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

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Risultati finali

data management plan

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

Pubblicazioni

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

Autori: 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
Pubblicato in: Nature Plants, Numero 8/4, 2022, Pagina/e 373-388, ISSN 2055-0278
Editore: Nature Publishing Group
DOI: 10.1038/s41477-022-01127-9

Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus

Autori: 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
Pubblicato in: PLOS Genetics, Numero 16/5, 2020, Pagina/e e1008769, ISSN 1553-7404
Editore: PLOS
DOI: 10.1371/journal.pgen.1008769

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

Autori: 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
Pubblicato in: GigaScience, Numero 10, 2023, Pagina/e giab013, ISSN 2047-217X
Editore: Oxford University Press
DOI: 10.1093/gigascience/giab013

Genomic Resources to Guide Improvement of the Shea Tree

Autori: 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
Pubblicato in: Frontiers in Plant Science, Numero 12, 2021, Pagina/e 720670, ISSN 1664-462X
Editore: 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

Autori: 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
Pubblicato in: New Phytologist, Numero 227/3, 2020, Pagina/e 930-943, ISSN 0028-646X
Editore: Blackwell Publishing Inc.
DOI: 10.1111/nph.16552

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

Autori: 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
Pubblicato in: Horticulture Research, Numero 10/9, 2023, Pagina/e uhad147, ISSN 2662-6810
Editore: Oxford University Press
DOI: 10.1093/hr/uhad147

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

Autori: Fabricio Almeida-Silva, Yves Van de Peer
Pubblicato in: Molecular Biology and Evolution, Numero 40/7, 2023, Pagina/e msad141, ISSN 0737-4038
Editore: 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

Autori: Quinten Bafort, Tian Wu, Annelore Natran, Olivier De Clerck, Yves Van de Peer
Pubblicato in: Evolution Letters, Numero 7/1, 2023, Pagina/e 37-47, ISSN 2056-3744
Editore: Oxford University Press
DOI: 10.1093/evlett/qrac003

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

Autori: 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
Pubblicato in: The Plant Journal, Numero 113/5, 2023, Pagina/e 1021-1034, ISSN 0960-7412
Editore: 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

Autori: 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
Pubblicato in: The Plant Journal, Numero 107/2, 2021, Pagina/e 613-628, ISSN 0960-7412
Editore: Blackwell Publishing Inc.
DOI: 10.1111/tpj.15298

Interspecific transfer of genetic information through polyploid bridges

Autori: Felipe Kauai, Quinten Bafort, Frederik Mortier, Marc Van Montagu, Dries Bonte, Yves Van de Peer
Pubblicato in: Proceedings of the National Academy of Sciences of the United States of America, Numero 121/21, 2024, Pagina/e e2400018121, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2400018121

Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons

Autori: 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
Pubblicato in: Proceedings of the National Academy of Sciences of the United States of America, Numero 00278424, 2022, Pagina/e e2208496119, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2208496119

Asymmetric genome merging leads to gene expression novelty through nucleo‐cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids

Autori: Lucas Prost‐Boxoen, Quinten Bafort, Antoine Van de Vloet, Fabricio Almeida‐Silva, Yunn Thet Paing, Griet Casteleyn, Sofie D'hondt, Olivier De Clerck, Yves Van de Peer
Pubblicato in: New Phytologist, Numero 245, 2025, Pagina/e 869-884, ISSN 0028-646X
Editore: Blackwell Publishing Inc.
DOI: 10.1111/nph.20249

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

Autori: Mehrshad Ebadi, Quinten Bafort, Eshchar Mizrachi, Pieter Audenaert, Pieter Simoens, Marc Van Montagu Dries Bonte & Yves Van de Peer
Pubblicato in: Proceedings of the National Academy of Sciences of the United States of America, Numero 120/41, 2023, Pagina/e e2307289120, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2307289120

Wolfberry genomes and the evolution of Lycium (Solanaceae)

Autori: 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
Pubblicato in: Communications Biology, Numero 4/1, 2021, Pagina/e 671, ISSN 2399-3642
Editore: Springer Nature
DOI: 10.1038/s42003-021-02152-8

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

Autori: 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
Pubblicato in: Horticulture Research, Numero 8/1, 2021, Pagina/e 188, ISSN 2052-7276
Editore: Nature Publishing Group
DOI: 10.1038/s41438-021-00599-8

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

Autori: Fabricio Almeida-Silva, Lucas Prost-Boxoen, Yves Van de Peer
Pubblicato in: New Phytologist, Numero 243/2, 2024, Pagina/e 811-819, ISSN 0028-646X
Editore: Blackwell Publishing Inc.
DOI: 10.1111/nph.19862

