OpenLB
Open Library of Bioscience
Advanced Search
Nature communications
Apr 29, 2025;16 (1): 4039.

Evolutionary history of magnoliid genomes and benzylisoquinoline alkaloid biosynthesis.

Yiheng Hu, Jinpeng Wang, Lumei Liu, Xin Yi, Xin Wang, Jianyu Wang, Ya'nan Hao, Liuyu Qin, Kunpeng Li, Yishan Feng, Zhongshuai Zhang, Hanying Wu, Yuannian Jiao
Author Information
  1. Yiheng Hu: State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, China.
  2. Jinpeng Wang: State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, China. ORCID
  3. Lumei Liu: State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, China.
  4. Xin Yi: State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, China.
  5. Xin Wang: State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, China. ORCID
  6. Jianyu Wang: State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, China.
  7. Ya'nan Hao: Department of Bioinformatics, School of Life Sciences, North China University of Science and Technology, Tangshan, China.
  8. Liuyu Qin: State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, China.
  9. Kunpeng Li: State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, China.
  10. Yishan Feng: Department of Bioinformatics, School of Life Sciences, North China University of Science and Technology, Tangshan, China.
  11. Zhongshuai Zhang: State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.
  12. Hanying Wu: Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China.
  13. Yuannian Jiao: State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, China. jiaoyn@ibcas.ac.cn. ORCID
PMID: 40301376 DOI: 10.1038/s41467-025-59343-8

Abstract

Benzylisoquinoline alkaloids (BIAs) are important metabolites synthesized in early-diverging eudicots and magnoliids, yet the genetic basis of BIA biosynthesis in magnoliids remains unclear. Here, we decode the genomes of two magnoliid species, Saruma henryi and Aristolochia manshuriensis, and reconstruct the ancestral magnoliid karyotype and infer the chromosomal rearrangement history following magnoliid diversification. Metabolomic, transcriptomic, and phylogenetic analyses reveal the intermediate chemical components and genetic basis of BIA biosynthesis in A. manshuriensis. Although the core enzymes involved in BIA synthesis appear to be largely conserved between early-diverging eudicots and magnoliids, the biosynthetic pathways in magnoliids seem to exhibit greater flexibility. Significantly, our investigation of the evolutionary history of BIA biosynthetic genes revealed that almost all were duplicated before the emergence of extant angiosperms, with only early-diverging eudicots and magnoliids preferentially retaining these duplicated genes, thereby enabling the biosynthesis of BIAs in these groups.

