Sequencing and Assembly of the Rice Variety N22 (Aus Group): a New Reference Genome to Study Comparative, Evolutionary and Functional Genomics of Rice

Since the release of 3000 resequenced rice genomes in May 2014, the global effort to drill deeper into this valuable data has begun to materialize. Current analyses can group the 3K set into 9-15 subpopulations. The goal of the international community is to genetically and phenotypically characterize natural variation that exists within IRRI’s 125K GeneBank accessions to address the most relevant traits for rice production, such as biotic and abiotic stress tolerances, and yield and grain quality. In support of this goal we plan to fully sequence and annotate the genomes and transcriptomes of 3-4 accessions from each subpopulation and map the 3K data to each genome for variation discovery and GWAS and genomic selection studies. 

Here we present the first high-quality genome sequence of an aus variety rice - Nagina22. N22 is a reference upland adapted rice. We produced and assembled 65 genome equivalents of PacBio long-read data that resulted in an assembly of 373Mb (1519 contigs, contig N50 of 906Kb, longest contig 3.5Mb). Contigs were assigned to pseudomolecules after alignment to the O. sativa ssp. japonica RefSeq thus providing a high quality reference sequence for aus rice. Genome annotation and comparative analyses define features of this variety and importantly provide a reference for the alignment of the resequencing data from the rice 3K project. With additional high-quality reference genome assemblies, the goal of characterizing and classifying the unlocked genetic potential of this vital crop will facilitate the next generation of green super crops to help feed the world.