Rice (Oryza sativa) is one of the most important crops in the world. It is the predominant staple food for a large fraction of the worlds population, especially in Asia, and provides more than one fth of the consumed by humans worldwide. In 2005, the International Rice Genome Sequencing Project published the rst rice genome of the Nipponbare variety using a high quality but expensive BAC-by-BAC approach. This sequence, along with a few other lower quality shotgun assemblies, has become an essential resource as the backbone for SNP analysis, RNA-seq, and other mapping-based assays of rice. However, these mapping-based approaches are challenged to properly analyze structural variations between the varieties, including of the hundreds of genes that dier between the major subpopulations.

To explore the true genomic complexities, we sequenced the Indica variety IR64 to more than 100x coverage using PacBio long read sequencing and also with Illumina short reads using the Allpaths-recipe with fragment, short-jump and long-jump libraries. After error correcting the PacBio reads using HGAP, more than 22x coverage was available in reads over 10kbp including many reads over 50kbp. We then assembled the PacBio reads using the Celera Assembler to produce a true reference quality assembly: the contig sizes approaches that of the BAC-by-BAC Nipponbare assembly, 4.0Mbp contig N50 versus 5.1Mbp respectively, compared to only 20kbp for the Illumina-only assembly. The reference quality PacBio assembly, with contigs spanning nearly entire chromosome arms, gives us signicantly greater power to analyze gene content, regulatory regions, and synteny across large genomic spans compared to mapping or short read assembly. From this we have isolated thousands of regions specic to Indica not present in Nipponbare spanning more than 20 megabases of sequence that was previously unresolved from the short read assembly. Many of the most signicant dierences contain genes and other loci associated with agriculturally important traits including hybrid sterility, submergence, and drought tolerance.