The evolutionary conundrum of whole‐genome duplication

Autori: Lorenzo Carretero‐Paulet, Yves Van de Peer
Pubblicato in: American Journal of Botany, Numero 107/8, 2020, Pagina/e 1101-1105, ISSN 0002-9122
Editore: Botanical Society of America, Inc.
DOI: 10.1002/ajb2.1520

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

Autori: Arthur Zwaenepoel, Yves Van de Peer
Pubblicato in: Molecular Biology and Evolution, Numero 37/9, 2020, Pagina/e 2734-2746, ISSN 0737-4038
Editore: Oxford University Press
DOI: 10.1093/molbev/msaa111

Flavonoids and anthocyanins in seagrasses: implications for climate change adaptation and resilience

Autori: Jana Botes, Xiao Ma, Jiyang Chang, Yves Van de Peer, Dave Kenneth Berger
Pubblicato in: Frontiers in Plant Science, Numero 15, 2025, Pagina/e 1520474, ISSN 1664-462X
Editore: Frontiers Media S. A.
DOI: 10.3389/fpls.2024.1520474

The Euscaphis japonica genome and the evolution of malvids

Autori: 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
Pubblicato in: The Plant Journal, Numero 108/5, 2021, Pagina/e 1382-1399, ISSN 0960-7412
Editore: Blackwell Publishing Inc.
DOI: 10.1111/tpj.15518

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

Autori: 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
Pubblicato in: Nature Communications, Numero 12/1, 2021, Pagina/e 4247, ISSN 2041-1723
Editore: 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

Autori: 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
Pubblicato in: Nature Communications, Numero 13/1, 2022, Pagina/e 1902, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-022-29561-5

The Cycas genome and the early evolution of seed plants

Autori: 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
Pubblicato in: Nature Plants, Numero 8/4, 2022, Pagina/e 389-401, ISSN 2055-0278
Editore: Nature Publishing Group
DOI: 10.1038/s41477-022-01129-7

The Cymbidium genome reveals the evolution of unique morphological traits

Autori: 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
Pubblicato in: Horticulture Research, Numero 8/1, 2021, Pagina/e 255, ISSN 2662-6810
Editore: Oxford University Press
DOI: 10.1038/s41438-021-00683-z

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

Autori: Yue Zhang, Xingyu Yang, Yves Van de Peer, Jinming Chen, Kathleen Marchal, Tao Shi
Pubblicato in: The Plant Journal, Numero 09607412, 2022, ISSN 0960-7412
Editore: Blackwell Publishing Inc.
DOI: 10.1111/tpj.15984

Origin and evolution of the triploid cultivated banana genome

Autori: 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
Pubblicato in: Nature Genetics, Numero 56/1, 2024, Pagina/e 136-142, ISSN 1061-4036
Editore: 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)

Autori: 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
Pubblicato in: Molecular Biology and Evolution, Numero 40/6, 2023, Pagina/e msad121, ISSN 0737-4038
Editore: Oxford University Press
DOI: 10.1093/molbev/msad121

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

Autori: Felipe Kauai; Frederik Mortier; Silvija Milosavljevic; Yves Van de Peer; Dries Bonte
Pubblicato in: PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Numero 290/1995, 2023, Pagina/e 20222456, ISSN 0962-8452
Editore: Royal Society of London
DOI: 10.1098/rspb.2022.2456

Diploid and tetraploid genomes of Acorus and the evolution of monocots

Autori: 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
Pubblicato in: Nature Communications, Numero 14/1, 2023, Pagina/e 3661, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-023-38829-3

A metabolic perspective on polyploid invasion and the emergence of life histories: Insights from a mechanistic model

Autori: Silvija Milosavljevic, Felipe Kauai, Frederik Mortier, Yves Van de Peer, Dries Bonte
Pubblicato in: American Journal of Botany, Numero 111, 2024, Pagina/e e16387, ISSN 0002-9122
Editore: Botanical Society of America, Inc.
DOI: 10.1002/ajb2.16387

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

Autori: 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
Pubblicato in: Horticulture Research, Numero 8/1, 2021, Pagina/e 177, ISSN 2052-7276
Editore: Nature Publishing Group
DOI: 10.1038/s41438-021-00614-y

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

Autori: Fabricio Almeida-Silva; Yves Van de Peer
Pubblicato in: Methods in Ecology and Evolution, Numero 14/12, 2023, Pagina/e 2942-2952, ISSN 2041-210X
Editore: John Wiley and Sons Inc.
DOI: 10.1111/2041-210x.14243

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

Autori: 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
Pubblicato in: The New Phytologist, Numero 234/1, 2022, Pagina/e 295-310, ISSN 0028-646X
Editore: Blackwell Publishing Inc.
DOI: 10.1111/nph.17949

