02211nas a2200457   4500000000100000000000100001008004100002260001200043100002800055700001700083700001800100700001600118700001600134700001700150700002200167700002000189700001600209700001500225700001700240700001400257700001600271700001400287700001500301700001300316700001800329700002100347700002000368700001700388700002000405700001600425700001200441700001700453700001800470700001300488700001900501700001500520700001700535245005100552520113600603022001401739       2025                            d  c02/20251 aBruno Contreras-Moreira1 aEshan Sharma1 aShradha Saraf1 aGuy Naamati1 aParul Gupta1 aJustin Elser1 aDmytro Chebotarov1 aKapeel Chougule1 aZhenyuan Lu1 aSharon Wei1 aAndrew Olson1 aIan Tsang1 aDisha Lodha1 aYong Zhou1 aZhichao Yu1 aWen Zhao1 aJianwei Zhang1 aSandeep Amberkar1 aKawinnat Sue-Ob1 aMaria Martin1 aKenneth McNally1 aDoreen Ware1 aZhi Sun1 aEric Deutsch1 aDario Copetti1 aRod Wing1 aPankaj Jaiswal1 aSarah Dyer1 aAndrew Jones00aA pan-gene catalogue of Asian cultivated rice.3 a<p>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 , , , and  varietal groups. The RPRP has been consistently annotated, supported by extensive experimental data and here we report the computational assignment, characterization and dissemination of stably identified pan-genes. We identified 25,178 core pan-genes 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, while cultivar-specific genes were enriched for domains under selective breeding pressure, such as for disease resistance. 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.</p>  a2692-8205