloe campanulata | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Hesperaloe parviflora | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Hesperelaea palmeri | Chloroplast
Mitochondrion | 5 | atp6, nad4L, ndhD, rps10, rps4 | 12 |
| Hesperis sylvestris | Chloroplast | 1 | ndhD | 1 |
| Hesperocallis undulata | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Hesperocyparis glabra | Plastid | 1 | clpP | 1 |
| Hesperoyucca whipplei | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Heteropogon contortus | Chloroplast | 2 | rpl2, rps19 | 6 |
| Heteropogon triticeus | Chloroplast | 2 | rpl2, rps19 | 6 |
| Heterothalamus alienus | Chloroplast | 2 | ndhD, psbL | 2 |
| Hevea brasiliensis | Chloroplast | 28 | atpI, cemA, clpP, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhG, ndhH, ndhK, petB, petD, petL, psbB, psbD, psbE, rpl23, rpoA, rpoB, rpoC1, rpoC2, rps12, rps14, rps16, rps18, rps2 | 49 |
| Hibiscus cannabinus | Mitochondrion | 5 | atp6, atp9, nad1, nad4L, rps10 | 11 |
| Hibiscus syriacus | Chloroplast | 1 | ndhD | 1 |
| Hickelia madagascariensis | Plastid | 1 | rpl2 | 4 |
| Hilaria cenchroides | Plastid | 1 | rpl2 | 4 |
| Hilaria rigida | Plastid | 1 | rpl2 | 4 |
| Hildaea pallens | Chloroplast | 1 | rpl2 | 4 |
| Hinterhubera ericoides | Chloroplast | 2 | ndhD, psbL | 2 |
| Hippophae rhamnoides | Chloroplast | 1 | ndhD | 1 |
| Hirtella physophora | Chloroplast | 1 | ndhD | 1 |
| Hirtella racemosa | Chloroplast | 1 | ndhD | 1 |
| Holcus lanatus | Chloroplast | 1 | rpl2 | 4 |
| Homalosorus pycnocarpos | Chloroplast | 63 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbL, psbM, rpl14, rpl16, rpl2, rpl21, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps14, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3, ycf4 | 144 |
| Homolepis aturensis | Chloroplast | 1 | rpl2 | 4 |
| Homolepis isocalycia | Chloroplast | 1 | rpl2 | 4 |
| Hordeum jubatum | Plastid | 1 | rpl2 | 4 |
| Hordeum vulgare subsp. vulgare | Chloroplast | 1 | rpl2 | 4 |
| Hosta minor | Chloroplast | 1 | rpl2 | 4 |
| Hosta ventricosa | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Humbertochloa bambusiuscula | Chloroplast | 1 | rpl2 | 4 |
| Humulus lupulus | Chloroplast | 1 | psbL | 1 |
| Huperzia lucidula | Chloroplast | 8 | atpI, ccsA, chlL, ndhD, ndhH, ndhJ, rpl36, rps16 | 9 |
| Huperzia serrata | Chloroplast | 5 | ccsA, chlL, ndhD, ndhH, ndhJ | 7 |
| Hydrangea hydrangeoides | Chloroplast | 2 | ndhD, psbL | 2 |
| Hydrangea luteovenosa | Chloroplast | 2 | ndhD, psbL | 2 |
| Hydrangea petiolaris | Chloroplast | 2 | ndhD, psbL | 2 |
| Hydrangea serrata | Chloroplast | 2 | ndhD, psbL | 2 |
| Hydrastis canadensis | Plastid | 2 | ndhD, rpl2 | 5 |
| Hymenasplenium unilaterale | Chloroplast | 57 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbL, psbM, psbT, rpl14, rpl2, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps16, rps18, rps19, rps2, rps3, rps4, rps7, ycf1, ycf2, ycf3, ycf4 | 125 |
| Hyoscyamus niger | Mitochondrion | 3 | cox1, rps10, rps4 | 3 |
| Hyparrhenia diplandra | Chloroplast | 2 | rpl2, rps19 | 6 |
| Hyparrhenia rufa | Chloroplast | 1 | rpl2 | 4 |
| Hyparrhenia subplumosa | Chloroplast | 1 | rpl2 | 4 |
| Hypnum imponens | Mitochondrion | 5 | atp1, ccmFN, cox3, tatC, trnI | 5 |
| Hypodematium crenatum | Chloroplast | 60 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbF, psbH, psbL, psbM, psbN, rpl14, rpl16, rpl2, rpl21, rpl22, rpl23, rpoA, rpoB, rpoC1, rpoC2, rps11, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3 | 136 |
| Hypolytrum nemorum | Chloroplast | 2 | rpl2, trnI-CAU | 6 |
| Hypseocharis bilobata | Chloroplast | 20 | atpA, atpF, atpI, ccsA, matK, ndhA, ndhB, ndhD, ndhF, ndhG, petB, psbE, psbF, psbL, rpl20, rpoB, rpoC1, rpoC2, rps14, rps2 | 60 |
| Ignatius tetrasporus | Chloroplast | 1 | trnI | 1 |
| Illicium oligandrum | Chloroplast | 2 | ndhD, psbL | 2 |
| Imperata cylindrica | Chloroplast | 1 | rpl2 | 4 |
| Indocalamus wilsonii | Chloroplast | 1 | rpl2 | 4 |
| Indosasa sinica | Chloroplast | 1 | rpl2 | 4 |
| Inga leiocalycina | Chloroplast | 2 | ndhD, psbL | 3 |
| Interfilum terricola | Chloroplast | 1 | trnI | 1 |
| Iochroma australe | Chloroplast | 2 | ndhD, ycf15 | 3 |
| Iochroma cardenasianum | Chloroplast | 2 | petB, psbL | 2 |
| Iochroma cyaneum | Chloroplast | 3 | ndhD, ndhF, psbL | 3 |
| Iochroma ellipticum | Chloroplast | 2 | ndhD, psbL | 2 |
| Iochroma lehmannii | Chloroplast | 1 | petB | 1 |
| Iochroma loxense | Chloroplast | 2 | ndhD, psbL | 2 |
| Iochroma nitidum | Chloroplast | 2 | ndhD, psbL | 2 |
| Iochroma salpoanum | Chloroplast | 2 | ndhD, psbL | 2 |
| Iochroma stenanthum | Chloroplast | 6 | ndhD, petD, petN, psbL, rps19, ycf15 | 6 |
| Iochroma tingoanum | Chloroplast | 4 | ndhD, petB, psbL, rps19 | 4 |
| Iochroma umbellatum | Chloroplast | 1 | psbL | 1 |
| Iodes cirrhosa | Chloroplast | 2 | ndhD, psbL | 2 |
| Ipomoea nil | Chloroplast
Mitochondrion | 5 | atp9, nad4L, ndhD, psbL, rps10 | 12 |
| Ipomoea purpurea | Chloroplast | 2 | ndhD, psbL | 2 |
| Ipomoea trifida | Plastid | 2 | ndhD, psbL | 2 |
| Iris gatesii | Plastid | 2 | ndhD, rpl2 | 5 |
| Iris sanguinea | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Isachne albens | Chloroplast | 2 | psbC, rpl2 | 5 |
| Isachne distichophylla | Plastid | 1 | rpl2 | 4 |
| Ischaemum afrum | Chloroplast | 1 | rpl2 | 4 |
| Iseilema macratherum | Chloroplast | 1 | rpl2 | 4 |
| Isoetes flaccida | Chloroplast | 35 | atpI, ccsA, cemA, chlL, matK, ndhA, ndhD, ndhF, ndhH, ndhJ, petB, petD, petG, petN, psaB, psaI, psbH, psbL, psbT, rbcL, rpl14, rpl20, rpl21, rpoA, rpoB, rpoC1, rpoC2, rps11, rps4, rps8, trnI-GAU, trnR-CCG, ycf1, ycf2, ycf4 | 39 |
| Jacobaea vulgaris | Chloroplast | 1 | psbL | 1 |
| Jasminum nudiflorum | Chloroplast | 1 | ndhD | 1 |
| Jasminum tortuosum | Plastid | 1 | ndhD | 1 |
| Jatropha curcas | Chloroplast | 1 | ndhD | 1 |
| Jenufa minuta | Chloroplast | 21 | ccsA, cemA, clpP, ftsH, orf125, orf204, orf306, orf333, orf579, orf608, orf700, rpl16, rpl2, rpoBa, rpoC1, rpoC2, rps2, trnI, ycf1, ycf3, ycf4 | 22 |
| Jenufa perforata | Chloroplast | 1 | trnI | 1 |
| Joinvillea ascendens | Chloroplast | 1 | rpl2 | 4 |
| Juglans cinerea | Chloroplast | 2 | ndhD, rpoB | 2 |
| Juglans hindsii | Chloroplast | 1 | ndhD | 1 |
| Juglans major | Chloroplast | 1 | ndhD | 1 |
| Juglans nigra | Chloroplast | 1 | ndhD | 1 |
| Juniperus bermudiana | Chloroplast | 1 | clpP | 1 |
| Juniperus monosperma | Chloroplast | 1 | clpP | 1 |
| Juniperus scopulorum | Chloroplast | 1 | clpP | 1 |
| Juniperus virginiana | Chloroplast | 1 | clpP | 1 |
| Kerriochloa siamensis | Chloroplast | 1 | rpl2 | 4 |
| Keteleeria davidiana | Chloroplast | 3 | psbI, psbZ, trnI | 4 |
| Kingdonia uniflora | Chloroplast | 1 | rpl2 | 4 |
| Klebsormidium nitens NIES-2285 | Chloroplast | 1 | psbF | 2 |
| Koliella corcontica | Chloroplast | 1 | trnI | 1 |
| Koliella longiseta | Chloroplast | 1 | trnI | 1 |
| Kolkwitzia amabilis | Chloroplast | 1 | psbL | 1 |
| Lactuca sativa | Chloroplast | 2 | ndhD, psbL | 2 |
| Laennecia sophiifolia | Chloroplast | 2 | ndhD, psbL | 2 |
| Laestadia muscicola | Chloroplast | 2 | ndhD, psbL | 2 |
| Lagenophora cuchumatanica | Chloroplast | 2 | ndhD, psbL | 2 |
