Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice
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 i...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-02-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-020-1938-2 |
| _version_ | 1818459689658089472 |
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| author | Jae Young Choi Zoe N. Lye Simon C. Groen Xiaoguang Dai Priyesh Rughani Sophie Zaaijer Eoghan D. Harrington Sissel Juul Michael D. Purugganan |
| author_facet | Jae Young Choi Zoe N. Lye Simon C. Groen Xiaoguang Dai Priyesh Rughani Sophie Zaaijer Eoghan D. Harrington Sissel Juul Michael D. Purugganan |
| author_sort | Jae Young Choi |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-14T23:18:21Z |
| format | Article |
| id | doaj.art-684ef4ff48e74bbeb5abee60a299b41a |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-14T23:18:21Z |
| publishDate | 2020-02-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-684ef4ff48e74bbeb5abee60a299b41a2022-12-21T22:44:01ZengBMCGenome Biology1474-760X2020-02-0121112710.1186/s13059-020-1938-2Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati riceJae Young Choi0Zoe N. Lye1Simon C. Groen2Xiaoguang Dai3Priyesh Rughani4Sophie Zaaijer5Eoghan D. Harrington6Sissel Juul7Michael D. Purugganan8Center for Genomics and Systems Biology, Department of Biology, New York UniversityCenter for Genomics and Systems Biology, Department of Biology, New York UniversityCenter for Genomics and Systems Biology, Department of Biology, New York UniversityOxford Nanopore TechnologiesOxford Nanopore TechnologiesNew York Genome CenterOxford Nanopore TechnologiesOxford Nanopore TechnologiesCenter for Genomics and Systems Biology, Department of Biology, New York UniversityAbstract 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.https://doi.org/10.1186/s13059-020-1938-2Oryza sativaAsian riceAromatic rice groupDomesticationCrop evolutionNanopore sequencing |
| spellingShingle | Jae Young Choi Zoe N. Lye Simon C. Groen Xiaoguang Dai Priyesh Rughani Sophie Zaaijer Eoghan D. Harrington Sissel Juul Michael D. Purugganan Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice Genome Biology Oryza sativa Asian rice Aromatic rice group Domestication Crop evolution Nanopore sequencing |
| title | Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice |
| title_full | Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice |
| title_fullStr | Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice |
| title_full_unstemmed | Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice |
| title_short | Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice |
| title_sort | nanopore sequencing based genome assembly and evolutionary genomics of circum basmati rice |
| topic | Oryza sativa Asian rice Aromatic rice group Domestication Crop evolution Nanopore sequencing |
| url | https://doi.org/10.1186/s13059-020-1938-2 |
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