School of Information and Computer, Anhui Agricultural University, Hefei, China.
School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China.
BMC Genomics. 2020 Jul 3;21(1):461. doi: 10.1186/s12864-020-06839-w.
Tea plant (Camellia sinensis) is one of the world's most important beverage crops due to its numerous secondary metabolites conferring tea quality and health effects. However, only a small fraction of tea genes (especially for those metabolite-related genes) have been functionally characterized to date. A cohesive bioinformatics platform is thus urgently needed to aid in the functional determination of the remaining genes.
TeaCoN, a database of gene co-expression network for tea plant, was established to provide genome-wide associations in gene co-expression to survey gene modules (i.e., co-expressed gene sets) for a function of interest. TeaCoN featured a comprehensive collection of 261 high-quality RNA-Seq experiments that covered a wide range of tea tissues as well as various treatments for tea plant. In the current version of TeaCoN, 31,968 (94% coverage of the genome) tea gene models were documented. Users can retrieve detailed co-expression information for gene(s) of interest in four aspects: 1) co-expressed genes with the corresponding Pearson correlation coefficients (PCC-values) and statistical P-values, 2) gene information (gene ID, description, symbol, alias, chromosomal location, GO and KEGG annotation), 3) expression profile heatmap of co-expressed genes across seven main tea tissues (e.g., leaf, bud, stem, root), and 4) network visualization of co-expressed genes. We also implemented a gene co-expression analysis, BLAST search function, GO and KEGG enrichment analysis, and genome browser to facilitate use of the database.
The TeaCoN project can serve as a beneficial platform for candidate gene screening and functional exploration of important agronomical traits in tea plant. TeaCoN is freely available at http://teacon.wchoda.com .
由于茶叶中具有多种次生代谢产物，赋予了茶叶品质和健康功效，因此茶树（Camellia sinensis）是世界上最重要的饮料作物之一。然而，迄今为止，仅有一小部分茶叶基因（特别是那些与代谢产物相关的基因）具有功能特征。因此，迫切需要一个整合的生物信息学平台来辅助其余基因的功能确定。
TeaCoN 是一个茶树基因共表达网络数据库，旨在提供全基因组基因共表达关联，以调查与特定功能相关的基因模块（即共表达基因集）。TeaCoN 包含了广泛的茶树组织以及各种茶树处理的 261 个高质量 RNA-Seq 实验的综合集合。在 TeaCoN 的当前版本中，记录了 31,968 个（基因组覆盖率为 94%）茶叶基因模型。用户可以从四个方面检索感兴趣基因的详细共表达信息：1）具有相应皮尔逊相关系数（PCC 值）和统计 P 值的共表达基因，2）基因信息（基因 ID、描述、符号、别名、染色体位置、GO 和 KEGG 注释），3）七个主要茶叶组织（如叶、芽、茎、根）中表达谱的共表达基因热图，以及 4）共表达基因的网络可视化。我们还实现了基因共表达分析、BLAST 搜索功能、GO 和 KEGG 富集分析以及基因组浏览器，以方便数据库的使用。
TeaCoN 项目可以作为一个有益的平台，用于筛选茶树重要农艺性状的候选基因和功能探索。TeaCoN 可免费在 http://teacon.wchoda.com 获得。
