The PanOryza pangene catalog of Asian cultivated rice

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dc.creatorContreras-Moreira, Bruno
dc.creatorSharma, Eshan
dc.creatorSaraf, Shradha
dc.creatorNaamati, Guy
dc.creatorGupta, Parul
dc.creatorElser, Justin
dc.creatorChebotarov, Dmytro
dc.creatorChougule, Kapeel
dc.creatorLu, Zhenyuan
dc.creatorWei, Sharon
dc.creatorOlson, Andrew
dc.creatorTsang, Ian
dc.creatorLodha, Disha
dc.creatorZhou, Yong
dc.creatorYu, Zhichao
dc.creatorZhao, Wen
dc.creatorZhang, Jianwei
dc.creatorAmberkar, Sandeep
dc.creatorSue-Ob, Kawinnat
dc.creatorSun, Zhi
dc.creatorMartin, Maria
dc.creatorMcNally, Kenneth L.
dc.creatorWare, Doreen
dc.creatorDeutsch, Eric W.
dc.creatorCopetti, Dario
dc.creatorWing, Rod A.
dc.creatorJaiswal, Pankaj
dc.creatorDyer, Sarah
dc.creatorJones, Andrew R.
dc.date2026
dc.date2026-04-01T01:17:52Z
dc.date.accessioned2026-06-27T04:12:51Z
dc.descriptionThe 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.
dc.formatapplication/pdf
dc.identifierhttps://hdl.handle.net/10568/182328
dc.identifier.urihttp://hdl.handle.net/123456789/25323
dc.languageen
dc.publisherCold Spring Harbor Laboratory Press
dc.rightsOpen Access
dc.sourceContreras-Moreira, Bruno, Eshan Sharma, Shradha Saraf, Guy Naamati, Parul Gupta, Justin Elser, Dmytro Chebotarov et al. "The PanOryza pangene catalog of Asian cultivated rice." Genome research 36, no. 1 (2026): 226-238.
dc.subjectoryza sativa
dc.subjectgenomes
dc.subjectgenetic diversity
dc.subjectpan-genomes
dc.subjectgene expression
dc.subjectProtein domains
dc.subjectplant breeding
dc.subjectdisease resistance
dc.subjectgenetic resources
dc.subjectvarieties
dc.titleThe PanOryza pangene catalog of Asian cultivated rice
dc.typeJournal Article

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Instituto Internacional de Investigación del Arroz (IRRI)