| Lagerstroemia fauriei | Chloroplast | 2 | ndhD, psbL | 2 |
| Lagerstroemia floribunda | Chloroplast | 2 | ndhD, psbL | 2 |
| Lagerstroemia guilinensis | Chloroplast | 2 | ndhD, psbL | 2 |
| Lagerstroemia indica | Chloroplast
Mitochondrion | 8 | atp6, atp9, mttB, nad1, ndhD, psbL, rpl22, rps10 | 26 |
| Lagerstroemia intermedia | Chloroplast | 2 | ndhD, psbL | 2 |
| Lagerstroemia speciosa | Chloroplast | 2 | ndhD, psbL | 2 |
| Lagerstroemia subcostata | Chloroplast | 4 | ndhD, psbI, psbL, rps15 | 4 |
| Larix decidua | Chloroplast | 2 | psbZ, trnI | 3 |
| Lasiacis nigra | Chloroplast | 1 | rpl2 | 4 |
| Lathyrus clymenum | Chloroplast | 1 | ndhD | 1 |
| Lathyrus davidii | Chloroplast | 1 | ndhD | 1 |
| Lathyrus graminifolius | Chloroplast | 1 | ndhD | 1 |
| Lathyrus inconspicuus | Chloroplast | 1 | ndhD | 1 |
| Lathyrus japonicus | Chloroplast | 1 | ndhD | 1 |
| Lathyrus littoralis | Chloroplast | 1 | ndhD | 1 |
| Lathyrus ochroleucus | Chloroplast | 1 | ndhD | 1 |
| Lathyrus odoratus | Chloroplast | 1 | ndhD | 1 |
| Lathyrus palustris | Chloroplast | 1 | ndhD | 1 |
| Lathyrus pubescens | Chloroplast | 1 | ndhD | 1 |
| Lathyrus sativus | Chloroplast | 1 | ndhD | 1 |
| Lathyrus tingitanus | Chloroplast | 1 | ndhD | 1 |
| Lecomtella madagascariensis | Chloroplast | 1 | rpl2 | 4 |
| Ledebouriella seseloides | Chloroplast | 1 | ndhD | 1 |
| Leersia japonica | Chloroplast | 1 | rpl2 | 4 |
| Leersia tisserantii | Plastid | 1 | rpl2 | 4 |
| Leitneria floridana | Chloroplast | 1 | ndhD | 1 |
| Lemna minor | Chloroplast | 2 | ndhD, rpl2 | 3 |
| Lens culinaris | Chloroplast | 1 | psbL | 1 |
| Leontopodium leiolepis | Chloroplast | 2 | ndhD, psbL | 2 |
| Lepidium virginicum JO26 | Chloroplast | 1 | ndhD | 1 |
| Lepidozamia peroffskyana | Chloroplast | 2 | petL, rps8 | 2 |
| Lepisorus clathratus | Chloroplast | 44 | accD, atpA, atpH, atpI, ccsA, chlB, chlL, infA, matK, ndhB, ndhC, ndhF, ndhI, Novel, petA, petB, petD, petN, psaB, psbB, psbC, psbD, psbH, psbJ, rpl16, rpl2, rpl21, rpl22, rpl23, rpl36, rpoB, rpoC1, rpoC2, rps11, rps15, rps16, rps2, rps3, rps4, rps7, ycf1, ycf2, ycf3, ycf4 | 110 |
| Leptaspis banksii | Chloroplast | 1 | rpl2 | 4 |
| Leptaspis zeylanica | Chloroplast | 1 | rpl2 | 4 |
| Leptochloa virgata | Chloroplast | 1 | rpl2 | 4 |
| Leucaena trichandra | Chloroplast | 2 | ndhD, psbL | 2 |
| Leucothrinax morrisii | Plastid | 3 | ndhD, rpl2, rps19 | 7 |
| Licania alba | Chloroplast | 1 | ndhD | 1 |
| Licania heteromorpha | Chloroplast | 1 | ndhD | 1 |
| Licania sprucei | Chloroplast | 1 | ndhD | 1 |
| Ligusticum tenuissimum | Chloroplast | 1 | ndhD | 1 |
| Lilium amabile | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Lilium callosum | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Lilium cernuum | Chloroplast | 1 | rpl2 | 2 |
| Lilium distichum | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Lilium hansonii | Chloroplast | 2 | ndhD, rpl2 | 3 |
| Lilium philadelphicum | Chloroplast | 3 | ndhD, rpl2, rps19 | 6 |
| Lilium sp. KHK-2014 | Chloroplast | 2 | ndhD, rpl2 | 3 |
| Lilium superbum | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Lilium tsingtauense | Chloroplast | 2 | ndhD, rpl2 | 3 |
| Limnopoa meeboldii | Chloroplast | 2 | psbC, rpl2 | 5 |
| Lindera glauca | Chloroplast | 1 | rpl2 | 2 |
| Linum usitatissimum | Chloroplast | 18 | accD, atpB, ccsA, clpP, matK, ndhA, ndhB, ndhD, ndhG, petB, psaI, rpl2, rpl20, rpoA, rpoC1, rpoC2, rps14, rps2 | 53 |
| Liquidambar formosana | Chloroplast | 2 | ndhD, psbL | 2 |
| Liriodendron chinense | Chloroplast | 2 | ndhD, psbL | 2 |
| Liriodendron tulipifera | Chloroplast
Mitochondrion | 16 | atp6, atp9, cox1, nad1, nad4L, ndhD, psbL, rpl16, rpl2, rps10, rps11, rps4, rrn5, rrnS, sdh4, trnI | 50 |
| Litchi chinensis | Chloroplast | 1 | ndhD | 1 |
| Lithachne pauciflora | Plastid | 1 | rpl2 | 4 |
| Littledalea racemosa | Chloroplast | 1 | rpl2 | 2 |
| Llerasia caucana | Chloroplast | 2 | ndhD, psbL | 2 |
| Lobosphaera incisa | Mitochondrion | 1 | trnI-1 | 1 |
| Lobosphaera incisa SAG 2468 | Chloroplast | 1 | trnI | 1 |
| Lobularia maritima | Chloroplast | 1 | ndhD | 1 |
| Lodoicea maldivica | Plastid | 4 | cemA, ndhD, rpl2, rps19 | 8 |
| Lolium multiflorum | Plastid | 1 | rpl2 | 4 |
| Lonicera japonica | Chloroplast | 3 | clpP, psbL, rps15 | 3 |
| Lotus japonicus | Chloroplast
Mitochondrion | 39 | atp1, atp4, atp6, atp8, atp9, ccmB, ccmC, ccmFc, ccmFn, cob, cox1, cox2, cox3, matR, mttB, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, nad9, ndhB, ndhD, psbL, pseudo-atp6, pseudo-cob, rpl16, rpl5, rps10, rps12, rps14, rps3, rps4, rps7, sdh4, trnI | 1120 |
| Loudetia simplex | Chloroplast | 1 | rpl2 | 4 |
| Loudetiopsis kerstingii | Chloroplast | 1 | rpl2 | 4 |
| Ludwigia octovalvis | Chloroplast | 2 | ndhD, psbL | 2 |
| Lupinus luteus | Chloroplast | 1 | psbL | 1 |
| Lupinus westianus | Chloroplast | 1 | psbL | 1 |
| Luzuriaga radicans | Chloroplast | 3 | ndhD, rpl2, rpl22 | 6 |
| Lychnis wilfordii | Chloroplast | 2 | ndhD, psbL | 2 |
| Lygeum spartum | Chloroplast | 1 | rpl2 | 4 |
| Lygodium japonicum | Chloroplast | 33 | accD, atpA, atpB, atpH, atpI, chlB, chlL, ndhA, ndhB, ndhF, ndhG, ndhH, petA, petB, petN, psbJ, psbM, psbN, rpl2, rpl22, rpl23, rpoA, rpoB, rpoC1, rpoC2, rps12, rps18, rps3, rps4, rps8, ycf2, ycf3, ycf4 | 44 |
| Lysimachia coreana | Plastid | 1 | ndhD | 1 |
| Maackia floribunda | Chloroplast | 2 | ndhD, psbL | 2 |
| Macadamia integrifolia | Chloroplast | 3 | ndhD, psbL, rpl2 | 6 |
| Macadamia ternifolia | Plastid | 3 | ndhD, psbL, rpl2 | 6 |
| Machilus balansae | Chloroplast | 5 | ndhB, ndhD, psbL, rpl2, rpoC2 | 9 |
| Machilus pauhoi | Chloroplast | 7 | ndhB, ndhD, psbL, rpl2, rpl22, rpoC2, ycf2 | 11 |
| Machilus thunbergii | Chloroplast | 7 | ndhB, ndhD, psbL, rpl2, rpl22, rpoC2, ycf2 | 11 |
| Machilus yunnanensis | Chloroplast | 5 | ndhB, ndhD, psbL, rpl2, rpoC2 | 9 |
| Macrothelypteris torresiana | Chloroplast | 61 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbL, psbM, rpl14, rpl16, rpl2, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3, ycf4 | 142 |
| Macrozamia mountperriensis | Chloroplast | 2 | petL, rps8 | 2 |
| Magnolia yunnanensis | Chloroplast | 3 | ndhD, psbL, rpl2 | 4 |
| Maianthemum bicolor | Chloroplast | 1 | rpl2 | 4 |
| Malus domestica | Mitochondrion | 1 | tRNA-Ile | 1 |
| Manfreda virginica | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Mangifera indica | Chloroplast | 1 | ndhD | 1 |
| Mankyua chejuensis | Chloroplast | 5 | accD, matK, ndhA, Novel, psaB | 8 |
| Marsilea crenata | Chloroplast | 42 | accD, atpA, atpI, ccsA, cemA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhE, ndhF, ndhG, ndhH, ndhI, petA, petB, petN, psaB, psaI, psbB, psbC, psbE, psbM, rpl2, rpl20, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps19, rps2, rps7, rps8, ycf1, ycf2, ycf3 | 51 |
| Marvania geminata | Chloroplast | 1 | trnI | 1 |
| Masdevallia coccinea | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Masdevallia picturata | Chloroplast | 5 | ndhD, petN, psbT, rpl2, rps19 | 9 |
| Matteuccia struthiopteris | Chloroplast | 63 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbL, psbM, psbT, rpl14, rpl16, rpl2, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3 | 145 |
