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

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

data management plan

as the open research pilot was checked, a data management will be delivered by month 6

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, Issue 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, Issue 16/5, 2020, Page(s) e1008769, ISSN 1553-7404
Publisher: PLOS
DOI: 10.1371/journal.pgen.1008769

Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (<i>Digitaria exilis</i>)

Author(s): Xuewen Wang, Shiyu Chen, Xiao Ma, Anna E J Yssel, Srinivasa R Chaluvadi, Matthew S Johnson, Prakash Gangashetty, Falalou Hamidou, Moussa D Sanogo, Arthur Zwaenepoel, Jason Wallace, Yves Van de Peer, Jeffrey L Bennetzen, Allen Van Deynze
Published in: GigaScience, Issue 10, 2023, Page(s) giab013, ISSN 2047-217X
Publisher: Oxford University Press
DOI: 10.1093/gigascience/giab013

Genomic Resources to Guide Improvement of the Shea Tree

Author(s): Iago Hale; Xiao Ma; Xiao Ma; Arthur T. O. Melo; Francis Kwame Padi; Prasad S. Hendre; Sarah B. Kingan; Shawn T. Sullivan; Shiyu Chen; Jean-Marc Boffa; Alice Muchugi; Alice Muchugi; Agyemang Danquah; Michael Teye Barnor; Ramni Jamnadass; Yves Van de Peer; Yves Van de Peer; Yves Van de Peer; Yves Van de Peer; Allen Van Deynze; Allen Van Deynze
Published in: Frontiers in Plant Science, Issue 12, 2021, Page(s) 720670, ISSN 1664-462X
Publisher: Frontiers Media S. A.
DOI: 10.3389/fpls.2021.720670

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, Issue 227/3, 2020, Page(s) 930-943, ISSN 0028-646X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/nph.16552

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

Author(s): Jia-Yu Xue, Hai-Yun Fan, Zhen Zeng, Yu-Han Zhou, Shuai-Ya Hu, Sai-Xi Li, Ying-Juan Cheng, Xiang-Ru Meng, Fei Chen, Zhu-Qing Shao, Yves Van de Peer
Published in: Horticulture Research, Issue 10/9, 2023, Page(s) uhad147, ISSN 2662-6810
Publisher: Oxford University Press
DOI: 10.1093/hr/uhad147

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

Author(s): Fabricio Almeida-Silva, Yves Van de Peer
Published in: Molecular Biology and Evolution, Issue 40/7, 2023, Page(s) msad141, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msad141

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

Author(s): Quinten Bafort, Tian Wu, Annelore Natran, Olivier De Clerck, Yves Van de Peer
Published in: Evolution Letters, Issue 7/1, 2023, Page(s) 37-47, ISSN 2056-3744
Publisher: Oxford University Press
DOI: 10.1093/evlett/qrac003

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

Author(s): Jia-Yu Xue, Zhen Li, Shuai-Ya Hu, Shu-Min Kao, Tao Zhao, Jie-Yu Wang, Yue Wang, Min Chen, Yichun Qiu, Hai-Yun Fan, Yang Liu, Zhu-Qing Shao, Yves Van de Peer
Published in: The Plant Journal, Issue 113/5, 2023, Page(s) 1021-1034, ISSN 0960-7412
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/tpj.16097

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, Issue 107/2, 2021, Page(s) 613-628, ISSN 0960-7412
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/tpj.15298

Interspecific transfer of genetic information through polyploid bridges

Author(s): Felipe Kauai, Quinten Bafort, Frederik Mortier, Marc Van Montagu, Dries Bonte, Yves Van de Peer
Published in: Proceedings of the National Academy of Sciences of the United States of America, Issue 121/21, 2024, Page(s) e2400018121, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2400018121

Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons

Author(s): Renhai Peng, Yanchao Xu, Shilin Tian, Turgay Unver, Zhen Liu, Zhongli Zhou, Xiaoyan Cai, Kunbo Wang, Yangyang Wei, Yuling Liu, Heng Wang, Guanjing Hu, Zhongren Zhang, Corrinne E Grover, Yuqing Hou, Yuhong Wang, Pengtao Li, Tao Wang, Quanwei Lu, Yuanyuan Wang, Justin L Conover, Hassan Ghazal, Qinglian Wang, Baohong Zhang, Marc Van Montagu, Yves Van de Peer, Jonathan F Wendel, Fang Liu
Published in: Proceedings of the National Academy of Sciences of the United States of America, Issue 00278424, 2022, Page(s) e2208496119, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2208496119

