Rice (Oryza sativa L.) is a major cereal crop that provides calories across the world. With a small genome, rice has been used extensively as a model for genetic and genomic studies in the Poaceae. Since the release of the first rice genome sequence in 2002, an improved reference genome assembly, multiple whole genome assemblies, extensive gene expression profiles, and resequencing data from over 3000 rice accessions have been generated. To facilitate access to the rice genome for plant biologists, we updated the Rice Genome Annotation Project database (RGAP; https://rice.uga.edu) with new datasets including 16 whole genome rice assemblies and sequence variants generated from multiple rice pan-genome projects including the 3000 Rice Genomes Project. We updated gene expression abundance data with 80 RNA-sequencing datasets and to facilitate gene function discovery, performed gene coexpression resulting in 39 coexpression modules that capture highly connected sets of co-regulated genes. To facilitate comparative genome analyses, 32 335 syntelogs were identified between the Nipponbare reference genome and other rice genomes and 19 371 syntelogs were identified between Nipponbare and four other Poaceae genomes. Infrastructure improvements to the RGAP database include an upgraded genome browser and data access portals, enhanced website security and increased performance of the website.

中文翻译：

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水稻基因组注释项目：用于挖掘水稻基因组的更新数据库


水稻 （Oryza sativa L.） 是一种主要的谷物作物，可在世界各地提供卡路里。由于基因组较小，水稻已被广泛用作禾本科遗传和基因组研究的模型。自 2002 年发布第一个水稻基因组序列以来，已经从 3000 多个水稻种质中生成了改进的参考基因组组装、多个全基因组组装、广泛的基因表达谱和重测序数据。为了方便植物生物学家访问水稻基因组，我们更新了水稻基因组注释项目数据库 （RGAP;https://rice.uga.edu），其中包含 16 个全基因组水稻组装和从多个水稻泛基因组项目（包括 3000 个水稻基因组计划）生成的序列变体。我们使用 80 个 RNA 测序数据集更新了基因表达丰度数据，为了促进基因功能的发现，我们进行了基因共表达，产生了 39 个共表达模块，这些模块捕获了高度连接的共调控基因集。为了便于比较基因组分析，在日本裸参考基因组和其他水稻基因组之间鉴定了 32 335 个同源物，在日本裸水稻和其他四个禾本科基因组之间鉴定了 19 371 个同源物。RGAP 数据库的基础设施改进包括升级的基因组浏览器和数据访问门户、增强的网站安全性和提高的网站性能。