Journal ArticleDOI
The ABC's of comparative genomics in the Brassicaceae: building blocks of crucifer genomes
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TLDR
This review summarizes recent advances in the understanding of phylogenetics, polyploidization and comparative genomics in the family Brassicaceae and integrates several of these findings into a simple system of 24 conserved chromosomal blocks (labeled A-X).About:
This article is published in Trends in Plant Science.The article was published on 2006-11-01. It has received 515 citations till now. The article focuses on the topics: Capsella rubella & Arabidopsis lyrata.read more
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Book ChapterDOI
Arabidopsis Genome Initiative
Ramesh Katam,Dilip R. Panthee,Evelina Y. Basenko,Rajib Bandopadhyay,Sheikh M. Basha,Kokiladevi Eswaran,Chittaranjan Kole +6 more
TL;DR: Arabidopsis (rockcress) is a genus in the family Brassicaceae as mentioned in this paper, which includes nine species and eight subspecies, and has 10 chromosomes in diploid stage.
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
The Capsella rubella genome and the genomic consequences of rapid mating system evolution
Tanja Slotte,Tanja Slotte,Khaled M. Hazzouri,Khaled M. Hazzouri,J. Arvid Ågren,Daniel Koenig,Florian Maumus,Ya-Long Guo,Kim A. Steige,Adrian E. Platts,Juan S. Escobar,L. Killian Newman,Wei Wang,Terezie Mandáková,Emilio Vello,Lisa M. Smith,Stefan R. Henz,Joshua G. Steffen,Joshua G. Steffen,Shohei Takuno,Shohei Takuno,Yaniv Brandvain,Graham Coop,Peter Andolfatto,Tina T. Hu,Mathieu Blanchette,Richard M. Clark,Hadi Quesneville,Magnus Nordborg,Brandon S. Gaut,Martin A. Lysak,Jerry Jenkins,Jane Grimwood,Jarrod Chapman,Simon E. Prochnik,Shengqiang Shu,Daniel S. Rokhsar,Daniel S. Rokhsar,Jeremy Schmutz,Detlef Weigel,Stephen I. Wright +40 more
TL;DR: The transition to selfing may be typified by parallel shifts in gene expression, along with a measurable reduction of purifying selection, similar to that seen in Arabidopsis, which self fertilization evolved about 1 million years ago.
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.
Journal ArticleDOI
Cabbage family affairs: the evolutionary history of Brassicaceae
TL;DR: This review examines recent outcomes from diverse botanical disciplines to synthesize for the first time a holistic view on the evolutionary history of the mustard family.
References
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Journal ArticleDOI
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
TL;DR: This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.
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Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
TL;DR: It is shown that a genome-wide duplication post-dates the divergence of Arabidopsis from most dicots, and that additional, more ancient duplication events affect more distant taxonomic comparisons.
Journal ArticleDOI
The origins of genomic duplications in Arabidopsis
TL;DR: It is shown that large segmental duplications cover much of the Arabidopsis thaliana genome and are primarily due to at least four different large-scale duplication events that occurred 100 to 200 million years ago.
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Comparative genetics in the grasses
Michael D. Gale,Katrien M. Devos +1 more
TL;DR: In this paper, a detailed analysis of the comparative maps of seven species, belonging to three subfamilies, and their applications are described, together with their applications, are described.
Journal ArticleDOI
Cereal Genome Evolution: Grasses, line up and form a circle
TL;DR: The genomes of six major grass species can be aligned by dissecting the individual chromosomes into segments and rearranging these linkage blocks into highly similar structures.
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