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Replaying the ‘genome duplication’ tape of life: the importance of polyploidy for adaptation in a changing environment

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Publications

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

Author(s): Ming-He Li, Ke-Wei Liu, Zhen Li, Hsiang-Chia Lu, Qin-Liang Ye, Diyang Zhang, Jie-Yu Wang, Yu-Feng Li, Zhi-Ming Zhong, Xuedie Liu, Xia Yu, Ding-Kun Liu, Xiong-De Tu, Bin Liu, Yang Hao, Xing-Yu Liao, Yu-Ting Jiang, Wei-Hong Sun, Jinliao Chen, Yan-Qiong Chen, Ye Ai, Jun-Wen Zhai, Sha-Sha Wu, Zhuang Zhou, Yu-Yun Hsiao, Wan-Lin Wu, You-Yi Chen, Yu-Fu Lin, Jui-Ling Hsu, Chia-Ying Li, Zhi-Wen Wang, Xiang
Published in: Nature Plants, 8/4, 2022, Page(s) 373-388, ISSN 2055-0278
Publisher: Nature Publishing Group
DOI: 10.1038/s41477-022-01127-9

Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus

Author(s): Polina Yu. Novikova, Ian G. Brennan, William Booker, Michael Mahony, Paul Doughty, Alan R. Lemmon, Emily Moriarty Lemmon, J. Dale Roberts, Levi Yant, Yves Van de Peer, J. Scott Keogh, Stephen C. Donnellan
Published in: PLOS Genetics, 16/5, 2020, Page(s) e1008769, ISSN 1553-7404
Publisher: PLOS
DOI: 10.1371/journal.pgen.1008769

The honeysuckle genome provides insight into the molecular mechanism of carotenoid metabolism underlying dynamic flower coloration

Author(s): Xiangdong Pu, Zhen Li, Ya Tian, Ranran Gao, Lijun Hao, Yating Hu, Chunnian He, Wei Sun, Meimei Xu, Reuben J. Peters, Yves Van de Peer, Zhichao Xu, Jingyuan Song
Published in: New Phytologist, 227/3, 2020, Page(s) 930-943, ISSN 0028-646X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/nph.16552

A chromosome‐level Amaranthus cruentus genome assembly highlights gene family evolution and biosynthetic gene clusters that may underpin the nutritional value of this traditional crop

Author(s): Xiao Ma, Fabián E Vaistij, Yi Li, Willem S Jansen van Rensburg, Sarah Harvey, Michael W Bairu, Sonja L Venter, Sydney Mavengahama, Zemin Ning, Ian A Graham, Allen Van Deynze, Yves Van de Peer, Katherine J Denby
Published in: The Plant Journal, 107/2, 2021, Page(s) 613-628, ISSN 0960-7412
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/tpj.15298

Wolfberry genomes and the evolution of Lycium (Solanaceae)

Author(s): You-Long Cao, Yan-long Li, Yun-Fang Fan, Zhen Li, Kouki Yoshida, Jie-Yu Wang, Xiao-Kai Ma, Ning Wang, Nobutaka Mitsuda, Toshihisa Kotake, Takeshi Ishimizu, Kun-Chan Tsai, Shan-Ce Niu, Diyang Zhang, Wei-Hong Sun, Qing Luo, Jian-Hua Zhao, Yue Yin, Bo Zhang, Jun-Yi Wang, Ken Qin, Wei An, Jun He, Guo-Li Dai, Ya-Jun Wang, Zhi-Gang Shi, En-Ning Jiao, Peng-Ju Wu, Xuedie Liu, Bin Liu, Xing-Yu Liao, Yu-Tin
Published in: Communications Biology, 4/1, 2021, Page(s) 671, ISSN 2399-3642
Publisher: Springer Nature
DOI: 10.1038/s42003-021-02152-8

A chromosome‐level Amaranthus cruentus genome assembly highlights gene family evolution and biosynthetic gene clusters that may underpin the nutritional value of this traditional crop

Author(s): Xiao Ma, Fabián E. Vaistij, Yi Li, Willem S. Jansen van Rensburg, Sarah Harvey, Michael W. Bairu, Sonja L. Venter, Sydney Mavengahama, Zemin Ning, Ian A. Graham, Allen Van Deynze, Yves Van de Peer, Katherine J. Denby
Published in: The Plant Journal, in press, 2021, ISSN 0960-7412
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/tpj.15298

The evolutionary conundrum of whole‐genome duplication

Author(s): Lorenzo Carretero‐Paulet, Yves Van de Peer
Published in: American Journal of Botany, 107/8, 2020, Page(s) 1101-1105, ISSN 0002-9122
Publisher: Botanical Society of America, Inc.
DOI: 10.1002/ajb2.1520

Model-Based Detection of Whole-Genome Duplications in a Phylogeny

Author(s): Arthur Zwaenepoel, Yves Van de Peer
Published in: Molecular Biology and Evolution, 37/9, 2020, Page(s) 2734-2746, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msaa111

