Indica Rice Genome Assembly and Annotation using Short and Long Read Sequences

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. Reference indica rice genome is not available to understand diversity existing in Indian germplasm. We here report the whole genome sequencing and annotation of indica cultivar, HR-12, which was released for commercial cultivation in India. This is also used as a parental line in rice breeding program. We have generated over 70x of Illumina data (2x100 nts) and 20x of PacBio data. Use long reads has significantly improved the quality of HR12 assembly by increasing four times N50 of contigs and reduced 40% of scaffolds. This approach has assembled over 90% (389 Mb) of estimated indica rice genome. We identified 2130 unique genes to HR-12 genome by comparing with 93-11 and Nipponbare. The HR12 assembly and genes can be used as a reference for genome will improve the understanding of Indica rice germplasm and genome assisted rice breeding.