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

Author(s): Mehrshad Ebadi, Quinten Bafort, Eshchar Mizrachi, Pieter Audenaert, Pieter Simoens, Marc Van Montagu Dries Bonte & Yves Van de Peer
Published in: Proceedings of the National Academy of Sciences of the United States of America, Issue 120/41, 2023, Page(s) e2307289120, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2307289120

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, Issue 4/1, 2021, Page(s) 671, ISSN 2399-3642
Publisher: Springer Nature
DOI: 10.1038/s42003-021-02152-8

Haplotype-resolved genome assembly and allele specific gene expression of cultivated ginger

Author(s): Shi-Ping Cheng, Kai-Hua Jia, Ren-Gang Zhang, Zhi-Chao Li, Shan-Shan Zhou, Tian-Le Shi, Ai-Chu Ma, Cong-Wen Yu, Chan Gao, Guang-Lei Cao, Hui Liu, Wei Zhao, Shuai Nie, Jing-Fang Guo, Si-Qian Jiao, Xue-Chan Tian, Xue-Mei Yan, Yu-Tao Bao, Quan-Zheng Yun, Ilga Porth, Yousry El-Kassaby, Xiao-Ru Wang, Zhen Li, Yves Van de Peer and Jian-Feng Mao
Published in: Horticulture Research, Issue 8/1, 2021, Page(s) 188, ISSN 2052-7276
Publisher: Nature Publishing Group
DOI: 10.1038/s41438-021-00599-8

HYBRIDEXPRESS: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors

Author(s): Fabricio Almeida-Silva, Lucas Prost-Boxoen, Yves Van de Peer
Published in: New Phytologist, Issue 243/2, 2024, Page(s) 811-819, ISSN 0028-646X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/nph.19862

The evolutionary conundrum of whole‐genome duplication

Author(s): Lorenzo Carretero‐Paulet, Yves Van de Peer
Published in: American Journal of Botany, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 8/1, 2021, Page(s) 255, ISSN 2662-6810
Publisher: Oxford University Press
DOI: 10.1038/s41438-021-00683-z

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

Author(s): Yue Zhang, Xingyu Yang, Yves Van de Peer, Jinming Chen, Kathleen Marchal, Tao Shi
Published in: The Plant Journal, Issue 09607412, 2022, ISSN 0960-7412
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/tpj.15984

Origin and evolution of the triploid cultivated banana genome

Author(s): Xiuxiu Li, Sheng Yu, Zhihao Chen, Xiaojun Chang, Yingzi Yun, Mengwei Jiang, Xuequn Chen, Xiaohui Wen, Hua Li, Wenjun Zhu, Shiyao Xu, Yanbing Xu, Xianjun Wang, Chen Zhang, Qiong Wu, Jin Hu, Zhenguo Lin, Jean-Marc Aury, Yves Van de Peer, Zonghua Wang, Xiaofan Zhou, Jihua Wang, Peitao Lü, Liangsheng Zhang
Published in: Nature Genetics, Issue 56/1, 2024, Page(s) 136-142, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-023-01589-3

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

Author(s): Yu Cao, Fabricio Almeida-Silva, Wei-Ping Zhang, Ya-Mei Ding, Dan Bai, Wei-Ning Bai, Bo-Wen Zhang, Yves Van de Peer, Da-Yong Zhang
Published in: Molecular Biology and Evolution, Issue 40/6, 2023, Page(s) msad121, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msad121

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

Author(s): Felipe Kauai; Frederik Mortier; Silvija Milosavljevic; Yves Van de Peer; Dries Bonte
Published in: PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Issue 290/1995, 2023, Page(s) 20222456, ISSN 0962-8452
Publisher: Royal Society of London
DOI: 10.1098/rspb.2022.2456

