title: Exploring the rice dispensable genome using a metagenome-like assembly strategy.
abstract: BACKGROUND
  The dispensable genome of a species, consisting of the dispensable sequences present only in a subset of individuals, is believed to play important roles in phenotypic variation and genome evolution. However, construction of the dispensable genome is costly and labor-intensive at present, and so the influence of the dispensable genome in genetic and functional genomic studies has not been fully explored.
  
  
  RESULTS
  We construct the dispensable genome of rice through a metagenome-like de novo assembly strategy based on low-coverage (1-3×) sequencing data of 1483 cultivated rice (Oryza sativa L.) accessions. Thousands of protein-coding genes are successfully assembled, including most of the known agronomically important genes absent from the Nipponbare rice reference genome. We develop an integration approach based on alignment and linkage disequilibrium, which is able to assign genomic positions relative to the reference genome for more than 78.2 % of the dispensable sequences. We carry out association mapping studies for rice grain width and 840 metabolic traits using 0.46 million polymorphisms between the dispensable sequences of different rice accessions. About 23.5 % of metabolic traits have more significant association signals with polymorphisms from dispensable sequences than with SNPs from the reference genome, and 41.6 % of trait-associated SNPs have concordant genomic locations with associated dispensable sequences.
  
  
  CONCLUSIONS
  Our results suggest the feasibility of building a species' dispensable genome using low-coverage population sequencing data. The constructed sequences will be helpful for understanding the rice dispensable genome and are complementary to the reference genome for identifying candidate genes associated with phenotypic variation.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China. ywww@webmail.hzau.edu.cn.
authors.forename: Wen
authors.initials: W
authors.lastname: Yao
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China. liguangwei@webmail.hzau.edu.cn.
authors.forename: Guangwei
authors.initials: G
authors.lastname: Li
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China. zhaohu@webmail.hzau.edu.cn.
authors.forename: Hu
authors.initials: H
authors.lastname: Zhao
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China. gwwang@mail.hzau.edu.cn.
authors.forename: Gongwei
authors.initials: G
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China. xmlian@mail.hzau.edu.cn.
authors.forename: Xingming
authors.initials: X
authors.lastname: Lian
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China. weibo.xie@mail.hzau.edu.cn.|Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China. weibo.xie@mail.hzau.edu.cn.
authors.forename: Weibo
authors.initials: W
authors.lastname: Xie
mesh_terms: D002874:Chromosome Mapping; D020451:Contig Mapping; D004251:DNA Transposable Elements; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D056186:Metagenomics / Q000379:methods; D058977:Molecular Sequence Annotation; D012275:Oryza / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements; D010940:Plant Proteins