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Nanopore-based genome assembly and the evolutionary genomics of basmati rice

View ORCID ProfileJae Young Choi, Zoe N. Lye, View ORCID ProfileSimon C. Groen, Xiaoguang Dai, Priyesh Rughani, Sophie Zaaijer, Eoghan D. Harrington, Sissel Juul, Michael D. Purugganan
doi: https://doi.org/10.1101/396515
Jae Young Choi
1Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA
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  • For correspondence: jyc387@nyu.edu mp132@nyu.edu
Zoe N. Lye
1Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA
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Simon C. Groen
1Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA
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Xiaoguang Dai
2Oxford Nanopore Technologies, New York, New York, USA
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Priyesh Rughani
2Oxford Nanopore Technologies, New York, New York, USA
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Sophie Zaaijer
3New York Genome Center, New York, New York, USA
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Eoghan D. Harrington
2Oxford Nanopore Technologies, New York, New York, USA
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Sissel Juul
2Oxford Nanopore Technologies, New York, New York, USA
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Michael D. Purugganan
1Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA
4Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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  • For correspondence: jyc387@nyu.edu mp132@nyu.edu
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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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  • New results and major analysis done in new version

  • DOI:10.5281/zenodo.3355330

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted August 13, 2019.
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Nanopore-based genome assembly and the evolutionary genomics of basmati rice
Jae Young Choi, Zoe N. Lye, Simon C. Groen, Xiaoguang Dai, Priyesh Rughani, Sophie Zaaijer, Eoghan D. Harrington, Sissel Juul, Michael D. Purugganan
bioRxiv 396515; doi: https://doi.org/10.1101/396515
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Nanopore-based genome assembly and the evolutionary genomics of basmati rice
Jae Young Choi, Zoe N. Lye, Simon C. Groen, Xiaoguang Dai, Priyesh Rughani, Sophie Zaaijer, Eoghan D. Harrington, Sissel Juul, Michael D. Purugganan
bioRxiv 396515; doi: https://doi.org/10.1101/396515

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