The Euscaphis japonica genome and the evolution of malvids

Author(s): Wei-Hong Sun, Zhen Li, Shuang Xiang, Lin Ni, Diyang Zhang, De-Qiang Chen, Meng-Yuan Qiu, Qi-Gong Zhang, Lin Xiao, Le Din, Yifan Li, Xing-Yu Liao, Xue-Die Liu, Yu-Ting Jiang, Pei-Lan Zhang, Hui Ni, Yifan Wang, Yi-Xun Yue, Xi Wu, Xiang-Qing Din, Wei Huang, Zhi-Wen Wang, Xiaokai Ma, Bobin Liu, Xiao-Xing Zou, Yves Van de Peer, Zhong-Jian Li, Shuang-Quan Zou
Published in: The Plant Journal, 108/5, 2021, Page(s) 1382-1399, ISSN 0960-7412
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/tpj.15518

The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts

Author(s): Tao Wan, Zhiming Liu, Ilia J. Leitch, Haiping Xin, Gillian Maggs-Kölling, Yanbing Gong, Zhen Li, Eugene Marais, Yiying Liao, Can Dai, Fan Liu, Qijia Wu, Chi Song, Yadong Zhou, Weichang Huang, Kai Jiang, Qi Wang, Yong Yang, Zhixiang Zhong, Ming Yang, Xue Yan, Guangwan Hu, Chen Hou, Yingjuan Su, Shixiu Feng, Ji Yang, Jijun Yan, Jinfang Chu, Fan Chen, Jinhua Ran, Xiaoquan Wang, Yves Van de Peer, And
Published in: Nature Communications, 12/1, 2021, Page(s) 4247, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-24528-4

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

Author(s): Zhen-Hui Wang, Xin-Feng Wang, Tianyuan Lu, Ming-Rui Li, Peng Jiang, Jing Zhao, Si-Tong Liu, Xue-Qi Fu, Jonathan F. Wendel, Yves Van de Peer, Bao Liu, Lin-Feng Li
Published in: Nature Communications, 13/1, 2022, Page(s) 1902, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-29561-5

The Cycas genome and the early evolution of seed plants

Author(s): Yang Liu, Sibo Wang, Linzhou Li, Ting Yang, Shanshan Dong, Tong Wei, Shengdan Wu, Yongbo Liu, Yiqing Gong, Xiuyan Feng, Jianchao Ma, Guanxiao Chang, Jinling Huang, Yong Yang, Hongli Wang, Min Liu, Yan Xu, Hongping Liang, Jin Yu, Yuqing Cai, Zhaowu Zhang, Yannan Fan, Weixue Mu, Sunil Kumar Sahu, Shuchun Liu, Xiaoan Lang, Leilei Yang, Na Li, Sadaf Habib, Yongqiong Yang, Anders J. Lindstrom, Pei Lian
Published in: Nature Plants, 8/4, 2022, Page(s) 389-401, ISSN 2055-0278
Publisher: Nature Publishing Group
DOI: 10.1038/s41477-022-01129-7

The Cymbidium genome reveals the evolution of unique morphological traits

Author(s): Ye Ai, Zhen Li, Wei-Hong Sun, Juan Chen, Diyang Zhang, Liang Ma, Qing-Hua Zhang, Ming-Kun Chen, Qing-Dong Zheng, Jiang-Feng Liu, Yu-Ting Jiang, Bai-Jun Li, Xuedie Liu, Xin-Yu Xu, Xia Yu, Yu Zheng, Xing-Yu Liao, Zhuang Zhou, Jie-Yu Wang, Zhi-Wen Wang, Tai-Xiang Xie, Shan-Hu Ma, Jie Zhou, Yu-Jie Ke, Yu-Zhen Zhou, Hsiang-Chia Lu, Ke-Wei Liu, Feng-Xi Yang, Gen-Fa Zhu, Laiqiang Huang, Dong-Hui Peng, Sh
Published in: Horticulture Research, 8/1, 2021, Page(s) 255, ISSN 2662-6810
Publisher: Oxford University Press
DOI: 10.1038/s41438-021-00683-z

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

Author(s): Lingfei Li, Xiaoli Chen, Dongming Fang, Shanshan Dong, Xing Guo, Na Li, Lucia Campos-Dominguez, Wenguang Wang, Yang Liu, Xiaoan Lang, Yang Peng, Daike Tian, Daniel C Thomas, Weixue Mu, Min Liu, Chenyu Wu, Ting Yang, Suzhou Zhang, Leilei Yang, Jianfen Yang, Zhong-Jian Liu, Liangsheng Zhang, Xingtan Zhang, Fei Chen, Yuannian Jiao, Yalong Guo, Mark Hughes, Wei Wang, Xiaofei Liu, Chunmei Zhong, Airong
Published in: The New Phytologist, 234/1, 2022, Page(s) 295-310, ISSN 0028-646X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/nph.17949

The genome of Corydalis reveals the evolution of benzylisoquinoline alkaloid biosynthesis in Ranunculales

Author(s): Zhichao Xu, Zhen Li, Fengming Ren, Ranran Gao, Zhe Wang, Jinlan Zhang, Tao Zhao, Xiao Ma, Xiangdong Pu, Tianyi Xin, Stephane Rombauts, Wei Sun, Yves Van de Peer, Shilin Chen, Jingyuan Song
Published in: The Plant Journal, 111/1, 2022, Page(s) 217-230, ISSN 0960-7412
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/tpj.15788

Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants

Author(s): Tao Shi, Razgar Seyed Rahmani, Paul F Gugger, Muhua Wang, Hui Li, Yue Zhang, Zhizhong Li, Qingfeng Wang, Yves Van de Peer, Kathleen Marchal, Jinming Chen
Published in: Molecular Biology and Evolution, 37/8, 2020, Page(s) 2394-2413, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msaa105

The evolutionary origin and domestication history of goldfish ( Carassius auratus )

Author(s): Duo Chen, Qing Zhang, Weiqi Tang, Zhen Huang, Gang Wang, Yongjun Wang, Jiaxian Shi, Huimin Xu, Lianyu Lin, Zhen Li, Wenchao Chi, Likun Huang, Jing Xia, Xingtan Zhang, Lin Guo, Yuanyuan Wang, Panpan Ma, Juan Tang, Gang Zhou, Min Liu, Fuyan Liu, Xiuting Hua, Baiyu Wang, Qiaochu Shen, Qing Jiang, Jingxian Lin, Xuequn Chen, Hongbo Wang, Meijie Dou, Lei Liu, Haoran Pan, Yiying Qi, Bin Wu, Jingping Fang
Published in: Proceedings of the National Academy of Sciences, 117/47, 2020, Page(s) 29775-29785, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2005545117

Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.)

Author(s): Qin Qiao, Patrick P Edger, Li Xue, La Qiong, Jie Lu, Yichen Zhang, Qiang Cao, Alan E Yocca, Adrian E Platts, Steven J Knapp, Marc Van Montagu, Yves Van de Peer, Jiajun Lei, Ticao Zhang
Published in: Proceedings of the National Academy of Sciences of the United States of America, 118/45, 2021, Page(s) e2105431118, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2105431118

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

Author(s): Theresa Catania, Yi Li, Thilo Winzer, David Harvey, Fergus Meade, Anna Caridi, Andrew Leech, Tony R Larson, Zemin Ning, Jiyang Chang, Yves Van de Peer, Ian A Graham
Published in: Nature Communications, 13/1, 2022, Page(s) 3150, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-30856-w

The emergence and evolution of intron‐poor and intronless genes in intron‐rich plant gene families

Author(s): Hui Liu, Hai‐Meng Lyu, Kaikai Zhu, Yves Van de Peer, Zong‐Ming (Max) Cheng
Published in: The Plant Journal, 105/4, 2021, Page(s) 1072-1082, ISSN 0960-7412
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/tpj.15088

Polyploidy: an evolutionary and ecological force in stressful times

Author(s): Yves Van de Peer, Tia-Lynn Ashman, Pamela S Soltis, Douglas E Soltis
Published in: The Plant Cell, 33/1, 2020, Page(s) 11-26, ISSN 1532-298X
Publisher: Oxford University Press
DOI: 10.1093/plcell/koaa015

Whole-genome microsynteny-based phylogeny of angiosperms

Author(s): Tao Zhao, Arthur Zwaenepoel, Jia-Yu Xue, Shu-Min Kao, Zhen Li, M. Eric Schranz, Yves Van de Peer
Published in: Nature Communications, 12/1, 2021, Page(s) 3495, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-23665-0

Polyploidy: A Biological Force From Cells to Ecosystems

Author(s): Donald T. Fox, Douglas E. Soltis, Pamela S. Soltis, Tia-Lynn Ashman, Yves Van de Peer
Published in: Trends in Cell Biology, 30/9, 2020, Page(s) 688-694, ISSN 0962-8924
Publisher: Elsevier BV
DOI: 10.1016/j.tcb.2020.06.006

Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production

Author(s): Chi Song, Fangfang Fu, Lulu Yang, Yan Niu, Zhaoyang Tian, Xiangxiang He, Xiaoming Yang, Jie Chen, Wei Sun, Tao Wan, Han Zhang, Yicheng Yang, Tian Xiao, Komivi Dossa, Xiangxiao Meng, Fuliang Cao, Yves Van de Peer, Guibin Wang, Shilin Chen
Published in: Communications Biology, 4/1, 2021, Page(s) 1203, ISSN 2399-3642
Publisher: Nature Publishing Group
DOI: 10.1038/s42003-021-02697-8

The Litsea genome and the evolution of the laurel family

Author(s): Yi-Cun Chen, Zhen Li, Yun-Xiao Zhao, Ming Gao, Jie-Yu Wang, Ke-Wei Liu, Xue Wang, Li-Wen Wu, Yu-Lian Jiao, Zi-Long Xu, Wen-Guang He, Qi-Yan Zhang, Chieh-Kai Liang, Yu-Yun Hsiao, Di-Yang Zhang, Si-Ren Lan, Laiqiang Huang, Wei Xu, Wen-Chieh Tsai, Zhong-Jian Liu, Yves Van de Peer, Yang-Dong Wang
Published in: Nature Communications, 11/1, 2020, Page(s) 1675, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-15493-5