RPAN: rice pan-genome browser for similar to 3000 rice genomes

文献类型： 外文期刊

第一作者： Sun, Chen

作者： Sun, Chen;Hu, Zhiqiang;Lu, Kuangchen;Zhao, Yue;Lu, Jinyuan;Wei, Chaochun;Zheng, Tianqing;Wang, Wensheng;Wang, Chunchao;Li, Zhikang;Shi, Jianxin;Zhang, Dabing;Sun, Chen;Hu, Zhiqiang;Wei, Chaochun;Zhang, Dabing

作者机构：

期刊名称：NUCLEIC ACIDS RESEARCH （ 影响因子：16.971； 五年影响因子：15.542 ）

ISSN： 0305-1048

年卷期： 2017 年 45 卷 2 期

页码：

收录情况： SCI

摘要： A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes with large-sized genomes. The Asian cultivated rice, Oryza sativa L., is one of the major food sources for the world and a model organism in plant biology. Recently, the 3000 Rice Genome Project (3K RGP) sequenced more than 3000 rice genomes with a mean sequencing depth of 14.3 x, which provided a tremendous resource for rice research. In this paper, we present a genome browser, Rice Pan-genomeBrowser (RPAN), as a tool to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding. It is available at http://cgm.sjtu.edu.cn/3kricedb/ or http://www.rmbreeding.cn/pan3k.

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