Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice Article Swipe
Yong Zhou
,
Zhichao Yu
,
Dmytro Chebotarov
,
Kapeel Chougule
,
Zhenyuan Lu
,
Luis F. Rivera
,
Nagarajan Kathiresan
,
Noor Al-Bader
,
Nahed Mohammed
,
Aseel Alsantely
,
Saule Mussurova
,
João Dourado Santos
,
Manjula Thimma
,
Maxim Troukhan
,
Alice Fornasiero
,
Carl D. Green
,
Dario Copetti
,
David Kudrna
,
Víctor Llaca
,
Mathias Lorieux
,
Andrea Zuccolo
,
Doreen Ware
,
Millicent D. Alexandrov Sanciangco
,
Jianwei Zhang
,
Rod A. Wing
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1038/s41467-023-37004-y
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1038/s41467-023-37004-y
Understanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Here, we utilize 73 high-quality genomes that encompass the subpopulation structure of Asian rice ( Oryza sativa ), plus the genomes of two wild relatives ( O. rufipogon and O. punctata ), to build a pan-genome inversion index of 1769 non-redundant inversions that span an average of ~29% of the O. sativa cv. Nipponbare reference genome sequence. Using this index, we estimate an inversion rate of ~700 inversions per million years in Asian rice, which is 16 to 50 times higher than previously estimated for plants. Detailed analyses of these inversions show evidence of their effects on gene expression, recombination rate, and linkage disequilibrium. Our study uncovers the prevalence and scale of large inversions (≥100 bp) across the pan-genome of Asian rice and hints at their largely unexplored role in functional biology and crop performance.
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Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1038/s41467-023-37004-y
- https://www.nature.com/articles/s41467-023-37004-y.pdf
- OA Status
- gold
- Cited By
- 75
- References
- 100
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4353018908
All OpenAlex metadata
Raw OpenAlex JSON
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https://openalex.org/W4353018908Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1038/s41467-023-37004-yDigital Object Identifier
- Title
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Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian riceWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2023Year of publication
- Publication date
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2023-03-21Full publication date if available
- Authors
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Yong Zhou, Zhichao Yu, Dmytro Chebotarov, Kapeel Chougule, Zhenyuan Lu, Luis F. Rivera, Nagarajan Kathiresan, Noor Al-Bader, Nahed Mohammed, Aseel Alsantely, Saule Mussurova, João Dourado Santos, Manjula Thimma, Maxim Troukhan, Alice Fornasiero, Carl D. Green, Dario Copetti, David Kudrna, Víctor Llaca, Mathias Lorieux, Andrea Zuccolo, Doreen Ware, Millicent D. Alexandrov Sanciangco, Jianwei Zhang, Rod A. WingList of authors in order
- Landing page
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https://doi.org/10.1038/s41467-023-37004-yPublisher landing page
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https://www.nature.com/articles/s41467-023-37004-y.pdfDirect link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://www.nature.com/articles/s41467-023-37004-y.pdfDirect OA link when available
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Genome, Biology, Evolutionary biology, Computational biology, Genetics, GeneTop concepts (fields/topics) attached by OpenAlex
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75Total citation count in OpenAlex
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2025: 30, 2024: 31, 2023: 14Per-year citation counts (last 5 years)
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100Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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