References

Plant J. 2004 Oct;40(2):302-13 [PMID: 15447655]
Plant J. 2023 Mar;113(5):1021-1034 [PMID: 36602036]
Nat Plants. 2019 Jan;5(1):63-73 [PMID: 30626928]
Nat Commun. 2021 Nov 26;12(1):6929 [PMID: 34836967]
J Plant Physiol. 2023 Jun;285:153983 [PMID: 37116390]
Front Plant Sci. 2021 Apr 12;12:642598 [PMID: 33912209]
Nat Commun. 2019 Oct 16;10(1):4702 [PMID: 31619678]
Mob DNA. 2015 Jun 02;6:11 [PMID: 26045719]
Genome Biol. 2019 Feb 11;20(1):29 [PMID: 30744646]
Mol Phylogenet Evol. 2014 Jan;70:84-93 [PMID: 24055602]
Nature. 2019 Oct;574(7780):679-685 [PMID: 31645766]
Plant Physiol. 2018 Feb;176(2):1410-1422 [PMID: 29233850]
Plant Commun. 2020 Feb 04;1(2):100027 [PMID: 33367231]
Plant J. 2009 Nov;60(4):729-43 [PMID: 19624470]
Am J Bot. 2018 Mar;105(3):348-363 [PMID: 29719043]
Syst Biol. 2022 Feb 10;71(2):301-319 [PMID: 33983440]
Proc Natl Acad Sci U S A. 1995 Mar 14;92(6):2071-5 [PMID: 7892226]
PLoS Comput Biol. 2022 Feb 4;18(2):e1009860 [PMID: 35120119]
Nucleic Acids Res. 2012 Apr;40(7):e49 [PMID: 22217600]
Nat Prod Rep. 2003 Dec;20(6):565-83 [PMID: 14700200]
Mol Biol Evol. 2000 Jan;17(1):32-43 [PMID: 10666704]
Mol Biol Evol. 2013 Apr;30(4):772-80 [PMID: 23329690]
Science. 2017 Apr 7;356(6333):92-95 [PMID: 28336562]
Am J Bot. 2004 Oct;91(10):1614-26 [PMID: 21652312]
Nat Biotechnol. 2011 May 15;29(7):644-52 [PMID: 21572440]
Curr Opin Biotechnol. 2008 Apr;19(2):173-80 [PMID: 18396034]
Nat Methods. 2022 Jun;19(6):679-682 [PMID: 35637307]
OMICS. 2012 May;16(5):284-7 [PMID: 22455463]
Bioinformatics. 2015 Jun 15;31(12):i44-52 [PMID: 26072508]
Nat Plants. 2021 Sep;7(9):1239-1253 [PMID: 34475528]
Nat Protoc. 2012 Mar 01;7(3):562-78 [PMID: 22383036]
Hortic Res. 2023 Apr 19;10(6):uhad073 [PMID: 37303613]
Genome Biol. 2020 Sep 14;21(1):245 [PMID: 32928274]
Nat Biotechnol. 2018 Nov;36(10):983-987 [PMID: 30247488]
Plant Cell. 2014 Jul;26(7):2792-802 [PMID: 25082857]
J Biomol NMR. 2006 Jan;34(1):41-56 [PMID: 16505963]
J Comput Biol. 2000;7(3-4):429-47 [PMID: 11108472]
Science. 2018 Oct 19;362(6412):343-347 [PMID: 30166436]
Mol Biol Evol. 2007 Aug;24(8):1586-91 [PMID: 17483113]
Plant Commun. 2020 Mar 09;1(2):100029 [PMID: 32685922]
Methods Mol Biol. 2019;1962:161-177 [PMID: 31020559]
Nat Rev Genet. 2017 Jul;18(7):411-424 [PMID: 28502977]
Bioinformatics. 2015 Oct 1;31(19):3210-2 [PMID: 26059717]
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W609-12 [PMID: 16845082]
J Ethnopharmacol. 2009 Aug 17;125(1):108-44 [PMID: 19505558]
Nature. 2021 Aug;596(7873):583-589 [PMID: 34265844]
Genetics. 1999 Apr;151(4):1531-45 [PMID: 10101175]
Science. 2002 Aug 9;297(5583):945-7 [PMID: 12169715]
Nat Genet. 2017 Apr;49(4):490-496 [PMID: 28288112]
Phytochemistry. 2005 Jun;66(11):1374-93 [PMID: 15925393]
Bioinformatics. 2016 Sep 15;32(18):2847-9 [PMID: 27207943]
PLoS One. 2013 Nov 12;8(11):e79204 [PMID: 24265760]
Mol Plant. 2020 Jan 6;13(1):59-71 [PMID: 31678615]
New Phytol. 2015 Jan;205(1):378-89 [PMID: 25138576]
Nucleic Acids Res. 2018 Jul 2;46(W1):W200-W204 [PMID: 29905871]
BMC Bioinformatics. 2008 Jan 14;9:18 [PMID: 18194517]
Am J Bot. 2002 Nov;89(11):1809-17 [PMID: 21665609]
Genomics Proteomics Bioinformatics. 2020 Jun;18(3):321-332 [PMID: 33137519]
Nat Commun. 2020 Apr 3;11(1):1675 [PMID: 32245969]
