2015-12-08: Exploring the rice dispensable genome using a metagenome-like assembly strategy Wen Yao, Guangwei Li, Hu Zhao, Gongwei Wang, Xingming Lian and Weibo Xie* Genome Biology 2015, 16(1): 1-20.

DOI: 10.1186/s13059-015-0757-3 pdf

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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.


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.


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.

2015-12-07: RiceVarMap: a comprehensive database of rice genomic variations Hu Zhao, Wen Yao, Yidan Ouyang, Wanneng Yang, Gongwei Wang, Xingming Lian, Yongzhong Xing, Lingling Chen and Weibo Xie* Nucleic Acids Research 2015, 43(D1): D1018-D1022.

DOI: 10.1093/nar/gku894 pdf

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Rice Variation Map (RiceVarMap, http:/ is a database of rice genomic variations. The database provides comprehensive information of 6 551 358 single nucleotide polymorphisms (SNPs) and 1 214 627 insertions/deletions (INDELs) identified from sequencing data of 1479 rice accessions. The SNP genotypes of all accessions were imputed and evaluated, resulting in an overall missing data rate of 0.42% and an estimated accuracy greater than 99%. The SNP/INDEL genotypes of all accessions are available for online query and download. Users can search SNPs/INDELs by identifiers of the SNPs/INDELs, genomic regions, gene identifiers and keywords of gene annotation. Allele frequencies within various subpopulations and the effects of the variation that may alter the protein sequence of a gene are also listed for each SNP/INDEL. The database also provides geographical details and phenotype images for various rice accessions. In particular, the database provides tools to construct haplotype networks and design PCR-primers by taking into account surrounding known genomic variations. These data and tools are highly useful for exploring genetic variations and evolution studies of rice and other species.