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The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes.

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 genus.

SUBMITTER: Liu S

PROVIDER: S-EPMC4279128 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature

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The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes.

Liu Shengyi S Liu Yumei Y Yang Xinhua X Tong Chaobo C Edwards David D Parkin Isobel A P IA Zhao Meixia M Ma Jianxin J Yu Jingyin J Huang Shunmou S Wang Xiyin X Wang Junyi J Lu Kun K Fang Zhiyuan Z Bancroft Ian I Yang Tae-Jin TJ Hu Qiong Q Wang Xinfa X Yue Zhen Z Li Haojie H Yang Linfeng L Wu Jian J Zhou Qing Q Wang Wanxin W King Graham J GJ Pires J Chris JC Lu Changxin C Wu Zhangyan Z Sampath Perumal P Wang Zhuo Z Guo Hui H Pan Shengkai S Yang Limei L Min Jiumeng J Zhang Dong D Jin Dianchuan D Li Wanshun W Belcram Harry H Tu Jinxing J Guan Mei M Qi Cunkou C Du Dezhi D Li Jiana J Jiang Liangcai L Batley Jacqueline J Sharpe Andrew G AG Park Beom-Seok BS Ruperao Pradeep P Cheng Feng F Waminal Nomar Espinosa NE Huang Yin Y Dong Caihua C Wang Li L Li Jingping J Hu Zhiyong Z Zhuang Mu M Huang Yi Y Huang Junyan J Shi Jiaqin J Mei Desheng D Liu Jing J Lee Tae-Ho TH Wang Jinpeng J Jin Huizhe H Li Zaiyun Z Li Xun X Zhang Jiefu J Xiao Lu L Zhou Yongming Y Liu Zhongsong Z Liu Xuequn X Qin Rui R Tang Xu X Liu Wenbin W Wang Yupeng Y Zhang Yangyong Y Lee Jonghoon J Kim Hyun Hee HH Denoeud France F Xu Xun X Liang Xinming X Hua Wei W Wang Xiaowu X Wang Jun J Chalhoub Boulos B Paterson Andrew H AH

Nature communications 20140523

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 ...[more]

PMID: 24852848

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Project description:BackgroundGlycosyltransferases comprise a highly divergent and polyphyletic multigene family that is involved in widespread modification of plant secondary metabolites in a process called glycosylation. According to conserved domains identified in their amino acid sequences, these glycosyltransferases can be classified into a single UDP-glycosyltransferase (UGT) 1 superfamily.ResultsWe performed genome-wide comparative analysis of UGT genes to trace evolutionary history in algae, bryophytes, pteridophytes, and angiosperms; then, we further investigated the expansion mechanisms and function characterization of UGT gene families in Brassica rapa and Brassica oleracea. Using Hidden Markov Model search, we identified 3, 21, 140, 200, 115, 147, and 147 UGTs in Chlamydomonas reinhardtii, Physcomitrella patens, Selaginella moellendorffii, Oryza sativa, Arabidopsis thaliana, B. rapa, and B. oleracea, respectively. Phylogenetic analysis revealed that UGT80 gene family is an ancient gene family, which is shared by all plants and UGT74 gene family is shared by ferns and angiosperms, but the remaining UGT gene families were shared by angiosperms. In dicot lineage, UGTs among three species were classified into three subgroups containing 3, 6, and 12 UGT gene families. Analysis of chromosomal distribution indicates that 98.6 and 71.4% of UGTs were located on B. rapa and B. oleracea pseudo-molecules, respectively. Expansion mechanism analyses uncovered that whole genome duplication event exerted larger influence than tandem duplication on expansion of UGT gene families in B. rapa, and B. oleracea. Analysis of selection forces of UGT orthologous gene pairs in B. rapa, and B. oleracea compared to A. thaliana suggested that orthologous genes in B. rapa, and B. oleracea have undergone negative selection, but there were no significant differences between A. thaliana -B. rapa and A. thaliana -B. oleracea lineages. Our comparisons of expression profiling illustrated that UGTs in B. rapa performed more discrete expression patterns than these in B. oleracea indicating stronger function divergence. Combing with phylogeny and expression analysis, the UGTs in B. rapa and B. oleracea experienced parallel evolution after they diverged from a common ancestor.ConclusionWe first traced the evolutionary history of UGT gene families in plants and revealed its evolutionary and functional characterization of UGTs in B. rapa, and B. oleracea. This study provides novel insights into the evolutionary history and functional divergence of important traits or phenotype-related gene families in plants.

Dataset Information

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes.

Publications

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes.

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