Annu Rev Plant Biol. 2008;59:735-69 [PMID: 18251710]
Nat Commun. 2020 Mar 18;11(1):1432 [PMID: 32188846]
Plant J. 2024 Jun;118(5):1439-1454 [PMID: 38379355]
Curr Protoc Bioinformatics. 2019 Mar;65(1):e57 [PMID: 30466165]
Genome Biol. 2019 Nov 14;20(1):238 [PMID: 31727128]
Nat Commun. 2023 Oct 17;14(1):6556 [PMID: 37848433]
Mol Biol Evol. 2020 May 1;37(5):1530-1534 [PMID: 32011700]
Curr Protoc Bioinformatics. 2009 Mar;Chapter 4:4.10.1-4.10.14 [PMID: 19274634]
Nat Methods. 2021 Feb;18(2):170-175 [PMID: 33526886]
Nat Plants. 2019 Aug;5(8):867-878 [PMID: 31332312]
Bioinformatics. 2010 Jul 1;26(13):1669-70 [PMID: 20472542]
Nature. 2011 May 5;473(7345):97-100 [PMID: 21478875]
J Biol Chem. 2020 Feb 7;295(6):1598-1612 [PMID: 31914404]
Phytochemistry. 2020 Feb;170:112193 [PMID: 31765874]
Nucleic Acids Res. 2021 Jan 8;49(D1):D412-D419 [PMID: 33125078]
Planta. 2014 Jul;240(1):19-32 [PMID: 24671624]
Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):E2274-E2283 [PMID: 29463716]
Nat Rev Cancer. 2022 Oct;22(10):576-591 [PMID: 35854147]
Eur J Biochem. 1967 Mar;1(1):70-2 [PMID: 6059349]
Nat Methods. 2015 Jan;12(1):59-60 [PMID: 25402007]
Nucleic Acids Res. 2014 Sep;42(15):e119 [PMID: 24990371]
Bioinformatics. 2009 Aug 1;25(15):1972-3 [PMID: 19505945]
Sci Rep. 2023 Feb 20;13(1):2955 [PMID: 36805479]
Bioinformatics. 2020 May 1;36(9):2896-2898 [PMID: 31971576]
Proc Natl Acad Sci U S A. 2007 Dec 4;104(49):19363-8 [PMID: 18048334]
Nat Methods. 2015 Apr;12(4):357-60 [PMID: 25751142]
Bioinformatics. 2006 May 15;22(10):1269-71 [PMID: 16543274]
Plant Commun. 2021 Dec 11;3(2):100268 [PMID: 35529951]
Bioinformatics. 2011 Mar 15;27(6):764-70 [PMID: 21217122]
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W265-8 [PMID: 17485477]
Genome Biol. 2008 Jan 11;9(1):R7 [PMID: 18190707]
Plant J. 2021 Dec;108(6):1662-1678 [PMID: 34624152]
Nat Methods. 2017 Jun;14(6):587-589 [PMID: 28481363]
Nat Genet. 2019 May;51(5):865-876 [PMID: 31043757]
J Biol Chem. 2008 Apr 4;283(14):8810-21 [PMID: 18230623]
Plant J. 2020 Aug;103(5):1910-1923 [PMID: 32524692]
Bioinformatics. 2018 Sep 15;34(18):3094-3100 [PMID: 29750242]
Plant J. 2022 Oct;112(2):535-548 [PMID: 36062348]
Hortic Res. 2022 Feb 11;: [PMID: 35147168]
Bioinformatics. 2018 Dec 15;34(24):4313-4314 [PMID: 29955821]
Plant Physiol. 2022 Nov 28;190(4):2430-2448 [PMID: 36053177]
Bioinformatics. 2004 Nov 1;20(16):2878-9 [PMID: 15145805]
BMC Bioinformatics. 2009 Dec 15;10:421 [PMID: 20003500]
J Mol Biol. 1990 Oct 5;215(3):403-10 [PMID: 2231712]
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7 [PMID: 15034147]
Mol Biol Evol. 2009 Jul;26(7):1641-50 [PMID: 19377059]
Bioinformatics. 2009 May 15;25(10):1329-30 [PMID: 19349283]
New Phytol. 2015 Jul;207(2):454-467 [PMID: 26053261]
BMC Bioinformatics. 2004 May 14;5:59 [PMID: 15144565]

Grants

  1. 32221001/National Natural Science Foundation of China (National Science Foundation of China)

MeSH Term

Benzylisoquinolines
Phylogeny
Evolution, Molecular
Genome, Plant
Biosynthetic Pathways
Alkaloids
Magnoliopsida

Chemicals

Benzylisoquinolines
Alkaloids
Journal Article

Links to CNCB-NGDC Resources

GWH: GWHFCTA00000000.1 (Aristolochia manshuriensis)
GWH: GWHFCTG00000000.1 (Saruma henryi)

Word Cloud

Similar Articles

Cited By