OpenLB
Open Library of Bioscience
Advanced Search
Frontiers in plant science
2023;14 1174972.

A chromosome-scale genome assembly of provides new insights into the evolution and adaptation of Fagaceae species.

Wei-Cheng Huang, Borong Liao, Hui Liu, Yi-Ye Liang, Xue-Yan Chen, Baosheng Wang, Hanhan Xia
Author Information
  1. Wei-Cheng Huang: College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China.
  2. Borong Liao: College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China.
  3. Hui Liu: Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
  4. Yi-Ye Liang: Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
  5. Xue-Yan Chen: Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
  6. Baosheng Wang: Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
  7. Hanhan Xia: College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China.
PMID: 37215286 DOI: 10.3389/fpls.2023.1174972

Abstract

Fagaceae species dominate forests and shrublands throughout the Northern Hemisphere, and have been used as models to investigate the processes and mechanisms of adaptation and speciation. Compared with the well-studied genus , genomic data is limited for the tropical-subtropical genus . is an ecologically and economically valuable species with a wide distribution in the evergreen broad-leaved forests of tropical-subtropical Asia. Here, we present a high-quality chromosome-scale reference genome of , obtained using a combination of Illumina and PacBio HiFi reads with Hi-C technology. The assembled genome size is 882.6 Mb with a contig N50 of 40.9 Mb and a BUSCO estimate of 99.5%, which are higher than those of recently published Fagaceae species. Genome annotation identified 37,750 protein-coding genes, of which 97.91% were functionally annotated. Repeat sequences constituted 50.95% of the genome and LTRs were the most abundant repetitive elements. Comparative genomic analysis revealed high genome synteny between and other Fagaceae species, despite the long divergence time between them. Considerable gene family expansion and contraction were detected in species. These expanded genes were involved in multiple important biological processes and molecular functions, which may have contributed to the adaptation of the genus to a tropical-subtropical climate. In summary, the genome assembly of provides important genomic resources for Fagaceae genomic research communities, and improves understanding of the adaptation and evolution of forest trees.

Keywords

Castanopsis hystrix cellulose synthase (CesA) gene chromosome-scale genome assembly comparative genomic analysis gene family

