Journal Article

Tea Plant Information Archive: a comprehensive genomics and bioinformatics platform for tea plant

Tong, Wei, Wu, Qiong, Li, Ye‐Yun, Li, Peng‐Hui, Li, Fang‐Dong, Zhao, Hui‐Juan, Xia, En‐Hua, Wan, Xiao‐Chun, Li, Ruo‐Pei, Zhang, Zheng‐Zhu, Wei, Chao‐Ling, Ge, Ruo‐Heng

2019

Overview

Summary Tea is the world's widely consumed nonalcohol beverage with essential economic and health benefits. Confronted with the increasing large‐scale omics‐data set particularly the genome sequence released in tea plant, the construction of a comprehensive knowledgebase is urgently needed to facilitate the utilization of these data sets towards molecular breeding. We hereby present the first integrative and specially designed web‐accessible database, Tea Plant Information Archive (TPIA; http://tpia.teaplant.org). The current release of TPIA employs the comprehensively annotated tea plant genome as framework and incorporates with abundant well‐organized transcriptomes, gene expressions (across species, tissues and stresses), orthologs and characteristic metabolites determining tea quality. It also hosts massive transcription factors, polymorphic simple sequence repeats, single nucleotide polymorphisms, correlations, manually curated functional genes and globally collected germplasm information. A variety of versatile analytic tools (e.g. JBrowse, blast, enrichment analysis, etc.) are established helping users to perform further comparative, evolutionary and functional analysis. We show a case application of TPIA that provides novel and interesting insights into the phytochemical content variation of section Thea of genus Camellia under a well‐resolved phylogenetic framework. The constructed knowledgebase of tea plant will serve as a central gateway for global tea community to better understand the tea plant biology that largely benefits the whole tea industry.

• Publisher: John Wiley & Sons, Inc,John Wiley and Sons Inc
• Subject: Annotations / Archives & records / Artificial chromosomes / beverages / Binding sites / Bioinformatics / bioinformatics platform / Biosynthesis / biotechnology / Caffeine / Camellia / Camellia sinensis - genetics / comparative genomics / Computational Biology / Construction planning / Datasets / DNA methylation / evolution biology / Functional analysis / Genes / Genetic aspects / Genetic engineering / Genome, Plant / Genomes / Genomics / Germplasm / industry / Knowledge bases (artificial intelligence) / knowledge database / Mathematical analysis / Metabolism / Metabolites / Nucleotide sequence / Nucleotides / Phylogenetics / Phylogeny / phytochemicals / Plant introductions / Quality / R&D / Research & development / Science / Simple sequence repeats / Single-nucleotide polymorphism / Tea / tea plant / Transcription factors / transcriptome