Research Explorer

Your browser does not support JavaScript or JavaScript is not enabled. Without JavaScript some functions of this webapplication may be disabled or cause error messages. To enable JavaScript, please consult the manual of your browser or contact your system administrator.

Project

Studying the mechanistic underpinnings and applications of polyploidy through genomics, experimental evolution, modeling, and Artificial Intelligence

Outputs and Outcomes

Publications

wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication

Hengchi ChenArthur ZwaenepoelYves Van de Peer

U Journal Article in Bioinformatics

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Jarkko SalojärviAditi RambaniZhe YuRomain GuyotSusan StricklerMaud LepelleyCui WangSitaram RajaramanPasi RastasChunfang ZhengDaniella Santos MuñozJoão MeidanisAlexandre Rossi PaschoalYves BawinTrevor J. KrabbenhoftZhen Qin WangSteven J. FleckRudy AusselLaurence BellangerAline CharpagneCoralie FournierMohamed KassamGregory LefebvreSylviane MétaironDéborah MoineMichel RigoreauJens StoltePerla HamonEmmanuel CouturonChristine Tranchant-DubreuilMinakshi MukherjeeTianying LanJan EngelhardtPeter StadlerSamara Mireza Correia De LemosSuzana Ivamoto SuzukiUcu SumiratChing Man WaiNicolas DauchotSimon Orozco-AriasAndrea GaravitoCatherine KiwukaPascal MusoliAnne NalukengeErwan GuichouxHavinga ReinoutMartin SmitLorenzo Carretero-PauletOliveiro Guerreiro FilhoMasako Toma BraghiniLilian PadilhaGustavo Hiroshi SeraTom RuttinkRobert HenryPierre MarracciniYves Van de PeerAlan AndradeDouglas DominguesGiovanni GiulianoLukas MuellerLuiz Filipe PereiraStephane PlaisanceValerie PoncetStephane RombautsDavid SankoffVictor A. AlbertDominique CrouzillatAlexandre de KochkoPatrick Descombes et al.

U Journal Article in Nature Genetics

Convergent and/or parallel evolution of RNA‐binding proteins in angiosperms after polyploidization

Liangyu GuoShuo WangXi JiaoXiaoxue YeDeyin DengHua LiuYan LiYves Van de PeerWenwu Wu

U Journal Article in New Phytologist

Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment

Xiao MaSteffen VannesteJiyang ChangLuca AmbrosinoKerrie BarryTill BayerAlexander A. BobrovLoriBeth BostonJustin E. CampbellHengchi ChenMaria Luisa ChiusanoEmanuela DattoloJane GrimwoodGuifen HeJerry JenkinsMarina KhachaturyanLázaro Marín-GuiraoAttila MesterházyDanish-Daniel MuhdJessica PazzagliaChris PlottShanmugam RajasekarStephane RombautsMiriam RuoccoAlison ScottMin Pau TanJozefien Van de VeldeBartel VanholmeJenell WebberLi Lian WongMi YanYeong Yik SungPolina NovikovaJeremy SchmutzThorsten B. H. ReuschGabriele ProcacciniJeanine L. OlsenYves Van de Peer et al.

A1 Journal Article in NATURE PLANTS

Understanding polyploid establishment : temporary persistence or stable coexistence?

Frederik MortierQuinten BafortSilvija MilosavljevićFelipe Kauai PereiraLucas ProstYves Van de PeerDries Bonte

A1 Journal Article in OIKOS

Origin and evolution of the triploid cultivated banana genome

Xiuxiu LiSheng YuZhihao ChengXiaojun ChangYingzi YunMengwei JiangXuequn ChenXiaohui WenHua LiWenjun ZhuShiyao XuYanbing XuXianjun WangChen ZhangQiong WuJin HuZhenguo LinJean-Marc AuryYves Van de PeerZonghua WangXiaofan ZhouJihua WangPeitao LüLiangsheng Zhang et al.