Diploid and tetraploid genomes of Acorus and the evolution of monocots

Author(s): Liang Ma, Ke-Wei Liu, Zhen Li, Yu-Yun Hsiao, Yiying Qi, Tao Fu, Guang-Da Tang, Diyang Zhang, Wei-Hong Sun, Ding-Kun Liu, Yuanyuan Li, Gui-Zhen Chen, Xue-Die Liu, Xing-Yu Liao, Yu-Ting Jiang, Xia Yu, Yang Hao, Jie Huang, Xue-Wei Zhao, Shijie Ke, You-Yi Chen, Wan-Lin Wu, Jui-Ling Hsu, Yu-Fu Lin, Ming-Der Huang, Chia-Ying Li, Laiqiang Huang, Zhi-Wen Wang, Xiang Zhao, Wen-Ying Zhong, Dong-Hui Peng, Sa
Published in: Nature Communications, Issue 14/1, 2023, Page(s) 3661, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-38829-3

Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome

Author(s): Kai-Hua Jia, Hui Liu, Ren-Gang Zhang, Jie Xu, Shan-Shan Zhou, Si-Qian Jiao, Xue-Mei Yan, Xue-Chan Tian, Tian-Le Shi, Hang Luo, Zhi-Chao Li, Yu-Tao Bao, Shuai Nie, Jing-Fang Guo, Ilga Porth, Yousry El-Kassaby, Xiao-Ru Wang, Charles Chen, Yves Van de Peer, Wei Zhao and Jian-Feng Mao
Published in: Horticulture Research, Issue 8/1, 2021, Page(s) 177, ISSN 2052-7276
Publisher: Nature Publishing Group
DOI: 10.1038/s41438-021-00614-y

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

Author(s): Fabricio Almeida-Silva; Yves Van de Peer
Published in: Methods in Ecology and Evolution, Issue 14/12, 2023, Page(s) 2942-2952, ISSN 2041-210X
Publisher: John Wiley and Sons Inc.
DOI: 10.1111/2041-210x.14243

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, Issue 234/1, 2022, Page(s) 295-310, ISSN 0028-646X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/nph.17949

The genome of the king protea, Protea cynaroides

Author(s): Jiyang Chang, Tuan A Duong, Cassandra Schoeman, Xiao Ma, Danielle Roodt, Nigel Barker, Zhen Li, Yves Van de Peer, Eshchar Mizrachi
Published in: The Plant Journal, Issue 113/2, 2023, Page(s) 262-276, ISSN 0960-7412
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/tpj.16044

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, Issue 111/1, 2022, Page(s) 217-230, ISSN 0960-7412
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/tpj.15788

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

Author(s): Liangyu Guo, Shuo Wang, Xi Jiao, Xiaoxue Ye, Deyin Deng, Hua Liu, Yan Li, Yves Van de Peer, Wenwu Wu
Published in: New Phytologist, Issue 242/3, 2024, Page(s) 1377-1393, ISSN 0028-646X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/nph.19656

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, Issue 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, Issue 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, Issue 118/45, 2021, Page(s) e2105431118, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2105431118

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

Author(s): Jiyang Chang, Juan Pablo Marczuk-Rojas, Carrie Waterman, Armando Garcia-Llanos, Shiyu Chen, Xiao Ma, Amanda Hulse-Kemp, Allen Van Deynze, Yves Van de Peer, Lorenzo Carretero-Paulet
Published in: Plant Genome, Issue 19403372, 2022, Page(s) e20238, ISSN 1940-3372
Publisher: Crop Science Society of America
DOI: 10.1002/tpg2.20238

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, Issue 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, Issue 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, Issue 33/1, 2020, Page(s) 11-26, ISSN 1532-298X
Publisher: Oxford University Press
DOI: 10.1093/plcell/koaa015

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

Author(s): Aiping Song, Jiangshuo Su, Haibin Wang, Zhongren Zhang, Xingtan Zhang, Yves Van de Peer, Fei Chen, Weimin Fang, Zhiyong Guan, Fei Zhang, Zhenxing Wang, Likai Wang, Baoqing Ding, Shuang Zhao, Lian Ding, Ye Liu, Lijie Zhou, Jun He, Diwen Jia, Jiali Zhang, Chuwen Chen, Zhongyu Yu, Daojin Sun, Jiafu Jiang, Sumei Chen & Fadi Chen
Published in: Nature Communications, Issue 14/1, 2023, Page(s) 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-37730-3

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

Author(s): Hengchi Chen, Arthur Zwaenepoel, Yves Van de Peer
Published in: Bioinformatics, Issue 40/5, 2024, Page(s) btae272, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btae272

