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Nucleic Acids Res. 2017 Jan 25;45(2):597-605. doi: 10.1093/nar/gkw958. Epub 2016 Dec 10.

RPAN: rice pan-genome browser for ∼3000 rice genomes.

Sun C1,2, Hu Z1,2, Zheng T3, Lu K1, Zhao Y1, Wang W3, Shi J4, Wang C3, Lu J1, Zhang D4,5, Li Z6, Wei C7,2.

Author information

1
Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
2
Shanghai Center for Bioinformation Technology, Shanghai 201203, China.
3
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
4
Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
5
School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia.
6
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China zhkli1953@126.com.
7
Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China ccwei@sjtu.edu.cn.

Abstract

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×, which provided a tremendous resource for rice research. In this paper, we present a genome browser, Rice Pan-genome Browser (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.

PMID:
27940610
PMCID:
PMC5314802
DOI:
10.1093/nar/gkw958
[Indexed for MEDLINE]
Free PMC Article

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