Comparative Analysis between Homoeologous Genome Segments of Brassica napus and Its Progenitor Species Reveals Extensive Sequence-Level Divergence
Foo Cheung,Martin Trick,Nizar Drou,Yong Pyo Lim,Jee Young Park,Soo Jin Kwon,Jin A Kim,Rod J. Scott,J. Chris Pires,Andrew H. Paterson,Christopher D. Town,Ian Bancroft +11 more
TLDR
The considerable variation that the authors observed, even between the different versions of the same Brassica genome, for gene fragments and annotated putative genes suggest that the concept of the pan-genome might be particularly appropriate when considering Brassica genomes.Abstract:
Homoeologous regions of Brassica genomes were analyzed at the sequence level. These represent segments of the Brassica A genome as found in Brassica rapa and Brassica napus and the corresponding segments of the Brassica C genome as found in Brassica oleracea and B. napus. Analysis of synonymous base substitution rates within modeled genes revealed a relatively broad range of times (0.12 to 1.37 million years ago) since the divergence of orthologous genome segments as represented in B. napus and the diploid species. Similar, and consistent, ranges were also identified for single nucleotide polymorphism and insertion-deletion variation. Genes conserved across the Brassica genomes and the homoeologous segments of the genome of Arabidopsis thaliana showed almost perfect collinearity. Numerous examples of apparent transduplication of gene fragments, as previously reported in B. oleracea, were observed in B. rapa and B. napus, indicating that this phenomenon is widespread in Brassica species. In the majority of the regions studied, the C genome segments were expanded in size relative to their A genome counterparts. The considerable variation that we observed, even between the different versions of the same Brassica genome, for gene fragments and annotated putative genes suggest that the concept of the pan-genome might be particularly appropriate when considering Brassica genomes.read more
Citations
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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
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
TL;DR: 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.
Journal ArticleDOI
Insights into the Maize Pan-Genome and Pan-Transcriptome
Candice N. Hirsch,Candice N. Hirsch,Jillian M. Foerster,James M. Johnson,Rajandeep S. Sekhon,Rajandeep S. Sekhon,German Muttoni,Brieanne Vaillancourt,Brieanne Vaillancourt,Francisco Peñagaricano,Erika Lindquist,Mary Ann Pedraza,Kerrie Barry,Natalia de Leon,Natalia de Leon,Shawn M. Kaeppler,Shawn M. Kaeppler,C. Robin Buell,C. Robin Buell +18 more
TL;DR: The dynamic nature of the maize pan-genome was revealed and it was demonstrated that a substantial portion of variation may lie outside the single reference genome for a species.
Journal ArticleDOI
Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus
TL;DR: In this paper, the authors conducted a cytological investigation of 50 resynthesized Brassica napus allopolyploids across generations S0:1 to S5:6 and in the S10:11 generation.
Journal ArticleDOI
Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea.
Isobel A. P. Parkin,Chushin Koh,Haibao Tang,Stephen J. Robinson,Sateesh Kagale,Sateesh Kagale,Wayne E. Clarke,Christopher D. Town,John Nixon,Vivek Krishnakumar,Shelby L. Bidwell,Harry Belcram,Matthew G. Links,Jérémy Just,Carling Clarke,Tricia Bender,Terry Huebert,Annaliese S. Mason,Chris J Pires,Guy C. Barker,Jonathan D. Moore,Peter Glen Walley,Sahana Manoli,Jacqueline Batley,David Edwards,Matthew N. Nelson,Xiyin Wang,Andrew H. Paterson,Graham J.W. King,Ian Bancroft,Boulos Chalhoub,Andrew G. Sharpe +31 more
TL;DR: Differential expression of the triplicated syntelogs and cytosine methylation levels across the sub-genomes suggest residual marks of the genome dominance that led to the current genome architecture, and epigenetic mechanisms play a role in the functional diversification of duplicate genes.
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