A1 Journal Article in NATURE GENETICS

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Jarkko SalojärviAditi RambaniZhe YuRomain GuyotSusan StricklerMaud LepelleyCui WangSitaram RajaramanPasi RastasChunfang ZhengDaniella Santos MuñozJoão MeidanisAlexandre Rossi PaschoalYves BawinTrevor KrabbenhoftZhen Qin WangSteven FleckRudy AusselLaurence BellangerAline CharpagneCoralie FournierMohamed KassamGregory LefebvreSylviane MétaironDéborah MoineMichel RigoreauJens StoltePerla HamonEmmanuel CouturonChristine Tranchant-DubreuilMinakshi MukherjeeTianying LanJan EngelhardtPeter StadlerSamara Mireza Correia De LemosSuzana Ivamoto SuzukiUcu SumiratWai Ching ManNicolas DauchotSimon Orozco-AriasAndrea GaravitoCatherine KiwukaPascal MusoliAnne NalukengeErwan GuichouxHavinga ReinoutMartin SmitLorenzo Carretero-PauletOliveiro Guerreiro FilhoMasako Toma BraghiniLilian PadilhaGustavo Hiroshi SeraTom RuttinkRobert HenryPierre MarracciniYves Van de PeerAlan AndradeDouglas DominguesGiovanni GiulianoLukas MuellerLuiz Filipe PereiraStephane PlaisanceValerie PoncetStephane RombautsDavid SankoffVictor A. AlbertDominique CrouzillatAlexandre de KochkoPatrick Descombes et al.

The Soybean Expression Atlas v2 : a comprehensive database of over 5000 RNA‐seq samples

Fabricio De Almeida SilvaFrancisnei Pedrosa‐SilvaThiago M. Venancio

A1 Journal Article in PLANT JOURNAL

Assessing the quality of comparative genomics data and results with the cogeqc R/Bioconductor package

Fabricio De Almeida SilvaYves Van de Peer

A1 Journal Article in METHODS IN ECOLOGY AND EVOLUTION

The duplication of genomes and genetic networks and its potential for evolutionary adaptation and survival during environmental turmoil

Mehrshad EbadiQuinten BafortEshchar MizrachiP. AudenaertPieter SimoensMarc Van MontaguDries BonteYves Van de Peer

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive regulatory networks for tomato organ development based on the genome and RNAome of microTom tomato

Jia-Yu XueHai-Yun FanZhen ZengYu-Han ZhouShuai-Ya HuSai-Xi LiYing-Juan ChengXiang-Ru MengFei ChenZhu-Qing ShaoYves Van de Peer et al.

A1 Journal Article in HORTICULTURE RESEARCH

Whole-genome duplications and the long-term evolution of gene regulatory networks in angiosperms

Fabricio De Almeida SilvaYves Van de Peer

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Diploid and tetraploid genomes of Acorus and the evolution of monocots

Liang MaKe-Wei LiuZhen LiYu-Yun HsiaoYiying QiTao FuGuang-Da TangDiyang ZhangWei-Hong SunDing-Kun LiuYuanyuan LiGui-Zhen ChenXue-Die LiuXing-Yu LiaoYu-Ting JiangXia YuYang HaoJie HuangXue-Wei ZhaoShijie KeYou-Yi ChenWan-Lin WuJui-Ling HsuYu-Fu LinMing-Der HuangChia-Ying LiLaiqiang HuangZhi-Wen WangXiang ZhaoWen-Ying ZhongDong-Hui PengSagheer AhmadSiren LanJi-Sen ZhangWen-Chieh TsaiYves Van de PeerZhong-Jian Liu et al.

A1 Journal Article in NATURE COMMUNICATIONS

Genomic insights into adaptation to karst limestone and incipient speciation in East Asian Platycarya spp. (Juglandaceae)

Yu CaoFabricio De Almeida SilvaWei-Ping ZhangYa-Mei DingDan BaiWei-Ning BaiBo-Wen ZhangYves Van de PeerDa-Yong Zhang

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum

Aiping SongJiangshuo SuHaibin WangZhongren ZhangXingtan ZhangYves Van de PeerFei ChenWeimin FangZhiyong GuanFei ZhangZhenxing WangLikai WangBaoqing DingShuang ZhaoLian DingYe LiuLijie ZhouJun HeDiwen JiaJiali ZhangChuwen ChenZhongyu YuDaojin SunJiafu JiangSumei ChenFadi Chen et al.

