The study involves sequencing the whole genome of five indica rice varieties namely, Nagina22, IR64, Anjali, Vandana and Pusa Basmati1. Paired-end genomic libraries were prepared and sequenced using Illumina platform and assembled to find sequence variations between these varieties and the japonica Nipponbare genomic sequence.. Indica Rice Genome sequencing

The study involves sequencing the whole genome of five indica rice varieties namely, Nagina22, IR64, Anjali, Vandana and Pusa Basmati1. Paired-end genomic libraries were prepared and sequenced using Illumina platform and assembled to find sequence variations between these varieties and the japonica Nipponbare genomic sequence. We assembled the pseudomolecules for the twelve chromosomes of rice and found several hundreds of SNPs between each variety and the reference Nipponbare. We also annotated these indica genomes on the lines of the reference annotations and also extracted the promoter regions i.e. the two kb region upstream of TSS for each gene. All this information has been stored and presented in a database called IRDb or the Indica Rice Database wherein all the assemblies can be downloaded as well. We also present the miRNA expression data, of N22 and PB1, along with transcriptome data, of N22 and IR64, of certain varieties. We also mapped the annotated gene boundaries to the known Quantitative Trait Loci to show physical overlap between protein coding and miRNA coding genes with the QTLs suggestive of their putative roles in the respective traits.