Nature Communications (Mar 2023)
Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice
- 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 Santos,
- Manjula Thimma,
- Maxim Troukhan,
- Alice Fornasiero,
- Carl D. Green,
- Dario Copetti,
- David Kudrna,
- Victor Llaca,
- Mathias Lorieux,
- Andrea Zuccolo,
- Doreen Ware,
- Kenneth McNally,
- Jianwei Zhang,
- Rod A. Wing
Affiliations
- Yong Zhou
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST)
- Zhichao Yu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University
- Dmytro Chebotarov
- International Rice Research Institute (IRRI), Los Baños
- Kapeel Chougule
- Cold Spring Harbor Laboratory
- Zhenyuan Lu
- Cold Spring Harbor Laboratory
- Luis F. Rivera
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST)
- Nagarajan Kathiresan
- Supercomputing Core Lab, King Abdullah University of Science and Technology (KAUST)
- Noor Al-Bader
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST)
- Nahed Mohammed
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST)
- Aseel Alsantely
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST)
- Saule Mussurova
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST)
- João Santos
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST)
- Manjula Thimma
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST)
- Maxim Troukhan
- Persephone Software, LLC
- Alice Fornasiero
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST)
- Carl D. Green
- Information Technology Department, King Abdullah University of Science and Technology (KAUST)
- Dario Copetti
- Arizona Genomics Institute (AGI), School of Plant Sciences, University of Arizona
- David Kudrna
- Arizona Genomics Institute (AGI), School of Plant Sciences, University of Arizona
- Victor Llaca
- Research and Development, Corteva Agriscience
- Mathias Lorieux
- DIADE, University of Montpellier, CIRAD, IRD
- Andrea Zuccolo
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST)
- Doreen Ware
- Cold Spring Harbor Laboratory
- Kenneth McNally
- International Rice Research Institute (IRRI), Los Baños
- Jianwei Zhang
- Arizona Genomics Institute (AGI), School of Plant Sciences, University of Arizona
- Rod A. Wing
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST)
- DOI
- https://doi.org/10.1038/s41467-023-37004-y
- Journal volume & issue
-
Vol. 14,
no. 1
pp. 1 – 14
Abstract
Pan-genomes provide useful resources for evolutionary studies, functional genomics and breeding of cultivated plants. Here, the authors report a new rice pan-genome including 73 Asian rice and two wild relatives (Oryza rufipogon and O. punctata), and reveal the prevalence and scale of large inversions across the pan-genome.