A1 Journal Article in NATURE COMMUNICATIONS

Neutral processes underlying the macro eco-evolutionary dynamics of mixed-ploidy systems

Felipe Kauai PereiraFrederik MortierSilvija MilosavljevićYves Van de PeerDries Bonte

A1 Journal Article in PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The immediate effects of polyploidization of Spirodela polyrhiza change in a strain-specific way along environmental gradients

Quinten BafortTian WuAnnelore NatranOlivier De ClerckYves Van de Peer

A1 Journal Article in EVOLUTION LETTERS

Studying whole-genome duplication using experimental evolution of Spirodela polyrhiza

Tian WuAnnelore NatranLucas ProstEylem Aydogdu LohausYves Van de PeerQuinten Bafort

Bookchapter in Polyploidy : methods and protocols

Inference of ancient polyploidy using transcriptome data

Jia LiYves Van de PeerZhen Li

Bookchapter in Polyploidy : methods and protocols

Studying whole-genome duplication using experimental evolution of Chlamydomonas

Quinten BafortLucas ProstEylem Aydogdu LohausAntoine Van de VloetGriet CasteleynYves Van de PeerOlivier De Clerck

Bookchapter in Polyploidy : methods and protocols

The Saururus chinensis genome provides insights into the evolution of pollination strategies and herbaceousness in magnoliids

Jia‐Yu XueZhen LiShuai‐Ya HuShu-Min KaoTao ZhaoJie‐Yu WangYue WangMin ChenYichun QiuHai‐Yun FanYang LiuZhu‐Qing ShaoYves Van de Peer et al.

A1 Journal Article in PLANT JOURNAL

syntenet : an R/Bioconductor package for the inference and analysis of synteny networks

Fabricio De Almeida SilvaTao ZhaoKristian K UllrichM Eric SchranzYves Van de Peer

A1 Journal Article in BIOINFORMATICS

The genome of the king protea, Protea cynaroides

Jiyang ChangTuan A. DuongCassandra SchoemanXiao MaDanielle RoodtNigel BarkerZhen LiYves Van de PeerEshchar Mizrachi

A1 Journal Article in PLANT JOURNAL

Revisiting ancient polyploidy in leptosporangiate ferns

Hengchi ChenYuhan FangArthur ZwaenepoelSanwen HuangYves Van de PeerZhen Li

A1 Journal Article in NEW PHYTOLOGIST

Evolution of isoform‐level gene expression patterns across tissues during lotus species divergence

Yue ZhangXingyu YangYves Van de PeerJinming ChenKathleen MarchalTao Shi

A1 Journal Article in PLANT JOURNAL

Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons

Renhai PengYanchao XuShilin TianTurgay UnverZhen LiuZhongli ZhouXiaoyan CaiKunbo WangYangyang WeiYuling LiuHeng WangGuanjing HuZhongren ZhangCorrinne E. GroverYuqing HouYuhong WangPengtao LiTao WangQuanwei LuYuanyuan WangJustin L. ConoverHassan GhazalQinglian WangBaohong ZhangMarc Van MontaguYves Van de PeerJonathan F. WendelFang Liu et al.

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genome of homosporous maidenhair fern sheds light on the euphyllophyte evolution and defences

Yuhan FangXing QinQinggang LiaoRan DuXizhi LuoQian ZhouZhen LiHengchi ChenWanting JinYaning YuanPengbo SunRui ZhangJiao ZhangLi WangShifeng ChengXueyong YangYuehong YanXingtan ZhangZhonghua ZhangShunong BaiYves Van de PeerWilliam John LucasSanwen HuangJianbin Yan et al.

A1 Journal Article in NATURE PLANTS

Chromosome‐scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication

Jiyang ChangJuan Pablo Marczuk‐RojasCarrie WatermanArmando Garcia‐LlanosShiyu ChenXiao MaAmanda Hulse‐KempAllen Van DeynzeYves Van de PeerLorenzo Carretero‐Paulet

A1 Journal Article in PLANT GENOME

Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe)

Ticao ZhangQin QiaoXiao DuXiao ZhangYali HouXin WeiChao SunRengang ZhangQuanzheng YunM. James C. CrabbeYves Van de PeerWenxuan Dong et al.

A1 Journal Article in JOURNAL OF INTEGRATIVE PLANT BIOLOGY

A functionally conserved STORR gene fusion in Papaver species that diverged 16.8 million years ago

Theresa CataniaYi LiThilo WinzerDavid HarveyFergus MeadeAnna CaridiAndrew LeechTony R. LarsonZemin NingJiyang ChangYves Van de PeerIan A. Graham et al.

