Abstract

India is believed to be a centre of origin and diversity of rice. India is the second largest rice producer in the world. Rice is a staple food for more than 60% of total population of India. More than 90% of rice cultivation in India belongs to indica type. However there is no reference rice genome available for indica type to understand the genetic diversity existing in Indian germplasm. With the advent of low cost NGS technologies, now it is possible to generate high quality rice genome assembly and annotation. Here we report the deep sequence of first indica cultivar, HR12 that was bred and released in India. The HR12 genome was assembled using combination of Illumina’s short reads and PacBio long reads (300bp to 51kb). Use of long reads has significantly improved the quality of HR12 assembly and annotation. HR12 rice assembly comprised over 90% (389 Mb) of estimated rice genome (430Mb). From our approach, the N50 of hybrid assembly was increased by four times and number of scaffolds was reduced by 40%. We annotated genes from HR12 assembly using various programs. HR12 genomic resources (assembly, annotated genes, repeats, variants etc) from this study will accelerate rice improvement programs in India and beyond.