Phylotranscriptomics reveals extensive gene duplication in the subtribe Gentianinae (Gentianaceae)

Journal of Systematics and Evolution - Tập 59 Số 6 - Trang 1198-1208 - 2021
Chunlin Chen1, Lei Zhang1, Jialiang Li1, Xingxing Mao1, Lushui Zhang1, Quanjun Hu1, Jianquan Liu1,2, Zhenxiang Xi1
1Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Laboratory of Hydraulics and Mountain River Engineering, College of Life Sciences Sichuan University Chengdu 610065 China
2State Key Laboratory of Grassland Agro-Ecosystems, College of Life Sciences Lanzhou University Lanzhou 730000 China

Tóm tắt

AbstractGene duplication plays an important role in plants for diversification and adaptation to new habitats. In this study, we aim to reconstruct the genome‐scale phylogeny and identify large‐scale gene duplication events for the subtribe Gentianinae (Gentianaceae), which is a great symbol of the alpine plants in the Qinghai–Tibet Plateau. We sequenced and assembled 70 transcriptomes from 67 species, representing all six recognized genera in the subtribe Gentianinae plus the closely related outgroups. Using phylogenomic approaches, the backbone relationships of Gentianinae were almost fully resolved with high bootstrap support. Although instances of conflicts were observed between nuclear and plastid phylogenies, six major clades of Gentianinae were consistently recovered in both phylogenies. In addition, we revealed a high occurrence of duplicated genes in our transcriptome assemblies. Using several gene tree reconciliation methods, we collectively identified 10 nodes in the species tree with large concentrations of duplicated genes. Further analysis indicated that many of these duplicated genes likely arose from hybrid polyploidy, which might also account for some of the topological incongruences between nuclear and plastid phylogenies in Gentianinae.

Từ khóa


Tài liệu tham khảo

10.1093/sysbio/sys078

10.1016/j.pbi.2012.03.010

10.1093/bioinformatics/btu170

10.1089/cmb.2009.0139

10.1111/nph.15357

10.1093/bioinformatics/btp348

10.1186/1471-2105-13-S10-S11

10.1089/106652700750050871

10.1093/aob/mci188

10.1126/science.1197761

Defoort J, 2019, The evolution of gene duplicates in angiosperms and the impact of protein–protein interactions and the mechanism of duplication, Genome Biology and Evolution, 11, 2292

10.1186/s13059-015-0721-2

10.1073/pnas.1404177111

10.12705/632.5

10.1111/jbi.12840

10.1111/brv.12107

10.1002/tax.596005

10.1073/pnas.0900906106

10.1111/j.1469-8137.2009.02923.x

10.1111/j.1095-8339.1996.tb00480.x

10.1186/1471-2105-13-S10-S14

10.1038/nbt.1883

10.1038/ng902

10.1038/nprot.2013.084

10.1186/gb-2007-8-7-r141

Ho TN, 2002, Metagentiana, a new genus of Gentianaceae, Botanical Bulletin of Academia Sinica, 43, 83

Ho TN, 2002, Reports on the chromesome numbers of 8 species in Gentiana (Gentianaceae), Acta Biologica Plateau Sinica, 15, 63

Ho TN, 2001, A worldwide monograph of Gentiana

10.1093/molbev/msv347

10.1098/rspb.1994.0058

10.1105/tpc.114.127597

10.1086/600082

10.1093/molbev/msz261

10.1086/376880

10.1155/2012/341932

10.1093/molbev/mst010

10.1016/j.pbi.2016.01.002

KunakhVA Mel'nykVM DrobykNM AndreevIO SpiridonovaKV TwardovskaMO KonvalyukII AdoninVI.2015. Genetic variation induced by tissue and organ culture inGentianaspecies. In: Rybczyński JJ Davey MR Mikuła A eds.The Gentianaceae – Volume 2: Biotechnology and Applications. Berlin Heidelberg: Springer Berlin Heidelberg.199–238.

10.1007/BF00984933

10.1111/nph.15386

10.1093/bioinformatics/btp352

LiH.2013. Aligning sequence reads clone sequences and assembly contigs with BWA‐MEM. arXiv: 1303.3997.

10.1093/gbe/evv048

10.1093/bioinformatics/btl158

10.1007/s11515-008-0076-0

10.1126/sciadv.1501084

10.1073/pnas.1710791115

10.1111/jbi.13229

10.1371/journal.pone.0153008

10.1186/1471-2164-13-246

10.1111/j.1365-294X.2005.02457.x

10.1007/s12041-013-0212-8

10.1111/jbi.12617

10.1126/science.1207205

10.1002/aps3.1038

McKain MR, 2016, A phylogenomic assessment of ancient polyploidy and genome evolution across the Poales, Genome Biology and Evolution, 8, 1150

10.1101/gr.107524.110

10.3732/ajb.1200330

10.1093/bioinformatics/btv234

10.1038/439670a

10.1073/pnas.1817937116

10.1371/journal.pone.0073667

10.1186/gb-2012-13-3-241

10.1007/978-3-642-86659-3

10.1038/s41586-019-1693-2

10.1104/pp.16.00523

10.1002/ajb2.1056

10.3732/ajb.0900287

10.1098/rsbl.2015.0086

10.1101/gr.172098.114

10.1186/s13059-019-1650-2

10.1093/sysbio/syy032

10.1016/j.pbi.2013.11.002

10.1111/j.0908-8857.2004.03297.x

10.1093/bioinformatics/btv351

10.1016/j.ympev.2018.10.001

10.1101/gr.196469.115

10.1093/bib/bbu015

10.1093/bioinformatics/btl446

StamatakisA HooverP RougemontJ.2008.A rapid bootstrap algorithm for the RAxML web servers.Systematic Biology57:758–771.

Struwe L, 2018, Gentianaceae, The Families and Genera of Vascular Plants, 15, 453

10.1111/nph.13491

10.1093/sysbio/syx044

Tiley GP, 2018, Assessing the performance of Ks plots for detecting ancient whole genome duplications, Genome Biology and Evolution, 10, 2882

10.1371/journal.pone.0080662

10.1111/mec.14096

10.1111/jse.12460

10.1038/s42003-018-0176-6

10.3389/fpls.2019.00534

10.1111/jse.12461

10.1093/molbev/msx319

10.1111/nph.14812

10.1093/molbev/msu245

10.1186/s12859-019-2670-3

10.1093/molbev/msm088

10.1016/j.ympev.2015.03.008

10.1007/BF00982961

10.1002/j.1537-2197.1996.tb12750.x

10.1007/BF00985670

10.1111/jse.12543

10.1016/S0169-5347(03)00033-8

10.3390/ijms19071962

Thông tin
Thông tin xuất bản

Journal of Systematics and Evolution

Tập 59 Số 6

1198-1208

Thông tin tác giả