Nanopore-based genome assembly and the evolutionary genomics of basmati rice
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Abstract
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 used long-read nanopore sequencing and assembled the genomes of two circum -basmati rice varieties, Basmati 334 and Dom Sufid.
RESULTS
We generated two high-quality, chromosome-level reference genomes that represented the 12 chromosomes of Oryza . The assemblies showed a contig N50 of 6.32Mb and 10.53Mb for Basmati 334 and Dom Sufid, respectively. Using our highly contiguous assemblies we characterized structural variations segregating across circum- basmati genomes. We discovered repeat expansions not observed in japonica—the rice group most closely related to circum- basmati—as well as presence/absence variants of over 20Mb, one of which was a circum- basmati-specific deletion of a gene regulating awn length. We further detected strong evidence of admixture between the circum- basmati and circum- aus groups. This gene flow had 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 showed three major geographically structured genetic groups: (1) Bhutan/Nepal group, (2) India/Bangladesh/Myanmar group, and (3) Iran/Pakistan group.
CONCLUSION
Availability of high-quality reference genomes from nanopore sequencing allowed functional and evolutionary genomic analyses, providing genome-wide evidence for gene flow between circum -aus and circum -basmati, the nature of circum -basmati structural variation, and the presence/absence of genes in this important and iconic rice variety group.
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Excerpt
What makes basmati rice differ from other varieties? How did they evolve? The sequencing of two high-quality basmati rice genomes provides clues to their evolutionary history.
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