Tree2GD: a phylogenomic method to detect large-scale gene duplication events

被引：9

作者：

Chen, Duoyuan ^{[1
]}

Zhang, Taikui ^{[1
,2
,3
]}

Chen, Yamao ^{[1
]}

Ma, Hong ^{[2
,3
]}

Qi, Ji ^{[1
]}

机构：

[1] Fudan Univ, Sch Life Sci, Inst Plant Biol, State Key Lab Genet Engn, Shanghai 200433, Peoples R China

[2] Penn State Univ, Dept Biol, Eberly Coll Sci, University Pk, PA 16802 USA

[3] Penn State Univ, Huck Inst Life Sci, University Pk, PA 16802 USA

来源：

BIOINFORMATICS | 2022年 / 38卷 / 23期

基金：

中国国家自然科学基金; 中国博士后科学基金;

关键词：

WHOLE-GENOME DUPLICATIONS; EVOLUTIONARY SIGNIFICANCE; PROVIDES INSIGHTS; MODEL SELECTION; POLYPLOIDY; ANCESTOR; PHYLOTRANSCRIPTOMICS; ALIGNMENT;

D O I：

10.1093/bioinformatics/btac669

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: Whole-genome duplication events have long been discovered throughout the evolution of eukaryotes, contributing to genome complexity and biodiversity and leaving traces in the descending organisms. Therefore, an accurate and rapid phylogenomic method is needed to identify the retained duplicated genes on various lineages across the target taxonomy. Results: Here, we present Tree2GD, an integrated method to identify large-scale gene duplication events by automatically perform multiple procedures, including sequence alignment, recognition of homolog, gene tree/species tree reconciliation, Ks distribution of gene duplicates and synteny analyses. Application of Tree2GD on 2 datasets, 12 metazoan genomes and 68 angiosperms, successfully identifies all reported whole-genome duplication events exhibited by these species, showing effectiveness and efficiency of Tree2GD on phylogenomic analyses of large-scale gene duplications.

引用

页码：5317 / 5321

页数：5

共 60 条

[21] Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype [J].

Jaillon, O ;

Aury, JM ;

Brunet, F ;

Petit, JL ;

Stange-Thomann, N ;

Mauceli, E ;

Bouneau, L ;

Fischer, C ;

Ozouf-Costaz, C ;

Bernot, A ;

Nicaud, S ;

Jaffe, D ;

Fisher, S ;

Lutfalla, G ;

Dossat, C ;

Segurens, B ;

Dasilva, C ;

Salanoubat, M ;

Levy, M ;

Boudet, N ;

Castellano, S ;

Anthouard, R ;

Jubin, C ;

Castelli, V ;

Katinka, M ;

Vacherie, B ;

Biémont, C ;

Skalli, Z ;

Cattolico, L ;

Poulain, J ;

de Berardinis, V ;

Cruaud, C ;

Duprat, S ;

Brottier, P ;

Coutanceau, JP ;

Gouzy, J ;

Parra, G ;

Lardier, G ;

Chapple, C ;

McKernan, KJ ;

McEwan, P ;

Bosak, S ;

Kellis, M ;

Volff, JN ;

Guigó, R ;

Zody, MC ;

Mesirov, J ;

Lindblad-Toh, K ;

Birren, B ;

Nusbaum, C .

NATURE, 2004, 431 (7011) :946-957

[22] Double the Genome, Double the Fun: Genome Duplications in Angiosperms [J].

Jiao, Yuannian .

MOLECULAR PLANT, 2018, 11 (03) :357-358

[23] Ancestral polyploidy in seed plants and angiosperms [J].

Jiao, Yuannian ;

Wickett, Norman J. ;

Ayyampalayam, Saravanaraj ;

Chanderbali, Andre S. ;

Landherr, Lena ;

Ralph, Paula E. ;

Tomsho, Lynn P. ;

Hu, Yi ;

Liang, Haiying ;

Soltis, Pamela S. ;

Soltis, Douglas E. ;

Clifton, Sandra W. ;

Schlarbaum, Scott E. ;

Schuster, Stephan C. ;

Ma, Hong ;

Leebens-Mack, Jim ;

dePamphilis, Claude W. .

NATURE, 2011, 473 (7345) :97-U113

[24]

Kalyaanamoorthy S, 2017, NAT METHODS, V14, P587, DOI [10.1038/NMETH.4285, 10.1038/nmeth.4285]

[25] Genome and evolution of the shade-requiring medicinal herb Panax ginseng [J].