| Matthiola incana | Chloroplast | 1 | ndhD | 1 |
| Mauritia flexuosa | Chloroplast | 1 | rpl2 | 4 |
| Medicago hybrida | Chloroplast | 3 | ndhD, psbL, rps15 | 3 |
| Medicago papillosa | Chloroplast | 1 | psbL | 1 |
| Medicago truncatula | Chloroplast
Mitochondrion | 5 | ccmFc, mttB, nad1, nad4L, psbL | 20 |
| Megaleranthis saniculifolia | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Megathyrsus maximus | Chloroplast | 1 | rpl2 | 4 |
| Melanocenchris abyssinica | Chloroplast | 1 | rpl2 | 4 |
| Melastoma candidum | Chloroplast | 1 | ndhD | 1 |
| Melica mutica | Plastid | 1 | rpl2 | 4 |
| Melica subulata | Plastid | 1 | rpl2 | 4 |
| Meliosma aff. cuneifolia Moore 333 | Chloroplast | 3 | ndhD, psbL, rpl2 | 6 |
| Melliodendron xylocarpum | Plastid | 1 | ndhD | 1 |
| Merianthera pulchra | Chloroplast | 1 | ndhD | 1 |
| Merxmuellera tsaratananensis | Chloroplast | 1 | rpl2 | 4 |
| Mesembryanthemum crystallinum | Chloroplast | 1 | psbL | 1 |
| Metanarthecium luteoviride | Chloroplast | 1 | rpl2 | 4 |
| Miconia dodecandra | Chloroplast | 1 | ndhD | 1 |
| Microspora stagnorum | Mitochondrion | 1 | trnI | 1 |
| Microthamnion kuetzingianum | Chloroplast | 1 | trnI | 1 |
| Mikania micrantha | Chloroplast | 1 | psbL | 1 |
| Milla biflora | Chloroplast | 1 | rpl2 | 4 |
| Millettia pinnata | Chloroplast
Mitochondrion | 53 | accD, atp1, atp4, atp6, atp8, atp9, atpA, atpF, ccmB, ccmC, ccmFc, ccmFn, cob, cox1, cox2, cox3, matR, mttB, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, nad9, ndhB, ndhD, ndhG, ndhH, petB, psbB, psbF, psbL, pseudo-nad6, rbcL, rpl16, rpl23, rpl5, rpoB, rpoC1, rpoC2, rps1, rps10, rps12, rps14, rps2, rps3, rps4, sdh4, trnI, trnW | 1138 |
| Mnesithea helferi | Chloroplast | 2 | rpl2, rps19 | 6 |
| Molinia caerulea | Plastid | 1 | rpl2 | 4 |
| Monachather paradoxus | Plastid | 1 | rpl2 | 4 |
| Monomastix sp. OKE-1 | Chloroplast
Mitochondrion | 1 | trnI | 4 |
| Monsonia emarginata | Chloroplast | 1 | psbL | 1 |
| Monsonia marlothii | Chloroplast | 1 | psbL | 1 |
| Monsonia speciosa | Plastid | 1 | psbL | 1 |
| Morus cathayana | Plastid | 3 | ndhD, psbL, trnI-CAU | 4 |
| Morus indica | Chloroplast | 2 | psbL, tRNA-Ile | 3 |
| Morus mongolica | Chloroplast | 2 | ndhD, psbL | 2 |
| Morus notabilis | Chloroplast | 1 | psbL | 1 |
| Musa balbisiana | Chloroplast | 1 | rpl2 | 4 |
| Musa itinerans | Chloroplast | 1 | rpl2 | 4 |
| Musa textilis | Plastid | 2 | ndhD, rpl2 | 5 |
| Mychonastes jurisii | Chloroplast | 1 | psaA | 3 |
| Myriopteris lindheimeri | Chloroplast | 48 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhE, ndhF, ndhG, ndhH, Novel, petA, petB, petD, petL, petN, psaB, psbC, psbF, psbJ, psbL, psbM, rpl14, rpl2, rpl21, rpl23, rpl32, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps19, rps2, rps3, rps7, rps8, ycf1, ycf2, ycf3 | 110 |
| Myrmecia israelensis | Chloroplast | 1 | trnI | 1 |
| Nandina domestica | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Nardus stricta | Chloroplast | 1 | rpl2 | 4 |
| Nassella hyalina | Chloroplast | 1 | rpl2 | 4 |
| Nasturtium officinale | Chloroplast | 1 | ndhD | 1 |
| Nelumbo lutea | Chloroplast | 2 | psbL, rpl2 | 5 |
| Nelumbo nucifera | Mitochondrion | 38 | atp1, atp4, atp6, atp8, atp9, ccmB, ccmFN, cob, cox1, cox2, cox3, matR, mttB, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, nad9, rpl16, rpl2, rpl5, rps1, rps10, rps11, rps13, rps14, rps19, rps2, rps3, rps4, rps7, sdh3a, sdh3b, sdh4 | 771 |
| Nematopoa longipes | Chloroplast | 2 | psbC, rpl2 | 5 |
| Neocinnamomum delavayi | Chloroplast | 3 | ndhD, psbL, rpl2 | 4 |
| Neocystis brevis | Chloroplast | 1 | trnI | 1 |
| Neodangemannia microcystis | Chloroplast | 1 | trnI | 1 |
| Neofinetia falcata | Chloroplast | 2 | rpl2, trnI-CAU | 6 |
| Neofinetia richardsiana | Chloroplast | 2 | rpl2, trnI-CAU | 6 |
| Neohouzeaua sp. Clark & Attigala 1712 | Plastid | 1 | rpl2 | 4 |
| Neololeba atra | Plastid | 1 | rpl2 | 4 |
| Neotorularia korolkowii | Chloroplast | 1 | ndhD | 1 |
| Neottia nidus-avis | Plastid | 2 | rpl2, rps18 | 5 |
| Nephroselmis astigmatica | Chloroplast | 1 | trnI | 1 |
| Nepsera aquatica | Chloroplast | 1 | ndhD | 1 |
| Nerium oleander | Plastid | 1 | ndhD | 1 |
| Netrium digitus | Chloroplast | 1 | trnI | 1 |
| Neyraudia reynaudiana | Chloroplast | 1 | rpl2 | 4 |
| Nicotiana attenuata | Chloroplast
Mitochondrion | 5 | cox1, ndhD, psbL, rps10, rps4 | 10 |
| Nicotiana sylvestris | Chloroplast | 16 | atpA, atpF, ndhA, ndhB, ndhD, ndhF, petB, psbE, psbL, rpl20, rpoA, rpoB, rpoC1, rpoC2, rps14, rps2 | 66 |
| Nicotiana tabacum | Mitochondrion
Plastid | 2 | psbL, rps10 | 4 |
| Nicotiana tomentosiformis | Chloroplast | 16 | atpA, atpF, ndhA, ndhB, ndhD, ndhF, petB, psbE, psbL, rpl20, rpoA, rpoB, rpoC1, rpoC2, rps14, rps2 | 33 |
| Nicotiana undulata | Chloroplast | 2 | ndhD, psbL | 2 |
| Nitella hyalina | Mitochondrion | 2 | nad9, rpl14 | 2 |
| Nolina atopocarpa | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Nothoceros aenigmaticus | Mitochondrion
Plastid | 109 | accD, atp1, atp4, atp6, atp9, atpA, atpB, atpE, atpF, atpH, atpI, ccsA, cemA, chlB, chlL, chlN, clpP, cob, cox1, cox2, cox3, cysA, cysT, infA, matK, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad9, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK, ORF-bryo1, ORF1031, ORF27, ORF473, ORF51, petA, petB, petD, petG, petL, petN, psaA, psaB, psaC, psaI, psaJ, psaM, psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ, rbcL, rpl14, rpl16, rpl20, rpl21, rpl22, rpl23, rpl32, rpl33, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps12, rps13, rps14, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, sdh4, tatC, trnI, ycf12, ycf2, ycf3, ycf4 | 388 |
| Nuphar advena | Chloroplast | 2 | ndhD, psbL | 2 |
| Nyholmiella obtusifolia | Mitochondrion | 2 | ccmFN, tatC | 2 |
| Nymphaea alba | Chloroplast | 1 | psbL | 1 |
| Nymphaea jamesoniana | Chloroplast | 1 | psbL | 1 |
| Nymphaea mexicana | Chloroplast | 1 | psbL | 1 |
| Nypa fruticans | Plastid | 2 | cemA, rpl2 | 5 |
| Oberonia japonica | Chloroplast | 1 | trnI-CAU | 2 |
| Ocimum basilicum | Chloroplast | 1 | ndhD | 1 |
| Oedocladium carolinianum | Chloroplast | 1 | trnI | 1 |
| Oenothera argillicola | Chloroplast | 1 | ndhD | 1 |
| Oenothera biennis | Chloroplast | 1 | ndhD | 1 |
| Oenothera elata subsp. hookeri | Plastid | 1 | ndhD | 1 |
| Oenothera glazioviana | Chloroplast | 1 | ndhD | 1 |
| Oenothera grandiflora Stockton 1 | Chloroplast | 1 | ndhD | 1 |
| Oenothera oakesiana strain ammophila | Chloroplast | 1 | ndhD | 1 |
| Oenothera parviflora | Chloroplast | 1 | ndhD | 1 |
| Oenothera villaricae berteriana Schwemmle | Chloroplast | 1 | ndhD | 1 |
| Olea europaea subsp. maroccana | Chloroplast | 1 | ndhD | 1 |
| Olea europaea var. sylvestris | Plastid | 1 | ndhD | 1 |
| Olea woodiana subsp. woodiana | Chloroplast | 1 | ndhD | 1 |
| Oligostachyum shiuyingianum | Chloroplast | 1 | rpl2 | 4 |
| Olmeca reflexa | Plastid | 1 | rpl2 | 4 |
| Oltmannsiellopsis viridis | Mitochondrion | 1 | trnI | 1 |
| Olyra latifolia | Plastid | 1 | rpl2 | 4 |
| Oncidium hybrid cultivar | Chloroplast | 2 | rpl2, trnI | 5 |
| Oncidium sphacelatum | Plastid | 1 | rpl2 | 4 |
| Oncinotis tenuiloba | Plastid | 1 | ndhD | 1 |
