title: The impact and origin of copy number variations in the Oryza species.
abstract: 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.
authors.affiliation: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
authors.forename: Zetao
authors.initials: Z
authors.lastname: Bai
authors.affiliation: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
authors.forename: Jinfeng
authors.initials: J
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Liao
authors.affiliation: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
authors.forename: Meijiao
authors.initials: M
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
authors.forename: Rong
authors.initials: R
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
authors.forename: Song
authors.initials: S
authors.lastname: Ge
authors.affiliation: Arizona Genomics Institute, School of Plant Science, University of Arizona, Tucson, AZ, 85721, USA.
authors.forename: Rod A
authors.initials: RA
authors.lastname: Wing
authors.affiliation: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. mschen@genetics.ac.cn.
authors.forename: Mingsheng
authors.initials: M
authors.lastname: Chen
mesh_terms: D056915:DNA Copy Number Variations; D018744:DNA, Plant / Q000235:genetics; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant
keywords: CNV genes; Copy number variation (CNV); Mutation mechanisms; NGS-based survey; Oryza species