The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes
Shengyi Liu,Yumei Liu,Xinhua Yang,Chaobo Tong,David Edwards,Isobel A. P. Parkin,Meixia Zhao,Jianxin Ma,Jingyin Yu,Shunmou Huang,Xiyin Wang,Junyi Wang,Kun Lu,Zhiyuan Fang,Ian Bancroft,Tae-Jin Yang,Qiong Hu,Xinfa Wang,Zhen Yue,Haojie Li,Linfeng Yang,Jian Wu,Qing Zhou,Wanxin Wang,Graham J.W. King,J. Chris Pires,Changxin Lu,Zhangyan Wu,Perumal Sampath,Zhuo Wang,Hui Guo,Shengkai Pan,Limei Yang,Jiumeng Min,Dong Zhang,Dianchuan Jin,Wanshun Li,Harry Belcram,Jinxing Tu,Mei Guan,Cunkou Qi,Dezhi Du,Jiana Li,Liangcai Jiang,Jacqueline Batley,Andrew G. Sharpe,Beom Seok Park,Pradeep Ruperao,Feng Cheng,Nomar Espinosa Waminal,Yin Huang,Caihua Dong,Li Wang,Jingping Li,Zhiyong Hu,Mu Zhuang,Yi Huang,Junyan Huang,Jiaqin Shi,Desheng Mei,Jing Liu,Tae-Ho Lee,Jinpeng Wang,Huizhe Jin,Zaiyun Li,Xun Li,Jiefu Zhang,Lu Xiao,Yongming Zhou,Zhongsong Liu,Xuequn Liu,Rui Qin,Xu Tang,Wenbin Liu,Yupeng Wang,Yangyong Zhang,Jonghoon Lee,Hyun Hee Kim,Xun Xu,Xinming Liang,Wei Hua,Xiaowu Wang,Jun Wang,Boulos Chalhoub,Andrew H. Paterson +84 more
TLDR
A draft genome sequence of Brassica oleracea is described, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks.Abstract:
Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear Brassica is an ideal model to increase knowledge of polyploid evolution Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B oleracea This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genusread more
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Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome
Boulos Chalhoub,Shengyi Liu,Isobel A. P. Parkin,Haibao Tang,Haibao Tang,Xiyin Wang,Julien Chiquet,Harry Belcram,Chaobo Tong,Birgit Samans,Margot Correa,Corinne Da Silva,Jérémy Just,Cyril Falentin,Chu Shin Koh,Isabelle Le Clainche,Maria Bernard,Pascal Bento,Benjamin Noel,Karine Labadie,Adriana Alberti,Mathieu Charles,Dominique Arnaud,Hui Guo,Christian Daviaud,Salman Alamery,Kamel Jabbari,Kamel Jabbari,Meixia Zhao,Patrick P. Edger,Houda Chelaifa,David C. Tack,Gilles Lassalle,Imen Mestiri,Nicolas Schnel,Marie-Christine Le Paslier,Guangyi Fan,Victor Renault,Philippe E. Bayer,Agnieszka A. Golicz,Sahana Manoli,Tae-Ho Lee,Vinh Ha Dinh Thi,Smahane Chalabi,Qiong Hu,Chuchuan Fan,Reece Tollenaere,Yunhai Lu,Christophe Battail,Jinxiong Shen,Christine Sidebottom,Xinfa Wang,Aurélie Canaguier,Aurélie Chauveau,Aurélie Bérard,G. Deniot,Mei Guan,Zhongsong Liu,Fengming Sun,Yong Pyo Lim,Eric Lyons,Christopher D. Town,Ian Bancroft,Xiaowu Wang,Jinling Meng,Jianxin Ma,J. Chris Pires,Graham J.W. King,Dominique Brunel,Régine Delourme,Michel Renard,Jean-Marc Aury,Keith L. Adams,Jacqueline Batley,Jacqueline Batley,Rod J. Snowdon,Jörg Tost,David Edwards,David Edwards,Yongming Zhou,Wei Hua,Andrew G. Sharpe,Andrew H. Paterson,Chunyun Guan,Patrick Wincker,Patrick Wincker,Patrick Wincker +86 more
TL;DR: The polyploid genome of Brassica napus, which originated from a recent combination of two distinct genomes approximately 7500 years ago and gave rise to the crops of rape oilseed, is sequenced.
Journal ArticleDOI
Sequencing of allotetraploid cotton ( Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement
Tianzhen Zhang,Yan Hu,Wenkai Jiang,Lei Fang,Xueying Guan,Jiedan Chen,Jinbo Zhang,Christopher A. Saski,Brian E. Scheffler,David M. Stelly,Amanda M. Hulse-Kemp,Qun Wan,Bingliang Liu,Chunxiao Liu,Sen Wang,Mengqiao Pan,Yangkun Wang,Dawei Wang,Wenxue Ye,Lijing Chang,Wenpan Zhang,Qingxin Song,Ryan C. Kirkbride,Xiao-Ya Chen,Elizabeth S. Dennis,Danny J. Llewellyn,Daniel G. Peterson,Peggy Thaxton,Don C. Jones,Qiong Wang,Xiaoyang Xu,Hua Zhang,Huaitong Wu,Lei Zhou,Gaofu Mei,Shuqi Chen,Yue Tian,Dan Xiang,Xinghe Li,Jian Ding,Qiyang Zuo,Linna Tao,Yunchao Liu,Ji Li,Yu Lin,Yuanyuan Hui,Zhisheng Cao,Caiping Cai,Xiefei Zhu,Zhi Jiang,Baoliang Zhou,Wangzhen Guo,Ruiqiang Li,Z. Jeffrey Chen +53 more
TL;DR: Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenomes, suggesting asymmetric evolution.
Journal ArticleDOI
Evolution by gene loss
Ricard Albalat,Cristian Cañestro +1 more
TL;DR: These questions are addressed, and insights are discussed from genomic studies of gene loss in populations and their relevance in evolutionary biology and biomedicine.
Journal ArticleDOI
Ensembl Genomes 2016: more genomes, more complexity
Paul J. Kersey,James E. Allen,Irina M. Armean,Sanjay Boddu,Bruce J. Bolt,Denise Carvalho-Silva,Mikkel B. Christensen,Paul Davis,Lee J. Falin,Christoph Grabmueller,Jay C. Humphrey,Arnaud Kerhornou,Julia Khobova,Naveen K. Aranganathan,Nicholas Langridge,Ernesto Lowy,Mark D. McDowall,Uma Maheswari,Michael Nuhn,Chuang Kee Ong,Bert Overduin,Michael Paulini,Helder Pedro,Emily Perry,Giulietta Spudich,Electra Tapanari,Brandon Walts,Gareth Williams,Marcela K. Tello-Ruiz,Joshua C. Stein,Sharon Wei,Doreen Ware,Dan Bolser,Kevin L. Howe,Eugene Kulesha,Daniel Lawson,Gareth Maslen,Daniel M. Staines +37 more
TL;DR: This paper provides an update to the previous publications about the Ensembl Genomes, with a focus on recent developments, including the development of new analyses and views to represent polyploid genomes and the continued up-scaling of the resource.
Journal ArticleDOI
Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants.
Xin Qiao,Qionghou Li,Hao Yin,Kaijie Qi,Leiting Li,Runze Wang,Shaoling Zhang,Andrew H. Paterson +7 more
TL;DR: A comprehensive landscape of different modes of gene duplication across the plant kingdom is identified by comparing 141 genomes, which provides a solid foundation for further investigation of the dynamic evolution of duplicate genes.
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