| Oncorachis ramosa | Chloroplast | 1 | rpl2 | 4 |
| Onoclea sensibilis | Chloroplast | 61 | accD, atpA, atpB, atpF, atpH, atpI, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbL, psbM, rpl14, rpl16, rpl2, rpl21, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps14, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3 | 137 |
| Oogamochlamys gigantea | Chloroplast | 1 | trnI | 1 |
| Ophioglossum californicum | Chloroplast
Mitochondrion | 47 | accD, atp1, atp4, atp6, atp8, atp9, chlL, cob, cox1, cox2, cox3, matR, mttB, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, nad9, ndhD, ndhF, Novel, petD, psaB, rpl16, rpl2, rpl5, rpl6, rps1, rps10, rps11, rps12, rps13, rps14, rps15, rps19, rps2, rps3, rps4, rps7, rrn18, sdh3, sdh4, ycf1 | 2162 |
| Opisthocentra clidemioides | Chloroplast | 1 | ndhD | 1 |
| Oplismenus hirtellus | Chloroplast | 1 | rpl2 | 4 |
| Oritrophium peruvianum | Chloroplast | 2 | ndhD, psbL | 2 |
| Orobanche californica | Chloroplast | 5 | atpA, atpF, matK, rpl32, ycf1 | 6 |
| Oropetium aristatum | Chloroplast | 1 | rpl2 | 4 |
| Orthotrichum diaphanum | Mitochondrion | 4 | nad9, rpL16, tatC, trnI | 5 |
| Orthotrichum macrocephalum | Mitochondrion | 4 | nad9, rpL16, tatC, trnI | 5 |
| Orthotrichum speciosum | Mitochondrion | 3 | ND9, rpL16, tatC | 4 |
| Orthotrichum stellatum | Mitochondrion | 3 | ccmFN, tatC, trnI | 3 |
| Orychophragmus diffusus | Chloroplast | 1 | ndhD | 1 |
| Orychophragmus hupehensis | Chloroplast | 1 | ndhD | 1 |
| Orychophragmus taibaiensis | Chloroplast | 1 | ndhD | 1 |
| Oryza alta | Chloroplast | 1 | rpl2 | 4 |
| Oryza australiensis | Chloroplast | 1 | rpl2 | 4 |
| Oryza barthii | Chloroplast | 1 | rpl2 | 4 |
| Oryza brachyantha | Chloroplast | 1 | rpl2 | 4 |
| Oryza eichingeri | Chloroplast | 1 | rpl2 | 4 |
| Oryza glumipatula | Chloroplast | 1 | rpl2 | 4 |
| Oryza grandiglumis | Chloroplast | 1 | rpl2 | 4 |
| Oryza latifolia | Chloroplast | 1 | rpl2 | 4 |
| Oryza longiglumis | Chloroplast | 1 | rpl2 | 4 |
| Oryza longistaminata | Chloroplast | 1 | rpl2 | 4 |
| Oryza meyeriana | Chloroplast | 1 | rpl2 | 4 |
| Oryza nivara SL10 | Chloroplast | 1 | rpl2 | 4 |
| Oryza officinalis | Chloroplast | 1 | rpl2 | 4 |
| Oryza punctata | Chloroplast | 1 | rpl2 | 4 |
| Oryza rhizomatis | Chloroplast | 1 | rpl2 | 4 |
| Oryza ridleyi | Chloroplast | 1 | rpl2 | 4 |
| Oryza sativa | Chloroplast | 1 | rpl2 | 4 |
| Oryza sativa Indica Group | Chloroplast
Mitochondrion | 6 | atp9, ccmFc, nad1, nad4L, ND5, rpl2 | 28 |
| Oryza sativa Japonica Group | Mitochondrion | 34 | atp1, atp6, atp9, ccmB, ccmC, ccmFc, ccmFn, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, nad9, orf25, orfB, orfX, rpl16, rpl2, rpl5, rps1, rps11, rps13, rps19, rps2, rps3, rps4, rps7 | 485 |
| Oryzopsis asperifolia | Plastid | 1 | rpl2 | 4 |
| Osmundastrum cinnamomeum | Chloroplast | 4 | atpH, petB, petN, rps7 | 5 |
| Ostericum grosseserratum | Chloroplast | 1 | ndhD | 1 |
| Osyris alba | Chloroplast | 1 | Novel | 1 |
| Otachyrium versicolor | Chloroplast | 1 | rpl2 | 4 |
| Otatea acuminata | Plastid | 1 | rpl2 | 4 |
| Oxyria sinensis | Chloroplast | 1 | ndhD | 1 |
| Oziroe biflora | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Pachycladon enysii | Chloroplast | 1 | ndhD | 1 |
| Pachysandra terminalis | Chloroplast | 3 | ndhD, psbL, rpl2 | 6 |
| Paeonia obovata | Chloroplast | 2 | ndhD, psbL | 2 |
| Panax japonicus | Chloroplast | 1 | ndhD | 1 |
| Panax notoginseng | Chloroplast | 1 | ndhD | 1 |
| Panax quinquefolius | Chloroplast | 1 | ndhD | 1 |
| Panax stipuleanatus | Chloroplast | 1 | ndhD | 1 |
| Panax vietnamensis | Chloroplast | 1 | ndhD | 1 |
| Panicum capillare | Chloroplast | 1 | rpl2 | 4 |
| Panicum lycopodioides | Chloroplast | 1 | rpl2 | 4 |
| Panicum miliaceum | Plastid | 1 | rpl2 | 5 |
| Panicum pygmaeum | Chloroplast | 1 | rpl2 | 4 |
| Panicum sumatrense | Chloroplast | 1 | rpl2 | 4 |
| Panicum virgatum | Chloroplast | 22 | atpA, matK, ndhA, ndhB, ndhD, ndhF, Novel, petB, psbB, psbE, psbF, rbcL, rpl2, rpl20, rpoA, rpoB, rpoC2, rps14, rps16, rps2, rps8, ycf3 | 35 |
| Papaver somniferum | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Paphiopedilum armeniacum | Chloroplast | 4 | petN, psbT, rpl2, rps19 | 8 |
| Paphiopedilum niveum | Chloroplast | 4 | petN, psbT, rpl2, rps19 | 7 |
| Parachlorella kessleri | Chloroplast | 1 | trnI | 2 |
| Paradoxia multiseta | Chloroplast | 1 | trnI | 1 |
| Parahyparrhenia siamensis | Chloroplast | 2 | rpl2, rps19 | 6 |
| Pararchidendron pruinosum | Chloroplast | 2 | ndhD, psbL | 3 |
| Parastrephia quadrangularis | Chloroplast | 2 | ndhD, psbL | 2 |
| Pariana radiciflora | Plastid | 1 | rpl2 | 4 |
| Parinari campestris | Chloroplast | 1 | ndhD | 1 |
| Paris cronquistii | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Paris luquanensis | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Paris mairei | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Paris marmorata | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Paris polyphylla var. chinensis | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Paris quadrifolia | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Paris verticillata | Plastid | 2 | ndhD, rpl2 | 5 |
| Paris vietnamensis | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Parkia javanica | Chloroplast | 2 | ndhD, psbL | 2 |
| Parthenium argentatum | Chloroplast | 1 | ndhD | 1 |
| Paspalidium geminatum | Chloroplast | 1 | rpl2 | 4 |
| Paspalum dilatatum | Chloroplast | 1 | rpl2 | 4 |
| Paspalum fimbriatum | Chloroplast | 1 | rpl2 | 4 |
| Paspalum glaziovii | Chloroplast | 1 | rpl2 | 4 |
| Paspalum paniculatum | Chloroplast | 1 | rpl2 | 4 |
| Paulownia coreana | Chloroplast | 1 | ndhD | 1 |
| Paulownia tomentosa | Chloroplast | 1 | ndhD | 1 |
| Pedinomonas tuberculata | Chloroplast | 1 | trnI | 1 |
| Pelargonium alternans | Chloroplast | 23 | atpA, atpF, ccsA, clpP, matK, ndhA, ndhB, ndhD, ndhF, ndhG, petB, petD, psbE, psbF, psbL, rpl2, rpl20, rpoB, rpoC1, rpoC2, rps14, rps2, ycf3 | 65 |
| Pelargonium australe | Chloroplast | 1 | psbL | 1 |
| Pelargonium citronellum | Chloroplast | 1 | psbL | 1 |
| Pelargonium cotyledonis | Chloroplast | 1 | psbL | 1 |
| Pelargonium cucullatum | Chloroplast | 1 | psbL | 1 |
| Pelargonium dichondrifolium | Chloroplast | 2 | ndhD, psbL | 2 |
| Pelargonium dolomiticum | Chloroplast | 1 | psbL | 1 |
| Pelargonium echinatum | Chloroplast | 1 | psbL | 1 |
| Pelargonium endlicherianum | Plastid | 1 | psbL | 2 |
| Pelargonium exhibens | Chloroplast | 1 | psbL | 1 |
| Pelargonium exstipulatum | Chloroplast | 2 | ndhD, psbL | 2 |
| Pelargonium fulgidum | Chloroplast | 1 | psbL | 1 |
| Pelargonium incrassatum | Chloroplast | 1 | psbL | 1 |
| Pelargonium myrrhifolium | Chloroplast | 1 | psbL | 1 |
| Pelargonium nanum | Chloroplast | 1 | psbL | 1 |
| Pelargonium quercifolium | Chloroplast | 1 | psbL | 1 |
| Pelargonium quinquelobatum | Plastid | 1 | psbL | 2 |
| Pelargonium spinosum | Plastid | 1 | psbL | 2 |
| Pelargonium tetragonum | Chloroplast | 1 | psbL | 1 |
| Pelargonium transvaalense | Chloroplast | 1 | psbL | 2 |
| Pelargonium trifidum | Chloroplast | 1 | psbL | 1 |
| Pelargonium x hortorum | Chloroplast | 2 | ndhD, psbL | 3 |
