CottonGen：棉花基因组学、遗传学和育种研究社区数据库,Plants

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CottonGen：棉花基因组学、遗传学和育种研究社区数据库
Plants ( IF 4.0 ) Pub Date : 2021-12-18 , DOI: 10.3390/plants10122805
Jing Yu ₁ , Sook Jung ₁ , Chun-Huai Cheng ₁ , Taein Lee ₁ , Ping Zheng ₁ , Katheryn Buble ₁ , James Crabb ₁ , Jodi Humann ₁ , Heidi Hough ₁ , Don Jones ₂ , J Todd Campbell ₃ , Josh Udall ₄ , Dorrie Main ₁

Affiliation

在过去的八年中，棉花研究界产生的全基因组、基因表达、SNP 基因分型和表型数据的数量呈指数增长。有效利用/再利用这些复杂的大型数据集以进行知识发现、翻译和作物改良应用，需要对它们进行整理，与其他类型的数据集成，并通过高效的在线搜索工具进行访问和分析。CottonGen 于 2012 年启动，是一个在线社区数据库，提供对综合同行评审的棉花基因组、遗传和育种数据以及分析工具的访问。由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，它一直是整合新数据并为信息检索提供必要接口的合乎逻辑的选择。CottonGen 中的存储库包含 CottonGen 团队整理的同事、基因、基因组、基因型、种质、图谱、标记、代谢物、表型、出版物、QTL、物种、转录组和性状数据。CottonGen 中包含的数据条目数量急剧增加，例如，自 2014 年以来，基因/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。新工具包括遗传图查看器、基因组浏览器、同线性查看器、代谢途径浏览器、序列检索、BLAST 和育种信息管理系统 (BIMS)，以及各种新数据类型的搜索页面。CottonGen 是国际棉花基因组计划的所在地，负责管理其选举并作为社区的沟通和协调中心。

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CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research

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.

更新日期：2021-12-18

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