Contreras-Moreira, Bruno, Sharma, Eshan, Saraf, Shradha, Naamati, Guy, Gupta, Parul, Elser, Justin, Chebotarov, Dmytro, Chougule, Kapeel, Lu, Zhenyuan, Wei, Sharon, Olson, Andrew, Tsang, Ian, Lodha, Disha, Zhou, Yong, Yu, Zhichao, Zhao, Wen, Zhang, Jianwei, Amberkar, Sandeep, Sue-Ob, Kawinnat, Sun, Zhi, Martin, Maria, McNally, Kenneth L, Ware, Doreen, Deutsch, Eric W, Copetti, Dario, Wing, Rod A, Jaiswal, Pankaj, Dyer, Sarah, Jones, Andrew R (December 2025) The PanOryza pangene catalog of Asian cultivated rice. Genome Research. ISSN 1088-9051 (Public Dataset)
![[thumbnail of 10.1101.gr.280790.125.pdf]](https://repository.cshl.edu/style/images/fileicons/application_pdf.png) |
PDF
10.1101.gr.280790.125.pdf - Published Version Available under License Creative Commons Attribution. Download (6MB) |
Abstract
The rice genome underpins fundamental research and breeding, but the Nipponbare (japonica) reference does not fully encompass the genetic diversity of Asian rice. To address this gap, the Rice Population Reference Panel (RPRP) was developed, comprising high-quality assemblies of 16 rice cultivars to represent the japonica, indica, aus, and aromatic varietal groups. The RPRP has been consistently annotated and supported by extensive experimental data, and here, we report the computational assignment, characterization, and dissemination of stably identified pangenes, collectively called the PanOryza data set. We identify 25,178 core pangenes shared across all cultivars, alongside cultivar-specific and family-enriched genes. Core genes exhibit higher gene expression and proteomic evidence, higher confidence protein domains, and AlphaFold structures, whereas cultivar-specific genes are enriched for domains under selective breeding pressure, such as for disease resistance. We identify more than 5000 genes absent in the IRGSP rice reference genome and present in at least two other Oryza cultivars. We demonstrate the utility of this resource through various examples of pangenes and their protein domains. This resource, integrated into public databases, enables researchers to explore genetic and functional diversity via a population-aware "reference guide" across rice genomes, advancing both basic and applied research.
| Item Type: | Paper |
|---|---|
| Subjects: | organism description > plant organism description > plant > rice |
| CSHL Authors: | |
| Communities: | CSHL labs > Ware lab |
| SWORD Depositor: | CSHL Elements |
| Depositing User: | CSHL Elements |
| Date: | 12 December 2025 |
| Date Deposited: | 18 Dec 2025 14:22 |
| Last Modified: | 05 Jan 2026 20:10 |
| PMCID: | PMC12758395 |
| Related URLs: | |
| Dataset ID: |
|
| URI: | https://repository.cshl.edu/id/eprint/42040 |
Actions (login required)
 |
Administrator's edit/view item |