title: RPAN: rice pan-genome browser for ∼3000 rice genomes.
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.
authors.affiliation: Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.|Shanghai Center for Bioinformation Technology, Shanghai 201203, China.
authors.forename: Chen
authors.identifier: 0000-0003-0657-207X
authors.initials: C
authors.lastname: Sun
authors.affiliation: Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.|Shanghai Center for Bioinformation Technology, Shanghai 201203, China.
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Hu
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Tianqing
authors.initials: T
authors.lastname: Zheng
authors.affiliation: Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Kuangchen
authors.initials: K
authors.lastname: Lu
authors.affiliation: Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Wensheng
authors.initials: W
authors.lastname: Wang
authors.affiliation: Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Jianxin
authors.initials: J
authors.lastname: Shi
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Chunchao
authors.initials: C
authors.lastname: Wang
authors.affiliation: Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Jinyuan
authors.initials: J
authors.lastname: Lu
authors.affiliation: Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.|School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia.
authors.forename: Dabing
authors.initials: D
authors.lastname: Zhang
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China zhkli1953@126.com.
authors.forename: Zhikang
authors.initials: Z
authors.lastname: Li
authors.affiliation: Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China ccwei@sjtu.edu.cn.|Shanghai Center for Bioinformation Technology, Shanghai 201203, China.
authors.forename: Chaochun
authors.initials: C
authors.lastname: Wei
mesh_terms: D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D058977:Molecular Sequence Annotation; D012275:Oryza / Q000235:genetics*; D012984:Software; D064878:Web Browser