@article{92,
  author = {Bruno Contreras-Moreira and Eshan Sharma and Shradha Saraf and Guy Naamati and Parul Gupta and Justin Elser and Dmytro Chebotarov and Kapeel Chougule and Zhenyuan Lu and Sharon Wei and Andrew Olson and Ian Tsang and Disha Lodha and Yong Zhou and Zhichao Yu and Wen Zhao and Jianwei Zhang and Sandeep Amberkar and Kawinnat Sue-Ob and Maria Martin and Kenneth McNally and Doreen Ware and Zhi Sun and Eric Deutsch and Dario Copetti and Rod Wing and Pankaj Jaiswal and Sarah Dyer and Andrew Jones},
  title = {A pan-gene catalogue of Asian cultivated rice.},
  abstract = {<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>},
  year = {2025},
  journal = {bioRxiv : the preprint server for biology},
  month = {02/2025},
  issn = {2692-8205},
  doi = {10.1101/2025.02.17.638606},
  language = {eng},
}