Syntenic gene analysis between Brassica rapa and other Brassicaceae species

doi:10.3389/fpls.2012.00198

	Syntenic gene analysis between Brassica rapa and other Brassicaceae species
	Cheng, Feng; Wu, Jian; Fang, Lu; Wang, Xiaowu
刊名	FRONTIERS IN PLANT SCIENCE
	2012
卷号	3 页码:-
关键词	synteny ortholog Brassica rapa Arabidopsis thaliana Arabidopsis lyrata Thellugiella parvula Brassicaceae
ISSN号	1664-462X
DOI	10.3389/fpls.2012.00198
通讯作者	Cheng, Feng
英文摘要	Chromosomal synteny analysis is important in genome comparison to reveal genomic evolution of related species. Shared synteny describes genomic fragments from different species that originated from an identical ancestor. Syntenic genes are orthologs located in these syntenic fragments, so they often share similar functions. Syntenic gene analysis is very important in Brassicaceae species to share gene annotations and investigate genome evolution. Here we designed and developed a direct and efficient tool, SynOrths, to identify pairwise syntenic genes between genomes of Brassicaceae species. SynOrths determines whether two genes are a conserved syntenic pair based not only on their sequence similarity, but also by the support of homologous flanking genes. Syntenic genes between Arabidopsis thaliana and Brassica rapa, Arabidopsis lyrata and B. rapa, and Thellungiella parvula and B. rapa were then identified using SynOrths. The occurrence of genome triplication in B. rapa was clearly observed, many genes that were evenly distributed in the genomes of A. thaliana, A. lyrata, and T. parvula had three syntenic copies in B. rapa. Additionally, there were many B. rapa genes that had no syntenic orthologs in A. thaliana, but some of these had syntenic orthologs in A. lyrata or T. parvula. Only 5,851 genes in B. rapa had no syntenic counterparts in any of the other three species. These 5,851 genes could have originated after B. rapa diverged from these species. A tool for syntenic gene analysis between species of Brassicaceae was developed, SynOrths, which could be used to accurately identify syntenic genes in differentiated but closely-related genomes. With this tool, we identified syntenic gene sets between B. rapa and each of A. thaliana, A. lyrata, T. parvula. Syntenic gene analysis is important for not only the gene annotation of newly sequenced Brassicaceae genomes by bridging them to model plant A. thaliana, but also the study of genome evolution in these species.
学科主题	Plant Sciences
语种	英语
出版者	FRONTIERS RESEARCH FOUNDATION
WOS记录号	WOS:000208837900195
内容类型	期刊论文
源URL	[http://111.203.20.206/handle/2HMLN22E/101121]
专题	蔬菜花卉研究所_生物技术研究室
作者单位	Chinese Acad Agr Sci, Inst Vegetables & Flowers, Beijing 100081, Peoples R China
推荐引用方式 GB/T 7714	Cheng, Feng,Wu, Jian,Fang, Lu,et al. Syntenic gene analysis between Brassica rapa and other Brassicaceae species[J]. FRONTIERS IN PLANT SCIENCE,2012,3:-.
APA	Cheng, Feng,Wu, Jian,Fang, Lu,&Wang, Xiaowu.(2012).Syntenic gene analysis between Brassica rapa and other Brassicaceae species.FRONTIERS IN PLANT SCIENCE,3,-.
MLA	Cheng, Feng,et al."Syntenic gene analysis between Brassica rapa and other Brassicaceae species".FRONTIERS IN PLANT SCIENCE 3(2012):-.