Construction Of Rice Pan-genome Browser

A pan-genome is the union of the gene sets of all individuals of a clade.We can study the evolution history of a clade through comparing the genomes among different individuals and populations.Pan-genome provides a new perspective for population genomics and expands our understanding about evolution.With the development of sequencing technologies and the decrease of the price,more and more large-sized genomes were sequenced and rice,one of the major food sources for human,was one of them.The rice pan-genome analyses provide a new dimension for us to understand rice genomics,and the results are of great importance for rice biology and rice breeding.Recently,the 3000 Rice Genomes Project(3K RGP)sequenced more than 3000 rice genomes with a mean sequencing depth of 14.3x,which provided a tremendous resource for rice research.However,it is a big challenge to visualize the results of rice pan-genome analysis with an intuitive way.Here,we present the Rice Pan-genome Browser(RPAN),a tool to search and visualize the rice pan-genome.RPAN contains a database of the basic information of rice accessions,genomic sequences,gene annotations,gene expression profiles and gene presence/absence variations(PAVs)of 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/.