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.

Genomic Breeding of Green Super Rice Varieties and Their Deployment in Asia and Africa

“…Based on the information on rice genomic variations, a new multifunctional and comprehensive rice functional genomics and breeding database (RFGB) has been established, which included a rice sequence polymorphism information retrieval system, an explorer visualization system of the genome, and data output system for specific genome regions (http://www. rmbre eding .cn/) (Sun et al 2016). Currently, the GSR project integrated the re-sequencing data of more than 6000 rice genomes worldwide, carried out haplotype analysis on the whole-genome structural variations, and investigated the selected genomic regions during the breeding process.…”

Rice Functional Genomics Research: Past Decade and Future

“…For example, the RiceVarMap website provides comprehensive information of 6 551 358 SNPs and 1 214 627 (InDels) identified from sequencing data of 1479 rice accessions (Zhao et al, 2015a). The Rice Pan-genome Browser (RPAN) is a tool to search and visualize the pan-genome derived from the 3K rice genome project (Sun et al, 2016a).…”

“…Recently, high-quality genomes for indica rice of Zhenshan 97 and Minghui 63 (Zhang et al, 2016) and Shuhui 498 (Du et al, 2017) were obtained using third-generation sequencing technology, providing additional high-quality genomes for the discovery of genes and structure variations in rice. The recent availability of the 3K genome sequences together with the already large amounts of rice sequencing data have provided an almost unlimited data resource for the studies of (annotated) non-coding portions and dispensable portions of the genome (3,000 rice genomes project, 2014; Sun et al, 2016a). In addition, understanding of the dispensable portions may in turn help the determination of the indispensable genome, which may be used for conceiving (or constructing) an essential rice genome in questing a rice version of Synthetic Genome.…”

Plant Pangenome: Impacts on Phenotypes and Evolution

“…Function-Based Definition. The function-based definition states that the pangenome is the sum of all genes within a given set of individuals; it can be extended at the gene family level, as in (31). This is similar to the definition used in bacteria, and relies on the identification of gene clusters (genes with close phylogenetic relationships, that may be scattered all along the genome).…”