| Pelatantheria scolopendrifolia | Chloroplast | 1 | trnI-CAU | 2 |
| Pentalinon luteum | Plastid | 1 | ndhD | 1 |
| Pentaphylax euryoides | Plastid | 1 | ndhD | 1 |
| Penthorum chinense | Chloroplast | 3 | ndhD, ndhH, psbL | 3 |
| Persea americana | Chloroplast | 5 | ndhB, ndhD, psbL, rpl2, rpoC2 | 9 |
| Petrosavia stellaris | Plastid | 1 | rpl2 | 1 |
| Peucedanum insolens | Chloroplast | 1 | ndhD | 1 |
| Peucedanum japonicum | Chloroplast | 1 | ndhD | 1 |
| Phacotus lenticularis | Chloroplast | 1 | trnI | 2 |
| Phaenanthoecium koestlinii | Chloroplast | 2 | psbC, rpl2 | 5 |
| Phaenosperma globosum | Plastid | 1 | rpl2 | 4 |
| Phaeoceros laevis | Mitochondrion | 22 | atp1, atp4, atp6, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad9, Novel, PhlaMp02, rps13, sdh4, tatC, trnY | 126 |
| Phalaenopsis aphrodite subsp. formosana | Chloroplast | 7 | ndhB, ndhC, ndhD, ndhJ, ndhK, rpl2, ycf1 | 11 |
| Phalaenopsis equestris | Chloroplast | 29 | accD, atpA, atpB, atpF, atpI, clpP, matK, ndhB, ndhC, ndhD, ndhJ, ndhK, petB, petL, psaI, psbF, psbH, rpl2, rpl23, rpoA, rpoB, rpoC1, rpoC2, rps14, rps16, rps2, rps8, ycf1, ycf3 | 50 |
| Phalaenopsis hybrid cultivar | Chloroplast | 1 | rpl2 | 2 |
| Phalaris arundinacea | Plastid | 1 | rpl2 | 4 |
| Pharus lappulaceus | Chloroplast | 1 | rpl2 | 4 |
| Pharus latifolius | Chloroplast | 1 | rpl2 | 4 |
| Phaseolus vulgaris | Chloroplast | 1 | ndhD | 1 |
| Phedimus takesimensis | Chloroplast | 1 | psbL | 1 |
| Pheidochloa gracilis | Chloroplast | 1 | rpl2 | 4 |
| Phelipanche purpurea | Chloroplast | 2 | rpl14, rps4 | 2 |
| Phellodendron amurense | Chloroplast | 1 | ndhD | 1 |
| Phlegmariurus squarrosus | Mitochondrion | 13 | atp9, cob, cox1, cox3, nad1, nad5, nad9, Novel, rpl6, rps12, rps13, rps2, sdh4 | 30 |
| Phleum alpinum | Plastid | 1 | rpl2 | 4 |
| Phoebe bournei | Chloroplast | 5 | ndhB, ndhD, psbL, rpl2, rpoC2 | 9 |
| Phoebe chekiangensis | Chloroplast | 5 | ndhB, ndhD, psbL, rpl2, rpoC2 | 9 |
| Phoebe omeiensis | Chloroplast | 5 | ndhB, ndhD, psbL, rpl2, rpoC2 | 9 |
| Phoebe sheareri | Chloroplast | 5 | ndhB, ndhD, psbL, rpl2, rpoC2 | 9 |
| Phoebe zhennan | Chloroplast | 5 | ndhB, ndhD, psbL, rpl2, rpoC2 | 9 |
| Phoenix dactylifera | Mitochondrion | 7 | atp1, atp4, atp9, nad1, nad4L, rpl16, rps19 | 56 |
| Phragmipedium longifolium | Chloroplast | 1 | rpl2 | 4 |
| Phragmites australis | Chloroplast | 1 | rpl2 | 4 |
| Phyllorachis sagittata | Chloroplast | 1 | rpl2 | 4 |
| Phyllostachys propinqua | Chloroplast | 1 | rpl2 | 4 |
| Physalis peruviana | Plastid | 2 | ndhD, psbL | 2 |
| Physcomitrella patens | Chloroplast | 1 | rps14 | 1 |
| Phytelephas aequatorialis | Plastid | 4 | cemA, ndhD, rpl2, rps19 | 8 |
| Picea abies | Chloroplast | 1 | trnI-CAU | 1 |
| Picea asperata | Chloroplast | 3 | petL, ycf1, ycf2 | 3 |
| Picea crassifolia | Chloroplast | 3 | petL, ycf1, ycf2 | 3 |
| Picea morrisonicola | Chloroplast | 4 | petA, petL, psbZ, trnI | 5 |
| Picocystis salinarum | Chloroplast | 1 | trnI | 1 |
| Pigafetta elata | Plastid | 1 | rpl2 | 4 |
| Pimenta dioica | Plastid | 1 | ndhD | 1 |
| Pinellia ternata | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Pinus sylvestris | Chloroplast | 3 | petL, psbZ, trnI-CAU | 4 |
| Pinus taiwanensis | Chloroplast | 1 | trnI | 2 |
| Piper auritum | Plastid | 2 | rpl2, rpoC2 | 5 |
| Piper cenocladum | Chloroplast | 3 | ndhD, petD, psbL | 4 |
| Piptadenia communis | Chloroplast | 2 | ndhD, psbL | 2 |
| Piptatherum songaricum | Chloroplast | 1 | rpl2 | 4 |
| Piptochaetium avenaceum | Plastid | 1 | rpl2 | 4 |
| Pisum sativum | Chloroplast | 1 | ndhD | 1 |
| Pithecellobium flexicaule | Chloroplast | 2 | ndhD, psbL | 3 |
| Plagiantha tenella | Chloroplast | 1 | rpl2 | 4 |
| Planctonema lauterbornii | Chloroplast | 1 | trnI | 1 |
| Platanus occidentalis | Chloroplast | 3 | ndhD, psbL, rpl2 | 6 |
| Pleioblastus maculatus | Chloroplast | 1 | rpl2 | 4 |
| Pleodorina starrii NIES-1363 | Plastid | 1 | trnI | 1 |
| Pleurospermum camtschaticum | Chloroplast | 1 | ndhD | 1 |
| Pleurozia purpurea | Mitochondrion | 8 | atp9, ccmB, cob, nad2, nad4, nad4L, nad6, sdh3 | 10 |
| Plinia trunciflora | Chloroplast | 2 | ndhD, psbL | 2 |
| Poa palustris | Plastid | 1 | rpl2 | 4 |
| Pogonatherum paniceum | Chloroplast | 1 | rpl2 | 4 |
| Pogostemon stellatus | Chloroplast | 1 | ndhD | 1 |
| Pogostemon yatabeanus | Chloroplast | 1 | ndhD | 1 |
| Polygonatum stenophyllum | Chloroplast | 1 | rpl2 | 4 |
| Polygonatum verticillatum | Chloroplast | 1 | ndhD | 1 |
| Polyspora axillaris | Plastid | 1 | ndhD | 1 |
| Polyspora dalgleishiana | Plastid | 1 | ndhD | 1 |
| Polyspora hainanensis | Plastid | 1 | ndhD | 1 |
| Polyspora longicarpa | Plastid | 1 | ndhD | 1 |
| Polyspora speciosa | Plastid | 1 | ndhD | 1 |
| Polytoca digitata | Chloroplast | 2 | rpl2, rps19 | 6 |
| Populus alba | Chloroplast | 1 | ndhD | 1 |
| Populus rotundifolia | Chloroplast | 1 | rpl2 | 1 |
| Populus trichocarpa | Chloroplast | 1 | ndhD | 1 |
| Portulaca oleracea | Chloroplast | 1 | psbL | 1 |
| Pouteria campechiana | Chloroplast | 2 | ndhD, trnI-CAU | 3 |
| Prasinoderma coloniale | Chloroplast | 1 | trnI | 1 |
| Premna microphylla | Chloroplast | 2 | ndhD, trnI-CAU | 3 |
| Primula poissonii | Chloroplast | 1 | ndhD | 1 |
| Prinsepia utilis | Plastid | 1 | psbL | 1 |
| Pritchardia thurstonii | Plastid | 2 | ndhD, rpl2 | 5 |
| Prunus cerasoides | Chloroplast | 1 | psbL | 1 |
| Prunus humilis | Chloroplast | 1 | psbL | 1 |
| Prunus kansuensis | Chloroplast | 1 | psbL | 1 |
| Prunus maximowiczii | Chloroplast | 1 | psbL | 1 |
| Prunus padus | Chloroplast | 1 | psbL | 1 |
| Prunus persica | Chloroplast | 1 | psbL | 1 |
| Prunus serotina | Chloroplast | 1 | psbL | 1 |
| Prunus yedoensis | Chloroplast | 1 | psbL | 1 |
| Przewalskia tangutica | Chloroplast | 2 | ndhD, psbL | 2 |
| Pseudocharacium americanum | Chloroplast | 1 | trnI | 1 |
| Pseudochlorella signiensis | Chloroplast | 2 | trnI, trnR | 2 |
| Pseudochloris wilhelmii | Chloroplast | 1 | trnI | 1 |
| Pseudolasiacis leptolomoides | Chloroplast | 1 | rpl2 | 4 |
| Pseudoneochloris marina | Chloroplast | 1 | trnI | 1 |
| Pseudophegopteris aurita | Chloroplast | 61 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbL, psbM, rpl14, rpl16, rpl2, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3, ycf4 | 140 |
| Pseudophoenix vinifera | Plastid | 1 | rpl2 | 4 |
| Pseudosorghum fasciculare | Chloroplast | 2 | rpl2, rps19 | 6 |
| Psidium guajava | Chloroplast | 3 | ndhD, psbL, trnI-CAU | 4 |
| Psilotum nudum | Mitochondrion | 45 | atp1, atp4, atp6, atp8, atp9, ccmB, ccmC, ccmFc, ccmFn, cob, cox1, cox2, cox3, matR, mttB, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, nad9, Novel, rpl16, rpl2, rpl5, rpl6, rps1, rps10, rps11, rps12, rps13, rps14, rps19, rps2, rps3, rps4, rps7, rrn18, rrn26, rrn5, sdh3, sdh4 | 984 |
| Pteridium aquilinum subsp. aquilinum | Chloroplast | 46 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, infA, matK, ndhC, ndhF, petA, petB, petN, psaA, psaB, psbB, psbC, psbD, psbE, psbL, psbM, rpl16, rpl2, rpl20, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps15, rps18, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3 | 120 |
| Pterogastra divaricata | Chloroplast | 1 | ndhD | 1 |
