TY  - JOUR
A1  - Contreras-Moreira, Bruno
A1  - Sharma, Eshan
A1  - Saraf, Shradha
A1  - Naamati, Guy
A1  - Gupta, Parul
A1  - Elser, Justin
A1  - Chebotarov, Dmytro
A1  - Chougule, Kapeel
A1  - Lu, Zhenyuan
A1  - Wei, Sharon
A1  - Olson, Andrew
A1  - Tsang, Ian
A1  - Lodha, Disha
A1  - Zhou, Yong
A1  - Yu, Zhichao
A1  - Zhao, Wen
A1  - Zhang, Jianwei
A1  - Amberkar, Sandeep
A1  - Sue-Ob, Kawinnat
A1  - Sun, Zhi
A1  - Martin, Maria
A1  - McNally, Kenneth L.
A1  - Ware, Doreen
A1  - Deutsch, Eric W.
A1  - Copetti, Dario
A1  - Wing, Rod A.
A1  - Jaiswal, Pankaj
A1  - Dyer, Sarah
A1  - Jones, Andrew R.
T1  - The PanOryza pangene catalog of Asian cultivated rice
Y1  - 2026/01/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 226 
EP  - 238 
DO  - 10.1101/gr.280790.125 
VL  - 36 
IS  - 1 
UR  - http://genome.cshlp.org/content/36/1/226.abstract 
N2  - 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. 
ER  -