Reference-guided de novo Genome Assembly of the Indica Type Rice Variety IR 64 Using Short-read Sequencing

Under the rice SNP consortium <http://www.ricesnp.org> activities with contributions by many partners, over 150 genomes of rice were re-sequenced at various depths to provide a SNP discovery pool of over 27 million SNPs.  These SNPs were used to select design Affymetrix arrays with ~1Mio SNP and other features.  A part of this work was the resequencing of the indica type mega-variety IR 64, to a depth of about ~60x coverage by Illumina technology with paired-end reads.  At IRRI, we applied  reference-guided de novo assembly approaches such as that developed by Schneeberger et al (2011, PNAS 108:10249-10254) to this data to create a genome build for IR 64.  Using the published Nipponbarre genome as reference, de novo assembled contigs of short reads mapping to Nipponbare give an overall reference genome coverage of 78% with n50 values ranging from 5.9 kb (Chr 12) to 8.9 kb (Chr 3).  Contigs built from mapped reads (per chromosome) + the pool of unmapped reads resulted in 81% coverage relative to Nipponbare and n50 values ranging from 2.6 kb (Chr 10) to 4.6 kb (Chr 1). Many of the regions of Nipponbare where IR 64 contigs do not map are regions known to be rich in transposable and other repetitive elements. This poster will present strategies we have explored to achieve a genome build of IR 64,  and proposed strategies to build an indica type reference genome from sequence data generated for multiple indica variety types.