A BAC-guided haplotype assembly pipeline increases the resolution of the virus resistance locus CMD2 in cassava

Autori: Luc Cornet, Syed Shan-e-Ali Zaidi, Jia Li, Yvan Ngapout, Sara Shakir, Loic Meunier, Caroline Callot, William Marande, Marc Hanikenne, Stephane Rombauts, Yves Van de Peer, Hervé Vanderschuren
Pubblicato in: Genome Biology, Numero 26, 2025, Pagina/e 185, ISSN 1474-760X
Editore: Springer Science and Business Media LLC
DOI: 10.1186/s13059-025-03620-8

The genome of the king protea, Protea cynaroides

Autori: Jiyang Chang, Tuan A Duong, Cassandra Schoeman, Xiao Ma, Danielle Roodt, Nigel Barker, Zhen Li, Yves Van de Peer, Eshchar Mizrachi
Pubblicato in: The Plant Journal, Numero 113/2, 2023, Pagina/e 262-276, ISSN 0960-7412
Editore: Blackwell Publishing Inc.
DOI: 10.1111/tpj.16044

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

Autori: 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
Pubblicato in: The Plant Journal, Numero 111/1, 2022, Pagina/e 217-230, ISSN 0960-7412
Editore: Blackwell Publishing Inc.
DOI: 10.1111/tpj.15788

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

Autori: Liangyu Guo, Shuo Wang, Xi Jiao, Xiaoxue Ye, Deyin Deng, Hua Liu, Yan Li, Yves Van de Peer, Wenwu Wu
Pubblicato in: New Phytologist, Numero 242/3, 2024, Pagina/e 1377-1393, ISSN 0028-646X
Editore: 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

Autori: 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
Pubblicato in: Molecular Biology and Evolution, Numero 37/8, 2020, Pagina/e 2394-2413, ISSN 0737-4038
Editore: Oxford University Press
DOI: 10.1093/molbev/msaa105

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

Autori: 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
Pubblicato in: Proceedings of the National Academy of Sciences, Numero 117/47, 2020, Pagina/e 29775-29785, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2005545117

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

Autori: 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
Pubblicato in: Proceedings of the National Academy of Sciences of the United States of America, Numero 118/45, 2021, Pagina/e e2105431118, ISSN 0027-8424
Editore: 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

Autori: 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
Pubblicato in: Plant Genome, Numero 19403372, 2022, Pagina/e e20238, ISSN 1940-3372
Editore: 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

Autori: 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
Pubblicato in: Nature Communications, Numero 13/1, 2022, Pagina/e 3150, ISSN 2041-1723
Editore: 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

Autori: Hui Liu, Hai‐Meng Lyu, Kaikai Zhu, Yves Van de Peer, Zong‐Ming (Max) Cheng
Pubblicato in: The Plant Journal, Numero 105/4, 2021, Pagina/e 1072-1082, ISSN 0960-7412
Editore: Blackwell Publishing Inc.
DOI: 10.1111/tpj.15088

Polyploidy: an evolutionary and ecological force in stressful times

Autori: Yves Van de Peer, Tia-Lynn Ashman, Pamela S Soltis, Douglas E Soltis
Pubblicato in: The Plant Cell, Numero 33/1, 2020, Pagina/e 11-26, ISSN 1532-298X
Editore: Oxford University Press
DOI: 10.1093/plcell/koaa015

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

Autori: 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
Pubblicato in: Nature Communications, Numero 14/1, 2023, Pagina/e 2021, ISSN 2041-1723
Editore: 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.

Autori: Hengchi Chen, Arthur Zwaenepoel, Yves Van de Peer
Pubblicato in: Bioinformatics, Numero 40/5, 2024, Pagina/e btae272, ISSN 1367-4803
Editore: 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

Autori: 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,
Pubblicato in: Nature Genetics, Numero 56, 2024, Pagina/e 721-731, ISSN 1061-4036
Editore: Nature Publishing Group
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Seagrass genomes reveal a hexaploid ancestry facilitating adaptation to the marine environment

Autori: 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
Pubblicato in: Nature Plants, Numero 10/2, 2024, Pagina/e 240-255, ISSN 2055-0278
Editore: Nature Publishing Group
DOI: 10.1038/s41477-023-01608-5

Whole-genome microsynteny-based phylogeny of angiosperms

Autori: Tao Zhao, Arthur Zwaenepoel, Jia-Yu Xue, Shu-Min Kao, Zhen Li, M. Eric Schranz, Yves Van de Peer
Pubblicato in: Nature Communications, Numero 12/1, 2021, Pagina/e 3495, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-021-23665-0

