A Reference Rice Genome Sequence in the 10K Genome Era

The reference rice genome of japonica cultivar Nipponbare was determined by a map-based sequencing method. Currently, thousands of rice cultivars and several wild species are being sequenced to unravel the genetic variation among diverse cultivars, landraces, and related genomes in the genus Oryza. It is therefore an urgent issue to provide an ultrahigh quality reference genome sequence so that single nucleotide variations can be detected accurately between cultivars. With the aid of a large amount of next-generation sequencing data, we could thoroughly examine the rice reference genome and correct the sequencing errors that were previously overlooked. Our genome-wide annotation identified or predicted 37,872 loci, of which over 3,000 loci were newly found. This genome assembly will further enhance future breeding strategies in the era of large-scale genomics.