References

Curr Protoc Bioinformatics. 2004 May;Chapter 4:Unit 4.10 [PMID: 18428725]
Proc Natl Acad Sci U S A. 2020 Apr 28;117(17):9451-9457 [PMID: 32300014]
Antiviral Res. 1995 Aug;27(4):367-74 [PMID: 8540756]
Nucleic Acids Res. 2003 Jan 1;31(1):365-70 [PMID: 12520024]
Biochem Biophys Res Commun. 2012 Mar 23;419(4):779-81 [PMID: 22390928]
Nat Plants. 2018 Jul;4(7):440-452 [PMID: 29915331]
Science. 2008 Apr 25;320(5875):486-8 [PMID: 18436778]
New Phytol. 2018 May;218(3):894-897 [PMID: 29658637]
New Phytol. 2020 May;226(4):987-1011 [PMID: 31630400]
G3 (Bethesda). 2016 Nov 8;6(11):3485-3495 [PMID: 27621377]
Gigascience. 2018 Jun 1;7(6): [PMID: 29893845]
Mol Ecol. 2016 Sep;25(18):4580-92 [PMID: 27447352]
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W435-9 [PMID: 16845043]
Plant Physiol. 2018 Feb;176(2):1410-1422 [PMID: 29233850]
Nat Plants. 2019 Aug;5(8):833-845 [PMID: 31383970]
Nucleic Acids Res. 2012 Apr;40(7):e49 [PMID: 22217600]
Sci Data. 2018 May 22;5:180069 [PMID: 29786699]
Biochimie. 1993;75(3-4):225-30 [PMID: 8507684]
Bioinformatics. 2017 Jul 15;33(14):2202-2204 [PMID: 28369201]
Front Plant Sci. 2022 Sep 23;13:1012277 [PMID: 36212339]
Plant Physiol Biochem. 2005 Aug;43(8):729-45 [PMID: 16122935]
Nucleic Acids Res. 2002 Jul 15;30(14):3059-66 [PMID: 12136088]
Plant Biotechnol J. 2022 Mar;20(3):538-553 [PMID: 34687252]
Front Plant Sci. 2022 Sep 23;13:1001583 [PMID: 36212310]
Mol Plant. 2021 Oct 4;14(10):1757-1767 [PMID: 34171480]
New Phytol. 2022 Jan;233(1):555-568 [PMID: 34637540]
Nucleic Acids Res. 2016 May 19;44(9):e89 [PMID: 26893356]
Nat Biotechnol. 2011 May 15;29(7):644-52 [PMID: 21572440]
Immunol Rev. 2004 Apr;198:267-84 [PMID: 15199968]
Plant Physiol. 2000 Oct;124(2):495-8 [PMID: 11027699]
Plant Physiol. 2002 Feb;128(2):336-40 [PMID: 11842136]
Bioinformatics. 2006 Jun 1;22(11):1399-401 [PMID: 16601003]
New Phytol. 2013 Jan;197(2):369-371 [PMID: 23253330]
Cytogenet Genome Res. 2005;110(1-4):462-7 [PMID: 16093699]
Nucleic Acids Res. 2009 Jan;37(Database issue):D211-5 [PMID: 18940856]
Curr Protoc Bioinformatics. 2007 Jun;Chapter 4:Unit 4.3 [PMID: 18428791]
Science. 2021 Nov 12;374(6569):eabi7489 [PMID: 34762468]
Bioinformatics. 2005 Jun;21 Suppl 1:i351-8 [PMID: 15961478]
Science. 2007 Nov 23;318(5854):1302-5 [PMID: 18033885]
Genome Res. 2004 May;14(5):988-95 [PMID: 15123596]
Genes (Basel). 2022 Dec 16;13(12): [PMID: 36553650]
New Phytol. 2020 May;226(4):1171-1182 [PMID: 31394003]
Nat Commun. 2022 Mar 14;13(1):1320 [PMID: 35288565]
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W29-37 [PMID: 21593126]
Phytochemistry. 2015 Apr;112:91-9 [PMID: 25104231]
Mol Plant. 2020 Aug 3;13(8):1194-1202 [PMID: 32585190]
Mol Ecol Resour. 2022 Aug;22(6):2396-2410 [PMID: 35377556]
Heredity (Edinb). 2014 Dec;113(6):533-41 [PMID: 24984608]
Nat Genet. 2000 May;25(1):25-9 [PMID: 10802651]
Mol Biol Evol. 2007 Aug;24(8):1586-91 [PMID: 17483113]
Nat Ecol Evol. 2022 Jul;6(7):924-935 [PMID: 35513577]
G3 (Bethesda). 2020 Oct 5;10(10):3565-3574 [PMID: 32847817]
Proc Natl Acad Sci U S A. 2007 Sep 25;104(39):15566-71 [PMID: 17878302]
Nucleic Acids Res. 2003 Jan 1;31(1):439-41 [PMID: 12520045]
Curr Opin Plant Biol. 2006 Dec;9(6):621-30 [PMID: 17011813]
Mol Ecol. 2023 Apr;32(7):1639-1655 [PMID: 36626136]
Hortic Res. 2022 Feb 19;: [PMID: 35184178]
Nucleic Acids Res. 2019 Jul 2;47(W1):W256-W259 [PMID: 30931475]
New Phytol. 2019 Jan;221(2):669-692 [PMID: 30368821]
Plant Biol (Stuttg). 2010 Mar;12(2):275-91 [PMID: 20398235]
Bioinformatics. 2020 Apr 1;36(7):2253-2255 [PMID: 31778144]
Nucleic Acids Res. 2014 Jan;42(Database issue):D222-30 [PMID: 24288371]
Methods Mol Biol. 2019;1962:227-245 [PMID: 31020564]
Cell Syst. 2016 Jul;3(1):99-101 [PMID: 27467250]
PLoS One. 2016 Oct 5;11(10):e0163962 [PMID: 27706213]
Science. 2019 Jun 07;364(6444): [PMID: 31171664]
Curr Opin Plant Biol. 2007 Jun;10(3):245-51 [PMID: 17434787]
Plant Cell. 2019 Sep;31(9):2089-2106 [PMID: 31311834]
Genome Biol. 2019 Nov 14;20(1):238 [PMID: 31727128]
Front Plant Sci. 2022 Nov 28;13:1049253 [PMID: 36518506]
Mol Biol Evol. 2015 Jan;32(1):268-74 [PMID: 25371430]
Nat Biotechnol. 2022 Sep;40(9):1332-1335 [PMID: 35332338]
Mol Ecol Resour. 2022 Apr;22(3):1178-1189 [PMID: 34689424]
Nat Rev Genet. 2010 Aug;11(8):539-48 [PMID: 20585331]
Annu Rev Plant Biol. 2014;65:505-30 [PMID: 24579996]
Bioinformatics. 2001 Sep;17(9):847-8 [PMID: 11590104]
J Mol Biol. 1997 Apr 25;268(1):78-94 [PMID: 9149143]
New Phytol. 2020 May;226(4):978-983 [PMID: 31378946]
Bioinformatics. 2009 Aug 1;25(15):1972-3 [PMID: 19505945]
Nat Commun. 2022 Apr 19;13(1):2047 [PMID: 35440538]
PLoS One. 2011;6(6):e21302 [PMID: 21701584]
Mol Plant. 2010 Jan;3(1):2-20 [PMID: 20035037]
Nat Methods. 2015 Apr;12(4):357-60 [PMID: 25751142]
Nucleic Acids Res. 2016 Jul 8;44(12):e113 [PMID: 27131372]
Bioinformatics. 2006 May 15;22(10):1269-71 [PMID: 16543274]
Genome Biol Evol. 2015 Jan 29;7(3):735-49 [PMID: 25637221]
Bioinformatics. 2011 Mar 15;27(6):764-70 [PMID: 21217122]
New Phytol. 2020 Apr;226(1):44-49 [PMID: 31797393]
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W265-8 [PMID: 17485477]
Genome Biol. 2008 Jan 11;9(1):R7 [PMID: 18190707]
Nucleic Acids Res. 2000 Jan 1;28(1):27-30 [PMID: 10592173]
Front Genet. 2022 Feb 08;12:691058 [PMID: 35211148]
Nucleic Acids Res. 2021 Sep 20;49(16):9077-9096 [PMID: 34417604]
Bioinformatics. 2004 Nov 1;20(16):2878-9 [PMID: 15145805]
Bioinformatics. 2013 Nov 15;29(22):2933-5 [PMID: 24008419]
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]
Journal Article

Links to CNCB-NGDC Resources

GWH: GWHBWDD00000000 (Castanopsis hystrix)

Word Cloud

Similar Articles

Cited By