Kim, Nam-Hoon ;

Jayakodi, Murukarthick ;

Lee, Sang-Choon ;

Choi, Beom-Soon ;

Jang, Woojong ;

Lee, Junki ;

Kim, Hyun Hee ;

Waminal, Nomar E. ;

Lakshmanan, Meiyappan ;

Nguyen, Binh Van ;

Lee, Yun Sun ;

Park, Hyun-Seung ;

Koo, Hyun Jo ;

Park, Jee Young ;

Perumal, Sampath ;

Joh, Ho Jun ;

Lee, Hana ;

Kim, Jinkyung ;

Kim, In Seo ;

Kim, Kyunghee ;

Koduru, Lokanand ;

Kang, Kyo Bin ;

Sung, Sang Hyun ;

Yu, Yeisoo ;

Park, Daniel S. ;

Choi, Doil ;

Seo, Eunyoung ;

Kim, Seungill ;

Kim, Young-Chang ;

Hyun, Dong Yun ;

Park, Youn-Il ;

Kim, Changsoo ;

Lee, Tae-Ho ;

Kim, Hyun Uk ;

Soh, Moon Soo ;

Lee, Yi ;

In, Jun Gyo ;

Kim, Heui-Soo ;

Kim, Yong-Min ;

Yang, Deok-Chun ;

Wing, Rod A. ;

Lee, Dong-Yup ;

Paterson, Andrew H. ;

Yang, Tae-Jin .

PLANT BIOTECHNOLOGY JOURNAL, 2018, 16 (11) :1904-1917

[26] Impact of whole-genome duplication events on diversification rates in angiosperms [J].

Landis, Jacob B. ;

Soltis, Douglas E. ;

Li, Zheng ;

Marx, Hannah E. ;

Barker, Michael S. ;

Tank, David C. ;

Soltis, Pamela S. .

AMERICAN JOURNAL OF BOTANY, 2018, 105 (03) :348-363

[27] One thousand plant transcriptomes and the phylogenomics of green plants [J].

Leebens-Mack, James H. ;

Barker, Michael S. ;

Carpenter, Eric J. ;

Deyholos, Michael K. ;

Gitzendanner, Matthew A. ;

Graham, Sean W. ;

Grosse, Ivo ;

Li, Zheng ;

Melkonian, Michael ;

Mirarab, Siavash ;

Porsch, Martin ;

Quint, Marcel ;

Rensing, Stefan A. ;

Soltis, Douglas E. ;

Soltis, Pamela S. ;

Stevenson, Dennis W. ;

Ullrich, Kristian K. ;

Wickett, Norman J. ;

DeGironimo, Lisa ;

Edger, Patrick P. ;

Jordon-Thaden, Ingrid E. ;

Joya, Steve ;

Liu, Tao ;

Melkonian, Barbara ;

Miles, Nicholas W. ;

Pokorny, Lisa ;

Quigley, Charlotte ;

Thomas, Philip ;

Villarreal, Juan Carlos ;

Augustin, Megan M. ;

Barrett, Matthew D. ;

Baucom, Regina S. ;

Beerling, David J. ;

Benstein, Ruben Maximilian ;

Biffin, Ed ;

Brockington, Samuel F. ;

Burge, Dylan O. ;

Burris, Jason N. ;

Burris, Kellie P. ;

Burtet-Sarramegna, Valerie ;

Caicedo, Ana L. ;

Cannon, Steven B. ;

Cebi, Zehra ;

Chang, Ying ;

Chater, Caspar ;

Cheeseman, John M. ;

Chen, Tao ;

Clarke, Neil D. ;

Clayton, Harmony ;

Covshoff, Sarah .

NATURE, 2019, 574 (7780) :679-+

[28]

Li Li H. H., 2019, The Pear Genome. Compendium of Plant Genomes, P279, DOI DOI 10.1007/978-3-030-11048-2_15

[29] Genome structure and evolution of Antirrhinum majus L [J].

Li, Miaomiao ;

Zhang, Dongfen ;

Gao, Qiang ;

Luo, Yingfeng ;

Zhang, Hui ;

Ma, Bin ;

Chen, Chunhai ;

Whibley, Annabel ;

Zhang, Yu'e ;

Cao, Yinghao ;

Li, Qun ;

Guo, Han ;

Li, Junhui ;

Song, Yanzhai ;

Zhang, Yue ;

Copsey, Lucy ;

Li, Yan ;

Li, Xiuxiu ;

Qi, Ming ;

Wang, Jiawei ;

Chen, Yan ;

Wang, Dan ;

Zhao, Jinyang ;

Liu, Guocheng ;

Wu, Bin ;

Yu, Lili ;

Xu, Chunyan ;

Li, Jiang ;

Zhao, Shancen ;

Zhang, Yijing ;

Hu, Songnian ;

Liang, Chengzhi ;

Yin, Ye ;

Coen, Enrico ;

Xue, Yongbiao .

NATURE PLANTS, 2019, 5 (02) :174-+

[30] Inferring putative ancient whole-genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions [J].

Li, Zheng ;

Barker, Michael S. .

GIGASCIENCE, 2020, 9 (02)

← 1 2 3 4 5 6 →