The impact and origin of copy number variations in the Oryza species

doi:10.1186/s12864-016-2589-2

	The impact and origin of copy number variations in the Oryza species
	Bai, Zetao ; Chen, Jinfeng ; Liao, Yi ; Wang, Meijiao ; Liu, Rong 1; Ge, Song1 ; Wing, Rod A.; Chen, Mingsheng
	2016
发表期刊	BMC GENOMICS
ISSN	1471-2164
卷号	17
摘要	Background: Copy number variation (CNV), a complex genomic rearrangement, has been extensively studied in humans and other organisms. In plants, CNVs of several genes were found to be responsible for various important traits; however, the cause and consequence of CNVs remains largely unknown. Recently released next-generation sequencing (NGS) data provide an opportunity for a genome-wide study of CNVs in rice. Results: Here, by an NGS-based approach, we generated a CNV map comprising 9,196 deletions compared to the reference genome 'Nipponbare'. Using Oryza glaberrima as the outgroup, 80 % of the CNV events turned out to be insertions in Nipponbare. There were 2,806 annotated genes affected by these CNV events. We experimentally validated 28 functional CNV genes including OsMADS56, BPH14, OsDCL2b and OsMADS30, implying that CNVs might have contributed to phenotypic variations in rice. Most CNV genes were found to be located in non-co-linear positions by comparison to O. glaberrima. One of the origins of these non-co-linear genes was genomic duplications caused by transposon activity or double-strand break repair. Comprehensive analysis of mutation mechanisms suggested an abundance of CNVs formed by non-homologous end-joining and mobile element insertion. Conclusions: This study showed the impact and origin of copy number variations in rice on a genomic scale.
关键词	Oryza species Copy number variation (CNV) NGS-based survey CNV genes Mutation mechanisms
学科领域	Biotechnology & Applied Microbiology ; Genetics & Heredity
DOI	10.1186/s12864-016-2589-2
收录类别	SCI
语种	英语
WOS关键词	GENOMIC STRUCTURAL VARIATION ; GENE MOVEMENT ; WHOLE-GENOME ; SHORT-READ ; REPRODUCTIVE DEVELOPMENT ; WIDE IDENTIFICATION ; RICE ; ARABIDOPSIS ; MECHANISMS ; SEQUENCE
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000373557000001
出版者	BMC
文献子类	Article
出版地	LONDON
资助机构	National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31171231, 31571309, 31371284] ; State Key Laboratory of Plant Genomics [SKLPG2011B0102] ; Direct For Biological SciencesNational Science Foundation (NSF)NSF - Directorate for Biological Sciences (BIO) [1026200] Funding Source: National Science Foundation
作者邮箱	mschen@genetics.ac.cn
作品OA属性	Green Published, gold
引用统计	被引频次：29[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/25012
专题	系统与进化植物学国家重点实验室
作者单位	1.Chinese Acad Sci, Inst Genet & Dev Biol, State Key Lab Plant Genom, Beijing 100101, Peoples R China 2.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 3.Wing, Rod A.] Univ Arizona, Arizona Genom Inst, Sch Plant Sci, Tucson, AZ 85721 USA
推荐引用方式 GB/T 7714	Bai, Zetao,Chen, Jinfeng,Liao, Yi,et al. The impact and origin of copy number variations in the Oryza species[J]. BMC GENOMICS,2016,17.
APA	Bai, Zetao.,Chen, Jinfeng.,Liao, Yi.,Wang, Meijiao.,Liu, Rong.,...&Chen, Mingsheng.(2016).The impact and origin of copy number variations in the Oryza species.BMC GENOMICS,17.
MLA	Bai, Zetao,et al."The impact and origin of copy number variations in the Oryza species".BMC GENOMICS 17(2016).

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