Yu Jing, Jung Sook, Cheng Chun-Huai, Lee Taein, Zheng Ping, Buble Katheryn, Crabb James, Humann Jodi, Hough Heidi, Jones Don, Campbell J Todd, Udall Josh, Main Dorrie
Department of Horticulture, Washington State University, Pullman, WA 99164, USA.
Cotton Incorporated, Cary, NC 27513, USA.
Plants (Basel). 2021 Dec 18;10(12):2805. doi: 10.3390/plants10122805.
Over the last eight years, the volume of whole genome, gene expression, SNP genotyping, and phenotype data generated by the cotton research community has exponentially increased. The efficient utilization/re-utilization of these complex and large datasets for knowledge discovery, translation, and application in crop improvement requires them to be curated, integrated with other types of data, and made available for access and analysis through efficient online search tools. Initiated in 2012, CottonGen is an online community database providing access to integrated peer-reviewed cotton genomic, genetic, and breeding data, and analysis tools. Used by cotton researchers worldwide, and managed by experts with crop-specific knowledge, it continuous to be the logical choice to integrate new data and provide necessary interfaces for information retrieval. The repository in CottonGen contains colleague, gene, genome, genotype, germplasm, map, marker, metabolite, phenotype, publication, QTL, species, transcriptome, and trait data curated by the CottonGen team. The number of data entries housed in CottonGen has increased dramatically, for example, since 2014 there has been an 18-fold increase in genes/mRNAs, a 23-fold increase in whole genomes, and a 372-fold increase in genotype data. New tools include a genetic map viewer, a genome browser, a synteny viewer, a metabolite pathways browser, sequence retrieval, BLAST, and a breeding information management system (BIMS), as well as various search pages for new data types. CottonGen serves as the home to the International Cotton Genome Initiative, managing its elections and serving as a communication and coordination hub for the community. With its extensive curation and integration of data and online tools, CottonGen will continue to facilitate utilization of its critical resources to empower research for cotton crop improvement.
在过去八年中，棉花研究界生成的全基因组、基因表达、单核苷酸多态性（SNP）基因分型和表型数据量呈指数级增长。要有效利用/再利用这些复杂的大型数据集以进行知识发现、转化并应用于作物改良，就需要对它们进行整理，与其他类型的数据整合，并通过高效的在线搜索工具供人访问和分析。CottonGen于2012年启动，是一个在线社区数据库，提供对经过同行评审的综合棉花基因组、遗传和育种数据以及分析工具的访问。它被全球棉花研究人员使用，并由具有作物特定知识的专家管理，仍然是整合新数据和提供信息检索必要接口的合理选择。CottonGen中的存储库包含由CottonGen团队整理的同行、基因、基因组、基因型、种质、图谱、标记、代谢物、表型、出版物、数量性状基因座（QTL）、物种、转录组和性状数据。例如，自2014年以来，CottonGen中存储的数据条目数量大幅增加，基因/信使核糖核酸（mRNA）增加了18倍，全基因组增加了23倍，基因型数据增加了372倍。新工具包括遗传图谱查看器、基因组浏览器、共线性查看器、代谢物途径浏览器、序列检索、BLAST和育种信息管理系统（BIMS），以及针对新数据类型的各种搜索页面。CottonGen是国际棉花基因组计划的所在地，管理其选举并作为该社区的沟通和协调中心。凭借其对数据和在线工具的广泛整理和整合，CottonGen将继续促进对其关键资源的利用，以推动棉花作物改良研究。