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

Author(s): Jarkko Salojärvi, Aditi Rambani, Zhe Yu, Romain Guyot, Susan Strickler, Maud Lepelley, Cui Wang, Sitaram Rajaraman, Pasi Rastas, Chunfang Zheng, Daniella Santos Muñoz, João Meidanis, Alexandre Rossi Paschoal, Yves Bawin, Trevor J. Krabbenhoft, Zhen Qin Wang, Steven J. Fleck, Rudy Aussel, Laurence Bellanger, Aline Charpagne, Coralie Fournier, Mohamed Kassam, Gregory Lefebvre, Sylviane Métairon,
Published in: Nature Genetics, Issue 56, 2024, Page(s) 721-731, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-024-01695-w

Seagrass genomes reveal a hexaploid ancestry facilitating adaptation to the marine environment

Author(s): Xiao Ma; Steffen Vanneste; Jiyang Chang; Luca Ambrosino; Kerrie Barry; Till Bayer; Alexander A. Bobrov; LoriBeth Boston; Justin E Campbell; Hengchi Chen; Maria Luisa Chiusano; Emanuela Dattolo; Jane Grimwood; Guifen He; Jerry Jenkins; Marina Khachaturyan; Lázaro Marín-Guirao; Attila Mesterházy; Danish-Daniel Muhd; Jessica Pazzaglia; Chris Plott; Shanmugam Rajasekar; Stephane Rombauts; Miriam Ru
Published in: Nature Plants, Issue 10/2, 2024, Page(s) 240-255, ISSN 2055-0278
Publisher: Nature Publishing Group
DOI: 10.1038/s41477-023-01608-5

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, Issue 12/1, 2021, Page(s) 3495, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-23665-0

Revisiting ancient polyploidy in leptosporangiate ferns

Author(s): Hengchi Chen, Yuhan Fang, Arthur Zwaenepoel, Sanwen Huang, Yves Van de Peer, Zhen Li
Published in: New Phytologist, 2023, ISSN 0028-646X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/nph.18607

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, Issue 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, Issue 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, Issue 11/1, 2020, Page(s) 1675, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-15493-5

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

Author(s): Fabricio Almeida-Silva, Tao Zhao, Kristian K Ullrich, M Eric Schranz, Yves Van de Peer
Published in: Bioinformatics, Issue 39/1, 2023, Page(s) btac806, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btac806

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

Author(s): Yuhan Fang, Xing Qin, Qinggang Liao, Ran Du, Xizhi Luo, Qian Zhou, Zhen Li, Hengchi Chen, Wanting Jin, Yaning Yuan, Pengbo Sun, Rui Zhang, Jiao Zhang, Li Wang, Shifeng Cheng, Xueyong Yang, Yuehong Yan, Xingtan Zhang, Zhonghua Zhang, Shunong Bai, Yves Van de Peer, William John Lucas, Sanwen Huang, Jianbin Yan
Published in: Nature Plants, Issue 20550278, 2022, Page(s) 1024-1037, ISSN 2055-0278
Publisher: Nature Publishing Group
DOI: 10.1038/s41477-022-01222-x

Studying whole-genome duplication using experimental evolution of Chlamydomonas

Author(s): Quinten Bafort, Lucas Prost, Eylem Aydogdu, Antoine Van de Vloet, Griet Casteleyn, Yves Van de Peer, Olivier De Clerck
Published in: Methods in Molecular Biology, Issue 2545, 2023, Page(s) 351-372, ISBN 978-1-0716-2561-3
Publisher: Humana
DOI: 10.1007/978-1-0716-2561-3_18

Inference of ancient polyploidy using transcriptome data

Author(s): Jia Li, Yves Van de Peer, Zhen Li
Published in: Methods in Molecular Biology, Issue 2545, 2023, Page(s) 47-76, ISBN 978-1-0716-2561-3
Publisher: Humana
DOI: 10.1007/978-1-0716-2561-3_3

Studying whole-genome duplication using experimental evolution of Spirodela polyrhiza

Author(s): Tian Wu, Annelore Natran, Lucas Prost, Eylem Aydogdu, Yves Van de Peer, Quinten Bafort
Published in: Methods in Molecular Biology, Issue 2545, 2023, Page(s) 373-390, ISBN 978-1-0716-2561-3
Publisher: Humana
DOI: 10.1007/978-1-0716-2561-3_19

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