| Pterygopleurum neurophyllum | Chloroplast | 1 | ndhD | 1 |
| Ptilidium pulcherrimum | Chloroplast | 5 | chlN, matK, rpl23, rpoC2, ycf68 | 6 |
| Ptychomnion cygnisetum | Mitochondrion | 7 | atp1, atp9, ccmFC, ccmFN, rps3, tatC, trnI | 8 |
| Puccinellia nuttalliana | Plastid | 1 | rpl2 | 4 |
| Puelia olyriformis | Chloroplast | 1 | rpl2 | 4 |
| Pugionium cornutum | Chloroplast | 1 | ndhD | 1 |
| Pugionium dolabratum | Chloroplast | 1 | ndhD | 1 |
| Punica granatum | Chloroplast | 2 | ndhD, psbL | 2 |
| Pyramimonas parkeae CCMP 726 | Chloroplast | 1 | trnI | 2 |
| Pyramimonas parkeae SCCAP K-0007 | Mitochondrion | 1 | trnI | 2 |
| Pyrenaria diospyricarpa | Plastid | 1 | ndhD | 1 |
| Pyrenaria khasiana | Plastid | 1 | ndhD | 1 |
| Pyrenaria menglaensis | Plastid | 1 | ndhD | 1 |
| Pyrenaria microcarpa | Plastid | 1 | ndhD | 1 |
| Pyrenaria oblongicarpa | Plastid | 1 | ndhD | 1 |
| Pyrenaria pingpienensis | Plastid | 1 | ndhD | 1 |
| Pyrus pashia | Chloroplast | 1 | psbL | 1 |
| Racomitrium elongatum | Mitochondrion | 1 | trnI | 1 |
| Racomitrium emersum | Mitochondrion | 1 | trnI | 1 |
| Racomitrium ericoides | Mitochondrion | 1 | trnI | 1 |
| Racomitrium lanuginosum | Mitochondrion | 1 | trnI | 1 |
| Raddia brasiliensis | Plastid | 1 | rpl2 | 4 |
| Raphanus sativus | Mitochondrion | 1 | cox2 | 2 |
| Ravenala madagascariensis | Plastid | 2 | rpl2, rpl33 | 5 |
| Rhachidosorus consimilis | Chloroplast | 60 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbL, psbM, rpl14, rpl16, rpl2, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3 | 140 |
| Rhazya stricta | Mitochondrion
Plastid | 13 | atp1, atp6, atp9, cox1, cox2, cox3, nad4, nad5, nad7, ndhD, rpl5, rps10, rps7 | 292 |
| Rheum palmatum | Chloroplast | 1 | ndhD | 1 |
| Rheum wittrockii | Plastid | 3 | ndhD, psbL, trnI-CAU | 3 |
| Rhexia virginica | Chloroplast | 1 | ndhD | 1 |
| Rhipidocladum pittieri | Chloroplast | 1 | rpl2 | 4 |
| Rhizanthella gardneri | Plastid | 3 | rpl16, rpl2, trnI | 5 |
| Rhus chinensis | Chloroplast | 1 | ndhD | 1 |
| Rhynchanthera bracteata | Chloroplast | 1 | ndhD | 1 |
| Rhynchoryza subulata | Plastid | 2 | rpl2, rps15 | 6 |
| Rottboellia cochinchinensis | Chloroplast | 1 | rpl2 | 4 |
| Roya obtusa | Chloroplast
Mitochondrion | 1 | trnI | 4 |
| Rytidosperma semiannulare | Chloroplast | 1 | rpl2 | 2 |
| Sabal domingensis | Plastid | 1 | rpl2 | 4 |
| Sabia yunnanensis | Chloroplast | 3 | ndhD, psbL, rpl2 | 6 |
| Saccharum arundinaceum | Chloroplast | 1 | rpl2 | 4 |
| Saccharum hildebrandtii | Chloroplast | 1 | rpl2 | 4 |
| Saccharum hybrid cultivar | Chloroplast | 1 | rpl2 | 4 |
| Saccharum hybrid cultivar SP80-3280 | Chloroplast | 13 | atpA, ndhA, ndhB, ndhD, ndhF, petB, rpl2, rpl20, rpoB, rpoC2, rps14, rps8, ycf3 | 25 |
| Saccharum officinarum | Chloroplast | 1 | rpl2 | 4 |
| Saccharum spontaneum | Chloroplast | 1 | rpl2 | 4 |
| Sacciolepis indica | Chloroplast | 1 | rpl2 | 4 |
| Sagittaria lichuanensis | Plastid | 1 | ndhD | 1 |
| Salacca ramosiana | Plastid | 3 | ndhD, rpl2, rps19 | 7 |
| Salicornia bigelovii | Chloroplast | 2 | ndhD, psbL | 2 |
| Salicornia brachiata | Chloroplast | 1 | psbL | 1 |
| Salicornia europaea | Chloroplast | 2 | ndhD, psbL | 2 |
| Salix arbutifolia | Chloroplast | 1 | ndhD | 1 |
| Salix babylonica | Chloroplast | 1 | ndhD | 1 |
| Salix purpurea | Chloroplast
Mitochondrion | 3 | ndhD, rpl10, rpl16 | 6 |
| Salix suchowensis | Chloroplast | 1 | ndhD | 1 |
| Salpinga maranonensis | Chloroplast | 1 | ndhD | 1 |
| Salvia miltiorrhiza | Mitochondrion | 4 | atp8, nad4L, rpl16, rps10 | 5 |
| Salvia rosmarinus | Chloroplast | 1 | ndhD | 1 |
| Samanea saman | Chloroplast | 2 | ndhD, psbL | 3 |
| Sambucus williamsii | Chloroplast | 1 | ndhD | 1 |
| Sanionia uncinata | Chloroplast
Mitochondrion | 7 | atp1, ccmFN, cox3, nad1, tatC, trnI, trnI-CAU | 16 |
| Saracha punctata | Chloroplast | 3 | ndhD, psbL, rps16 | 4 |
| Sarcinofilum mucosum | Chloroplast | 1 | trnI | 1 |
| Sarocalamus faberi | Chloroplast | 1 | rpl2 | 2 |
| Sartidia dewinteri | Chloroplast | 1 | rpl2 | 4 |
| Sartidia isaloensis | Chloroplast | 1 | rpl2 | 4 |
| Sartidia perrieri | Chloroplast | 1 | rpl2 | 4 |
| Saussurea chabyoungsanica | Chloroplast | 2 | ndhD, psbL | 2 |
| Saussurea involucrata | Chloroplast | 1 | psbL | 1 |
| Schefflera heptaphylla | Chloroplast | 1 | ndhD | 1 |
| Scherffelia dubia | Plastid | 1 | trnI | 1 |
| Schima argentea | Plastid | 1 | ndhD | 1 |
| Schima brevipedicellata | Plastid | 1 | ndhD | 1 |
| Schima crenata | Plastid | 1 | ndhD | 1 |
| Schima khasiana | Plastid | 1 | ndhD | 1 |
| Schima multibracteata | Plastid | 1 | ndhD | 1 |
| Schima noronhae | Plastid | 1 | ndhD | 1 |
| Schima remotiserrata | Plastid | 1 | ndhD | 1 |
| Schima sericans | Plastid | 1 | ndhD | 1 |
| Schima sinensis | Plastid | 1 | ndhD | 1 |
| Schima superba | Plastid | 1 | ndhD | 1 |
| Schima wallichii | Plastid | 1 | ndhD | 1 |
| Schisandra chinensis | Chloroplast | 2 | ndhD, psbL | 2 |
| Schismus arabicus | Chloroplast | 1 | rpl2 | 4 |
| Schizachyrium brevifolium | Chloroplast | 2 | rpl2, rps19 | 5 |
| Schizachyrium exile | Chloroplast | 2 | rpl2, rps19 | 6 |
| Schizachyrium imberbe | Chloroplast | 2 | rpl2, rps19 | 6 |
| Schizachyrium sanguineum | Chloroplast | 2 | rpl2, rps19 | 6 |
| Schizachyrium scoparium | Chloroplast | 2 | rpl2, rps19 | 6 |
| Schizachyrium spicatum | Chloroplast | 2 | rpl2, rps19 | 6 |
| Schizachyrium tenerum | Chloroplast | 2 | rpl2, rps19 | 6 |
| Schizaea elegans | Chloroplast | 35 | accD, atpA, atpB, atpH, atpI, ccsA, chlB, chlL, infA, Novel, petA, petD, petN, psaA, psaB, psaC, psbB, psbE, psbL, rpl14, rpl16, rpl2, rpl32, rpoA, rpoB, rpoC1, rpoC2, rps11, rps15, rps2, rps3, rps4, ycf1, ycf2, ycf4 | 89 |
| Schizaea pectinata | Chloroplast | 39 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, petA, petD, petN, psaA, psaB, psaC, psaJ, psbB, psbE, psbL, rpl2, rpl32, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps14, rps15, rps16, rps2, rps3, rps4, ycf1, ycf2, ycf4 | 103 |
| Schizomeris leibleinii | Chloroplast | 1 | trnI | 1 |
| Schoenolirion croceum | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Schwalbea americana | Chloroplast | 1 | ndhK | 1 |
| Sciadopitys verticillata | Chloroplast | 1 | rps8 | 1 |
| Scopolia parviflora | Chloroplast | 2 | ndhD, psbL | 2 |
| Secale cereale | Chloroplast | 1 | rpl2 | 2 |
| Sedum oryzifolium | Chloroplast | 3 | ndhD, psbL, rpl22 | 3 |
| Sedum sarmentosum | Chloroplast | 5 | ndhD, ndhH, psbL, rpl22, rpoC1 | 5 |
| Senegalia laeta | Chloroplast | 2 | ndhD, psbL | 2 |
| Senna tora | Chloroplast | 2 | ndhD, psbL | 2 |
| Sequoia sempervirens | Chloroplast | 1 | rpl16 | 1 |
| Serenoa repens | Plastid | 1 | rpl2 | 4 |
| Sesamum indicum | Chloroplast | 1 | ndhD | 1 |
| Setaria viridis | Chloroplast | 1 | rpl2 | 4 |
| Silene capitata | Chloroplast | 2 | ndhD, psbL | 2 |
| Silene chalcedonica | Chloroplast | 2 | ndhD, psbL | 2 |
| Silene conica | Chloroplast | 12 | atpA, matK, ndhA, ndhB, ndhD, ndhG, petL, psbZ, rpoA, rpoB, rps2, trnI-CAU | 26 |
| Silene conoidea | Chloroplast | 2 | ndhD, psbL | 2 |
| Silene latifolia | Chloroplast | 13 | atpA, clpP, matK, ndhA, ndhB, ndhD, petL, psbF, psbL, psbZ, rpoB, rps2, trnI-CAU | 26 |
