Nanopore sequencing based genome assembly and evolutionary genomics of circum basmati rice
Background The circum basmati group of cultivated Asian rice Oryza sativa contains many iconic varieties and is widespread in the Indian subcontinent. Despite its economic and cultural importance, a high quality reference genome is currently lacking, and the group's evolutionary history is not fully resolved. To address these gaps, we use long read nanopore sequencing and assemble the genomes of two circum basmati rice varieties. Results We generate two high quality, chromosome level reference genomes that represent the 12 chromosomes of Oryza The assemblies show a contig N50 of 6.32 Mb and 10.53 Mb for Basmati 334 and Dom Sufid, respectively. Using our highly contiguous assemblies, we characterize structural variations segregating across circum basmati genomes. We discover repeat expansions not observed in japonica the rice group most closely related to circum basmati as well as the presence and absence variants of over 20 Mb, one of which is a circum basmati specific deletion of a gene regulating awn length. We further detect strong evidence of admixture between the circum basmati and circum aus groups. This gene flow has its greatest effect on chromosome 10, causing both structural variation and single nucleotide polymorphism to deviate from genome wide history. Lastly, population genomic analysis of 78 circum basmati varieties shows three major geographically structured genetic groups: Bhutan/Nepal, India/Bangladesh/Myanmar, and Iran/Pakistan. Conclusion The availability of high quality reference genomes allows functional and evolutionary genomic analyses providing genome wide evidence for gene flow between circum aus and circum basmati, describes the nature of circum basmati structural variation, and reveals the presence/absence variation in this important and iconic rice variety group.
Genome Biology