Background: 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. Description: 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. Conclusion: 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.
CITATION STYLE
Zhang, R., Ma, Y., Hu, X., Chen, Y., He, X., Wang, P., … Zhang, S. (2020). TeaCoN: A database of gene co-expression network for tea plant (Camellia sinensis). BMC Genomics, 21(1). https://doi.org/10.1186/s12864-020-06839-w
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