| Silene noctiflora | Chloroplast | 13 | atpA, matK, ndhA, ndhB, ndhD, ndhG, petL, psbL, psbZ, rpoA, rpoB, rps2, trnI-CAU | 25 |
| Silene paradoxa | Chloroplast | 2 | ndhD, psbL | 2 |
| Silene vulgaris | Chloroplast
Mitochondrion | 15 | atpA, clpP, matK, ndhA, ndhB, ndhD, ndhG, petL, psbL, psbZ, rpoA, rpoB, rps2, trnI-CAT, trnI-CAU | 56 |
| Sinadoxa corydalifolia | Chloroplast | 1 | ndhD | 1 |
| Sinalliaria limprichtiana | Chloroplast | 1 | ndhD | 1 |
| Sinalliaria limprichtiana var. grandifolia | Chloroplast | 2 | ndhD, trnI | 2 |
| Sinapis arvensis | Mitochondrion | 2 | matR, nad1 | 6 |
| Sinojackia rehderiana | Plastid | 1 | ndhD | 1 |
| Sinojackia xylocarpa | Chloroplast | 1 | ndhD | 1 |
| Sinowilsonia henryi | Chloroplast | 1 | ndhD | 1 |
| Siphocampylus krauseanus | Chloroplast | 1 | ndhD | 1 |
| Sladenia celastrifolia | Plastid | 1 | ndhD | 1 |
| Sobralia aff. bouchei HTK-2015 | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Sobralia callosa | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Solanum berthaultii | Chloroplast | 2 | ndhD, psbL | 2 |
| Solanum bulbocastanum | Chloroplast | 2 | ndhD, psbL | 2 |
| Solanum cheesmaniae | Chloroplast | 2 | ndhD, psbL | 2 |
| Solanum chilense | Chloroplast | 2 | ndhD, psbL | 2 |
| Solanum commersonii Lz3.2 | Chloroplast | 2 | ndhD, psbL | 2 |
| Solanum galapagense | Chloroplast | 2 | ndhD, psbL | 2 |
| Solanum habrochaites | Chloroplast | 2 | ndhD, psbL | 2 |
| Solanum lycopersicum | Chloroplast
Mitochondrion | 20 | atpF, cox1, ndhA, ndhB, ndhD, ndhF, ndhG, petB, psbE, psbL, rpl20, rpoA, rpoB, rpoC1, rpoC2, rps10, rps12, rps14, rps2, rps4 | 126 |
| Solanum melongena | Plastid | 1 | ndhD | 1 |
| Solanum neorickii | Chloroplast | 3 | ndhD, psbL, psbT | 3 |
| Solanum nigrum | Chloroplast | 2 | ndhD, psbL | 2 |
| Solanum pennellii | Chloroplast
Mitochondrion | 5 | cox1, ndhD, psbL, rps10, rps4 | 12 |
| Solanum peruvianum | Chloroplast | 3 | ndhD, psbL, psbT | 3 |
| Solanum pimpinellifolium | Chloroplast | 2 | ndhD, psbL | 2 |
| Solanum tuberosum | Chloroplast | 2 | ndhD, psbL | 2 |
| Soliva sessilis | Chloroplast | 2 | ndhD, psbL | 2 |
| Sophora alopecuroides | Chloroplast | 2 | ndhD, psbL | 8 |
| Sorghastrum nutans | Chloroplast | 1 | rpl2 | 4 |
| Sorghum bicolor | Chloroplast
Mitochondrion | 5 | ccmFC, nad1, nad4L, rpl2, trnI | 16 |
| Sphagnum palustre | Mitochondrion | 3 | atp1, tatC, trnI | 4 |
| Spinacia oleracea | Plastid | 1 | psbL | 1 |
| Spirodela polyrhiza 7498 | Chloroplast
Mitochondrion | 7 | atp4, cox2, nad1, nad4L, ndhD, rpl20, rpoC1 | 24 |
| Spirogyra maxima | Chloroplast | 1 | trnI | 1 |
| Sporobolus heterolepis | Plastid | 1 | rpl2 | 4 |
| Sporobolus maritimus | Chloroplast | 1 | rpl2 | 4 |
| Sporobolus michauxianus | Plastid | 1 | rpl2 | 4 |
| Stangeria eriopus | Chloroplast | 2 | petL, trnI | 2 |
| Stegnogramma sagittifolia | Chloroplast | 59 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbL, psbM, rpl14, rpl16, rpl2, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps16, rps18, rps19, rps2, rps3, rps4, rps7, ycf1, ycf2, ycf3 | 140 |
| Steinchisma laxum | Chloroplast | 1 | rpl2 | 4 |
| Stenotaphrum secundatum | Chloroplast | 1 | rpl2 | 4 |
| Stephania japonica | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Stewartia calcicola | Plastid | 1 | ndhD | 1 |
| Stewartia cordifolia | Plastid | 1 | ndhD | 1 |
| Stewartia crassifolia | Plastid | 1 | ndhD | 1 |
| Stewartia malacodendron | Plastid | 1 | ndhD | 1 |
| Stewartia ovata | Plastid | 1 | ndhD | 1 |
| Stewartia pseudocamellia | Plastid | 1 | ndhD | 1 |
| Stewartia pteropetiolata | Plastid | 1 | ndhD | 1 |
| Stewartia rostrata | Plastid | 1 | ndhD | 1 |
| Stewartia rubiginosa | Plastid | 1 | ndhD | 1 |
| Stewartia sinensis | Plastid | 1 | ndhD | 1 |
| Stichococcus bacillaris | Chloroplast | 1 | trnI | 1 |
| Stipa hymenoides | Plastid | 1 | rpl2 | 4 |
| Stipagrostis hirtigluma | Chloroplast | 1 | rpl2 | 4 |
| Stockwellia quadrifida | Chloroplast | 1 | ndhD | 1 |
| Stoneobryum mirum | Mitochondrion | 1 | trnI | 1 |
| Stratiotes aloides | Mitochondrion | 2 | nad1, nad4L | 2 |
| Streptochaeta spicata | Chloroplast | 1 | rpl2 | 4 |
| Streptostachys asperifolia | Chloroplast | 1 | rpl2 | 4 |
| Styppeiochloa gynoglossa | Chloroplast | 2 | psbC, rpl2 | 5 |
| Styrax grandiflorus | Chloroplast | 1 | ndhD | 1 |
| Syagrus coronata | Chloroplast | 1 | rpl2 | 4 |
| Symbiochloris reticulata | Chloroplast | 1 | trnI | 1 |
| Symplocarpus renifolius | Chloroplast | 1 | ndhD | 1 |
| Symplocos costaricana | Plastid | 1 | ndhD | 1 |
| Symplocos paniculata | Plastid | 1 | ndhD | 1 |
| Syntrichia filaris | Mitochondrion | 4 | nad9, Novel, rpl16, tatC | 5 |
| Syntrichia ruralis | Chloroplast | 3 | atpF, ndhA, rpoB | 3 |
| Tacca leontopetaloides | Chloroplast | 2 | rpl2, trnI-CAU | 6 |
| Tahina spectabilis | Plastid | 1 | rpl2 | 2 |
| Taiwania cryptomerioides | Chloroplast | 1 | trnI | 2 |
| Takakia lepidozioides | Chloroplast | 27 | atpH, ccsA, ndhA, ndhD, ndhG, petB, petD, petG, petL, psaB, psbB, psbD, psbH, psbL, psbZ, rpl14, rpl2, rpl33, rpoA, rpoC1, rpoC2, rps15, rps4, rps7, trnL-UAA, ycf1, ycf4 | 34 |
| Talipariti hamabo | Chloroplast | 1 | ndhD | 1 |
| Tamarindus indica | Chloroplast | 2 | ndhD, psbL | 2 |
| Taraxacum amplum | Chloroplast | 2 | ndhD, psbL | 2 |
| Taraxacum brevicorniculatum | Chloroplast | 1 | psbL | 1 |
| Taraxacum kok-saghyz | Chloroplast | 1 | psbL | 1 |
| Taraxacum mongolicum | Chloroplast | 2 | ndhD, psbL | 2 |
| Taraxacum obtusifrons | Chloroplast | 2 | ndhD, psbL | 2 |
| Taraxacum officinale | Chloroplast | 2 | ndhD, psbL | 2 |
| Taraxacum platycarpum | Chloroplast | 2 | ndhD, psbL | 2 |
| Tarenaya hassleriana | Chloroplast | 1 | ndhD | 1 |
| Tectona grandis | Chloroplast | 2 | ndhD, trnI | 6 |
| Tenaxia guillarmodiae | Plastid | 1 | rpl2 | 4 |
| Ternstroemia gymnanthera | Plastid | 1 | ndhD | 1 |
| Tetracentron sinense | Chloroplast | 3 | ndhD, psbL, rpl2 | 6 |
| Tetradesmus obliquus UTEX 393 | Chloroplast | 1 | trnI | 3 |
| Tetradoxa omeiensis | Chloroplast | 1 | ndhD | 1 |
| Tetraphis pellucida | Chloroplast
Mitochondrion | 4 | nad9, petA, rpl16, tatC | 10 |
| Tetraplodon fuegianus | Mitochondrion | 3 | ccmC, tatC, trnI | 3 |
| Tetrastigma hemsleyanum | Chloroplast | 1 | psbL | 1 |
| Thalictrum coreanum | Plastid | 2 | ndhD, rpl2 | 5 |
| Thamnocalamus spathiflorus | Chloroplast | 1 | rpl2 | 4 |
| Themeda arguens | Chloroplast | 2 | rpl2, rps19 | 6 |
| Themeda arundinacea | Chloroplast | 2 | rpl2, rps19 | 5 |
| Themeda quadrivalvis | Chloroplast | 1 | rpl2 | 4 |
| Themeda triandra | Chloroplast | 2 | rpl2, rps19 | 5 |
| Themeda villosa | Chloroplast | 2 | rpl2, rps19 | 6 |
| Thlaspi arvense | Chloroplast | 1 | ndhD | 1 |
| Thrixspermum japonicum | Chloroplast | 1 | trnI-CAU | 2 |
| Thyridolepis xerophila | Chloroplast | 1 | rpl2 | 4 |
| Thysanolaena latifolia | Plastid | 1 | rpl2 | 4 |
| Tibetia liangshanensis | Chloroplast | 2 | ndhD, psbL | 2 |
| Tibouchina longifolia | Chloroplast | 1 | ndhD | 1 |
| Tigridiopalma magnifica | Chloroplast | 1 | ndhD | 1 |
| Tilia amurensis | Plastid | 1 | ndhD | 1 |
| Tilia mandshurica | Plastid | 1 | ndhD | 1 |
| Tilia oliveri | Plastid | 1 | ndhD | 1 |
