@article{Contreras-Moreira01012026,
author = {Contreras-Moreira, Bruno and Sharma, Eshan and Saraf, Shradha and Naamati, Guy and Gupta, Parul and Elser, Justin and Chebotarov, Dmytro and Chougule, Kapeel and Lu, Zhenyuan and Wei, Sharon and Olson, Andrew and Tsang, Ian and Lodha, Disha and Zhou, Yong and Yu, Zhichao and Zhao, Wen and Zhang, Jianwei and Amberkar, Sandeep and Sue-Ob, Kawinnat and Sun, Zhi and Martin, Maria and McNally, Kenneth L. and Ware, Doreen and Deutsch, Eric W. and Copetti, Dario and Wing, Rod A. and Jaiswal, Pankaj and Dyer, Sarah and Jones, Andrew R.}, 
title = {The PanOryza pangene catalog of Asian cultivated rice},
volume = {36}, 
number = {1}, 
pages = {226-238}, 
year = {2026}, 
doi = {10.1101/gr.280790.125}, 
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.}, 
URL = {http://genome.cshlp.org/content/36/1/226.abstract}, 
eprint = {http://genome.cshlp.org/content/36/1/226.full.pdf+html}, 
journal = {Genome Research} 
}