Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice

Zhou, Yong, Yu, Zhichao, Chebotarov, Dmytro, Chougule, Kapeel, Lu, Zhenyuan, Rivera, Luis F, Kathiresan, Nagarajan, Al-Bader, Noor, Mohammed, Nahed, Alsantely, Aseel, Mussurova, Saule, Santos, João, Thimma, Manjula, Troukhan, Maxim, Fornasiero, Alice, Green, Carl D, Copetti, Dario, Kudrna, David, Llaca, Victor, Lorieux, Mathias, Zuccolo, Andrea, Ware, Doreen, McNally, Kenneth, Zhang, Jianwei, Wing, Rod A (March 2023) Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice. Nature Communications, 14 (1). p. 1567. ISSN 2041-1723

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Abstract

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.

Item Type:	Paper
Subjects:	bioinformatics > genomics and proteomics > analysis and processing bioinformatics bioinformatics > genomics and proteomics organism description > plant > Oryza evolution organism description > plant organism description > plant > rice
CSHL Authors:	Chougule, Kapeel Lu, Zhenyuan Ware, Doreen H.
Communities:	CSHL labs > Ware lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	21 March 2023
Date Deposited:	01 Nov 2023 17:16
Last Modified:	11 Jan 2024 15:13
PMCID:	PMC10030860
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/41291

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