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Genome Biol. 2020 Feb 5;21(1):21. doi: 10.1186/s13059-020-1938-2.

Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice.

Author information

1
Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA. jyc387@nyu.edu.
2
Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA.
3
Oxford Nanopore Technologies, New York, NY, USA.
4
New York Genome Center, New York, NY, USA.
5
Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA. mp132@nyu.edu.
6
Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates. mp132@nyu.edu.

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 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.

KEYWORDS:

Admixture; Aromatic rice group; Asian rice; Aus; Awnless; Basmati; Crop evolution; De novo genome assembly; Domestication; Indica; Japonica; Nanopore sequencing; Oryza sativa

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