RT Journal
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
JF Genome Research 
JO Genome Research 
YR 2026 
FD January 01 
VO 36 
IS 1 
SP 226 
OP 238 
DO 10.1101/gr.280790.125 
UL http://genome.cshlp.org/content/36/1/226.abstract 
AB 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.