A1 Journal Article in NATURE COMMUNICATIONS

Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax

Zhen-Hui WangXin-Feng WangTianyuan LuMing-Rui LiPeng JiangJing ZhaoSi-Tong LiuXue-Qi FuJonathan F. WendelYves Van de PeerBao LiuLin-Feng Li et al.

A1 Journal Article in NATURE COMMUNICATIONS

Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy

Ming-He LiKe-Wei LiuZhen LiHsiang-Chia LuQin-Liang YeDiyang ZhangJie-Yu WangYu-Feng LiZhi-Ming ZhongXuedie LiuXia YuDing-Kun LiuXiong-De TuBin LiuYang HaoXing-Yu LiaoYu-Ting JiangWei-Hong SunJinliao ChenYan-Qiong ChenYe AiJun-Wen ZhaiSha-Sha WuZhuang ZhouYu-Yun HsiaoWan-Lin WuYou-Yi ChenYu-Fu LinJui-Ling HsuChia-Ying LiZhi-Wen WangXiang ZhaoWen-Ying ZhongXiao-Kai MaLiang MaJie HuangGui-Zhen ChenMing-Zhong HuangLaiqiang HuangDong-Hui PengYi-Bo LuoShuang-Quan ZouShi-Pin ChenSiren LanWen-Chieh TsaiYves Van de PeerZhong-Jian Liu et al.

A1 Journal Article in NATURE PLANTS

The Cycas genome and the early evolution of seed plants

Yang LiuSibo WangLinzhou LiTing YangShanshan DongTong WeiShengdan WuYongbo LiuYiqing GongXiuyan FengJianchao MaGuanxiao ChangJinling HuangYong YangHongli WangMin LiuYan XuHongping LiangJin YuYuqing CaiZhaowu ZhangYannan FanWeixue MuSunil Kumar SahuShuchun LiuXiaoan LangLeilei YangNa LiSadaf HabibYongqiong YangAnders J. LindstromPei LiangBernard GoffinetSumaira ZamanJill L. WegrzynDexiang LiJian LiuJie CuiEva C. SonnenscheinXiaobo WangJue RuanJia-Yu XueZhu-Qing ShaoChi SongGuangyi FanZhen LiLiangsheng ZhangJianquan LiuZhong-Jian LiuYuannian JiaoXiao-Quan WangHong WuErtao WangMichael LisbyHuanming YangJian WangXin LiuXun XuNan LiPamela S. SoltisYves Van de PeerDouglas E. SoltisXun GongHuan LiuShouzhou Zhang et al.

A1 Journal Article in NATURE PLANTS

Genomes shed light on the evolution of Begonia, a mega‐diverse genus

Lingfei LiXiaoli ChenDongming FangShanshan DongXing GuoNa LiLucia Campos‐DominguezWenguang WangYang LiuXiaoan LangYang PengDaike TianDaniel C. ThomasWeixue MuMin LiuChenyu WuTing YangSuzhou ZhangLeilei YangJianfen YangZhong‐Jian LiuLiangsheng ZhangXingtan ZhangFei ChenYuannian JiaoYalong GuoMark HughesWei WangXiaofei LiuChunmei ZhongAirong LiSunil Kumar SahuHuanming YangErnest WuJoel SharbroughMichael LisbyXin LiuXun XuDouglas E. SoltisYves Van de PeerCatherine KidnerShouzhou ZhangHuan Liu et al.

A1 Journal Article in NEW PHYTOLOGIST

Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production

Chi SongFangfang FuLulu YangYan NiuZhaoyang TianXiangxiang HeXiaoming YangJie ChenWei SunTao WanHan ZhangYicheng YangTian XiaoKomivi DossaXiangxiao MengFuliang CaoYves Van de PeerGuibin WangShilin Chen et al.

A1 Journal Article in COMMUNICATIONS BIOLOGY

The Euscaphis japonica genome and the evolution of malvids

Wei‐Hong SunZhen LiShuang XiangLin NiDiyang ZhangDe‐Qiang ChenMeng‐Yuan QiuQi‐Gong ZhangLin XiaoLe DinYifan LiXing‐Yu LiaoXue‐Die LiuYu‐Ting JiangPei‐Lan ZhangHui NiYifan WangYi‐Xun YueXi WuXiang‐Qing DinWei HuangZhi‐Wen WangXiaokai MaBobin LiuXiao‐Xing ZouYves Van de PeerZhong‐Jian LiuShuang‐Quan Zou et al.

A1 Journal Article in PLANT JOURNAL