Draft Genome Sequence of Oryza sativa Subspecies indica cultivar, HR-12

Indian subcontinent is the center of origin and diversity for Rice (Oryza sativa L.). The O. sativa ssp. indica is a major food crop grown in India, which occupies first and second position in area and production, respectively. Reference genome sequences of indica (cv. 93-11) and japonica (cv. Nipponbare) (Yu et al., Science 2002, 296: 79-92; Goff et al., Science 2002, 296: 92-100) may not be useful to understand genomes of rice cultivars in India, due to lack of annotation of indica and distant nature of japonica genomes. To create our own reference rice genome, we sequenced the whole genome of an indica rice cultivar “HR-12” to support India’s rice improvement program. De novo sequencing (paired end: 2x100 nts and mate-paired: 2 to 20 kb insert size) was carried out using next-generation sequencer, Illumina HiSeq 1000. The first version (v1.0) de novo assemblies (~30X genome coverage) were generated using Velvet and SOAPDenovo programs. This resulted approximately 315 Mb contigs from 365 Mb scaffold genomic size. About 90% of Nipponabare genes (http://rice.plantbiology.msu.edu/) are detected in the HR12 genome draft. The draft genome assembly (version 1) of HR-12 is submitted to NCBI/GenBank. This genome will be used as a reference for subsequent indica rice genomic studies.