Revisiting ancient polyploidy in leptosporangiate ferns

Autori: Hengchi Chen, Yuhan Fang, Arthur Zwaenepoel, Sanwen Huang, Yves Van de Peer, Zhen Li
Pubblicato in: New Phytologist, 2023, ISSN 0028-646X
Editore: Blackwell Publishing Inc.
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Polyploidy: A Biological Force From Cells to Ecosystems

Autori: Donald T. Fox, Douglas E. Soltis, Pamela S. Soltis, Tia-Lynn Ashman, Yves Van de Peer
Pubblicato in: Trends in Cell Biology, Numero 30/9, 2020, Pagina/e 688-694, ISSN 0962-8924
Editore: Elsevier BV
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Deciphering the biosynthetic pathway of triterpene saponins in Prunella vulgaris

Autori: Si‐Jie Liu, Zhengtai Liu, Bing‐Yan Shao, Tao Li, Xinning Zhu, Ren Wang, Lei Shi, Sheng Xu, Yves Van de Peer, Jia‐Yu Xue
Pubblicato in: The Plant Journal, Numero 121, 2025, Pagina/e e17220, ISSN 0960-7412
Editore: Blackwell Publishing Inc.
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Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production

Autori: 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
Pubblicato in: Communications Biology, Numero 4/1, 2021, Pagina/e 1203, ISSN 2399-3642
Editore: Nature Publishing Group
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Dosage sensitivity shapes balanced expression and gene longevity of homoeologs after whole-genome duplications in angiosperms

Autori: Tao Shi, Zhiyan Gao, Jinming Chen, Yves Van de Peer
Pubblicato in: The Plant Cell, Numero 36, 2024, Pagina/e 4323-4337, ISSN 1040-4651
Editore: American Society of Plant Biologists
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doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications

Autori: Fabricio Almeida-Silva, Yves Van de Peer
Pubblicato in: Bioinformatics, Numero 41, 2025, Pagina/e btaf043, ISSN 1367-4811
Editore: Oxford University Press (OUP)
DOI: 10.1093/bioinformatics/btaf043

The immediate metabolomic effects of whole‐genome duplication in the greater duckweed, Spirodela polyrhiza

Autori: Tian Wu, Quinten Bafort, Frederik Mortier, Fabricio Almeida‐Silva, Annelore Natran, Yves Van de Peer
Pubblicato in: American Journal of Botany, Numero 111, 2024, Pagina/e e16383, ISSN 0002-9122
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Expanding the toolkit for ploidy manipulation in Chlamydomonas reinhardtii

Autori: Antoine Van de Vloet, Lucas Prost‐Boxoen, Quinten Bafort, Yunn Thet Paing, Griet Casteleyn, Lucile Jomat, Stéphane D. Lemaire, Olivier De Clerck, Yves Van de Peer
Pubblicato in: New Phytologist, Numero 246, 2025, Pagina/e 1403-1412, ISSN 0028-646X
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The Litsea genome and the evolution of the laurel family

Autori: 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
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Editore: Nature Publishing Group
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syntenet: an R/Bioconductor package for the inference and analysis of synteny networks

Autori: Fabricio Almeida-Silva, Tao Zhao, Kristian K Ullrich, M Eric Schranz, Yves Van de Peer
Pubblicato in: Bioinformatics, Numero 39/1, 2023, Pagina/e btac806, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btac806

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

Autori: 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
Pubblicato in: Nature Plants, Numero 20550278, 2022, Pagina/e 1024-1037, ISSN 2055-0278
Editore: Nature Publishing Group
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Studying whole-genome duplication using experimental evolution of Chlamydomonas

Autori: Quinten Bafort, Lucas Prost, Eylem Aydogdu, Antoine Van de Vloet, Griet Casteleyn, Yves Van de Peer, Olivier De Clerck
Pubblicato in: Methods in Molecular Biology, Numero 2545, 2023, Pagina/e 351-372, ISBN 978-1-0716-2561-3
Editore: Humana
DOI: 10.1007/978-1-0716-2561-3_18

Inference of ancient polyploidy using transcriptome data

Autori: Jia Li, Yves Van de Peer, Zhen Li
Pubblicato in: Methods in Molecular Biology, Numero 2545, 2023, Pagina/e 47-76, ISBN 978-1-0716-2561-3
Editore: Humana
DOI: 10.1007/978-1-0716-2561-3_3

Studying whole-genome duplication using experimental evolution of Spirodela polyrhiza

Autori: Tian Wu, Annelore Natran, Lucas Prost, Eylem Aydogdu, Yves Van de Peer, Quinten Bafort
Pubblicato in: Methods in Molecular Biology, Numero 2545, 2023, Pagina/e 373-390, ISBN 978-1-0716-2561-3
Editore: Humana
DOI: 10.1007/978-1-0716-2561-3_19

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