| Tilia paucicostata | Plastid | 1 | ndhD | 1 |
| Tofieldia thibetica | Plastid | 2 | ndhD, rpl2 | 3 |
| Torreya fargesii | Chloroplast | 1 | rps11 | 1 |
| Torreyochloa pallida | Plastid | 1 | rpl2 | 4 |
| Trachelium caeruleum | Chloroplast | 1 | psbL | 1 |
| Treubaria triappendiculata | Chloroplast | 1 | trnI | 1 |
| Treubia lacunosa | Mitochondrion | 1 | sdh3 | 1 |
| Tribolium hispidum | Chloroplast | 1 | rpl2 | 4 |
| Tricholaena monachne | Chloroplast | 1 | rpl2 | 4 |
| Trichoneura grandiglumis | Chloroplast | 1 | rpl2 | 4 |
| Trifolium aureum | Plastid | 1 | psbL | 1 |
| Trifolium boissieri | Chloroplast | 2 | ndhD, psbL | 2 |
| Trifolium glanduliferum | Chloroplast | 2 | ndhD, psbL | 2 |
| Trifolium grandiflorum | Plastid | 1 | psbL | 1 |
| Trifolium meduseum | Chloroplast | 2 | ndhD, psbL | 2 |
| Trifolium repens | Plastid | 1 | psbL | 1 |
| Trifolium strictum | Chloroplast | 2 | ndhD, psbL | 2 |
| Trifolium subterraneum | Chloroplast | 1 | psbL | 1 |
| Trillium cuneatum | Plastid | 3 | ndhD, rpl2, trnI-CAU | 7 |
| Trillium decumbens | Plastid | 3 | ndhD, rpl2, trnI-CAU | 7 |
| Trillium maculatum | Plastid | 1 | rpl2 | 4 |
| Trillium tschonoskii | Plastid | 1 | rpl2 | 4 |
| Triolena amazonica | Chloroplast | 1 | ndhD | 1 |
| Tripsacum dactyloides | Mitochondrion | 5 | ccmFC, ccmFC-1, nad1, nad4L, trnI | 7 |
| Trisetum cernuum | Plastid | 1 | rpl2 | 4 |
| Tristachya humbertii | Chloroplast | 1 | rpl2 | 4 |
| Tristachya leucothrix | Chloroplast | 1 | rpl2 | 4 |
| Trithrinax brasiliensis | Plastid | 1 | rpl2 | 4 |
| Triticum aestivum | Chloroplast | 2 | ndhB, rpl2 | 4 |
| Triticum urartu | Chloroplast | 1 | rpl2 | 2 |
| Trochodendron aralioides | Chloroplast | 3 | ndhD, psbL, rpl2 | 4 |
| Tupiella akineta UTEX 1912 | Mitochondrion | 1 | trnI | 1 |
| Tutcheria championii | Plastid | 1 | ndhD | 1 |
| Typha latifolia | Chloroplast | 1 | rpl2 | 4 |
| Ulota hutchinsiae | Mitochondrion | 3 | ccmFN, tatC, trnI | 3 |
| Uniola paniculata | Chloroplast | 1 | rpl2 | 4 |
| Urochloa reptans | Chloroplast | 1 | rpl2 | 4 |
| Utricularia macrorhiza | Chloroplast | 2 | ndhD, psbL | 2 |
| Vaccinium macrocarpon | Mitochondrion | 1 | mttB | 1 |
| Vachellia flava | Chloroplast | 2 | ndhD, psbL | 2 |
| Vachellia seyal | Chloroplast | 2 | ndhD, psbL | 2 |
| Vanilla planifolia | Chloroplast | 4 | petN, psbT, rpl2, rps19 | 8 |
| Vaseyochloa multinervosa | Chloroplast | 1 | rpl2 | 4 |
| Veitchia arecina | Plastid | 1 | rpl2 | 4 |
| Veratrum patulum | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Vernicia fordii | Chloroplast | 1 | ndhD | 1 |
| Viburnum utile | Chloroplast | 2 | ndhD, psbL | 2 |
| Vicia sativa | Chloroplast | 1 | psbL | 1 |
| Victoria cruziana | Chloroplast | 1 | psbL | 1 |
| Vigna angularis | Chloroplast
Mitochondrion | 7 | ccmFc, mttB, nad1, nad4L, nad5, ndhD, rps10 | 26 |
| Vigna radiata var. radiata | Chloroplast
Mitochondrion | 7 | ccmFc, mttB, nad1, nad4L, nad5, ndhD, rps10 | 12 |
| Vigna unguiculata | Chloroplast | 1 | ndhD | 1 |
| Viscum album | Chloroplast | 1 | Novel | 1 |
| Viscum coloratum | Chloroplast | 1 | psbL | 1 |
| Viscum crassulae | Chloroplast | 1 | Novel | 1 |
| Viscum minimum | Chloroplast | 1 | psbL | 1 |
| Vitis acerifolia | Chloroplast | 3 | ndhD, psbL, rpl22 | 3 |
| Vitis aestivalis | Chloroplast | 3 | ndhD, psbL, rpl22 | 3 |
| Vitis amurensis | Chloroplast | 3 | ndhD, psbL, rpl22 | 3 |
| Vitis cinerea | Chloroplast | 5 | ndhD, psbL, rpl22, rps12, rps19 | 5 |
| Vitis coignetiae | Chloroplast | 5 | ndhD, psbL, rpl22, rps12, rps19 | 7 |
| Vitis cordifolia | Chloroplast | 5 | ndhD, psbL, rpl22, rps12, rps19 | 7 |
| Vitis ficifolia | Chloroplast | 5 | ndhD, psbL, rpl22, rps12, rps19 | 7 |
| Vitis mustangensis | Chloroplast | 3 | ndhD, psbL, rpl22 | 3 |
| Vitis rotundifolia | Chloroplast | 2 | ndhD, psbL | 2 |
| Vitis rupestris | Chloroplast | 5 | ndhD, psbL, rpl22, rps12, rps19 | 5 |
| Vitis vinifera | Chloroplast
Mitochondrion | 4 | nad4L, ndhD, psbL, rps10 | 10 |
| Vitis x champinii | Chloroplast | 4 | ndhD, psbL, rpl22, rps19 | 4 |
| Wallichia densiflora | Plastid | 3 | ndhD, rpl2, rps19 | 5 |
| Washingtonia robusta | Plastid | 3 | ndhD, rpl2, rps19 | 6 |
| Watanabea reniformis | Chloroplast | 1 | trnI | 1 |
| Welwitschia mirabilis | Mitochondrion | 10 | atp4, ccmFC, matR, mttB, nad6, nad9, rps3, rps4, sdh4, trnI-CAU | 10 |
| Westoniella kohkemperi | Chloroplast | 2 | ndhD, psbL | 2 |
| Whiteochloa capillipes | Chloroplast | 1 | rpl2 | 4 |
| Wisteria floribunda | Chloroplast | 2 | ndhD, psbL | 2 |
| Wisteria sinensis | Chloroplast | 2 | ndhD, psbL | 2 |
| Woodsia macrochlaena | Chloroplast | 62 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbL, psbM, rpl14, rpl16, rpl2, rpl20, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf3 | 144 |
| Woodsia polystichoides | Chloroplast | 59 | accD, atpA, atpB, atpF, atpH, atpI, chlB, chlL, chlN, infA, matK, ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhK, Novel, petA, petB, petD, petN, psaB, psaC, psbB, psbC, psbD, psbE, psbF, psbH, psbL, psbM, rpl14, rpl2, rpl20, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps15, rps16, rps18, rps19, rps2, rps3, rps4, rps7, ycf1, ycf2, ycf3 | 138 |
| Woodwardia unigemmata | Chloroplast | 53 | accD, atpA, atpB, atpF, atpH, atpI, ccsA, chlB, chlL, infA, matK, ndhB, ndhC, ndhF, ndhG, ndhH, Novel, petA, petB, petN, psaB, psbB, psbC, psbD, psbE, psbI, psbJ, psbL, psbM, rpl14, rpl16, rpl2, rpl21, rpl22, rpl23, rpl36, rpoA, rpoB, rpoC1, rpoC2, rps11, rps12, rps15, rps16, rps18, rps2, rps3, rps4, rps7, rps8, ycf1, ycf2, ycf4 | 126 |
| Xanthorrhoea preissii | Chloroplast | 1 | rpl2 | 4 |
| Xerophyllum tenax | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Xylochloris irregularis | Chloroplast | 1 | trnI | 1 |
| Yucca brevifolia | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Yucca filamentosa | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Yucca queretaroensis | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Yucca schidigera | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Yushania levigata | Chloroplast | 1 | rpl2 | 4 |
| Zamia furfuracea | Chloroplast | 3 | petL, psbZ, trnI | 3 |
| Zantedeschia aethiopica | Chloroplast | 2 | ndhD, rpl2 | 5 |
| Zanthoxylum piperitum | Chloroplast | 1 | ndhD | 1 |
| Zanthoxylum schinifolium | Chloroplast | 1 | ndhD | 1 |
| Zea diploperennis | Plastid | 1 | rpl2 | 4 |
| Zea luxurians | Mitochondrion
Plastid | 5 | ccmFC-1, nad1, nad4L, rpl2, trnI-1 | 16 |
| Zea mays subsp. mays | Mitochondrion | 11 | atp4, atp9, cox2, mat-r, nad1, nad3, nad4L, nad5, nad6, rps12, rps13 | 348 |
| Zea mays subsp. parviglumis | Mitochondrion | 4 | ccmFC, nad1, nad4L, trnI-1 | 4 |
| Zea perennis | Mitochondrion
Plastid | 5 | ccmFC, nad1, nad4L, rpl2, trnI-1 | 16 |
| Zeugites pittieri | Chloroplast | 1 | rpl2 | 4 |
| Zingiber spectabile | Plastid | 1 | rpl2 | 4 |
| Zizania aquatica | Plastid | 1 | rpl2 | 4 |
| Zizania latifolia | Chloroplast | 1 | rpl2 | 4 |
| Ziziphus jujuba | Chloroplast
Mitochondrion | 8 | atp6, atp9, nad1, nad4L, ndhD, psbL, rps10, sdh4 | 26 |
| Zostera marina | Mitochondrion | 2 | nad1, nad4L | 2 |
| Zoysia macrantha | Plastid | 1 | rpl2 | 4 |
| Zygodon viridissimus | Mitochondrion | 1 | trnI | 1 |