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

Abstract

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.

From Chloroplast Biogenesis to Chlorophyll Accumulation: The Interplay of Light and Hormones on Gene Expression in Camellia sinensis cv. Shuchazao Leaves

“…Functional annotation revealed 57823, 40003, 34066, 11963, and 34972 unigenes with alignments to NR (non-redundant protein database), Swiss-Prot (Annotated protein sequence database), KOG (Clusters of orthologous groups for eukaryotic complete genomes), KEGG (Kyoto encyclopedia of genes and genomes) and GO (Gene ontology) databases, respectively. Selected unigenes were validated according to the tea plant genome in the Tea Plant Information Archive (TPIA) (Wei et al, 2018;Xia et al, 2019)…”

Transcriptome and Phytochemical Analyses Provide New Insights Into Long Non-Coding RNAs Modulating Characteristic Secondary Metabolites of Oolong Tea (Camellia sinensis) in Solar-Withering

“…Additionally, the 5.8S ribosomal RNA (5.8S rRNA) and U6 small nuclear RNA (U6 snRNA) were used to normalize the miRNA expression level. The relative expression levels were calculated according to the 2 −DDCt method, and all qRT-PCR primers were designed with the automated primer design tool of the Tea Plant Information Archive ( Supplementary Table S1) (Xia et al, 2019). All qRT-PCR analyses were performed with three biological replicates.…”

Identification of Genic SSRs Provide a Perspective for Studying Environmental Adaptation in the Endemic Shrub Tetraena mongolica

“…By comparing our finding with some other SSR development projects performed using CandiSSR, we found a similar polymorphic genic SSRs generation rate among these different studies. For example, 497 polymorphic genic SSRs were identified in the comparison of the transcriptomes representing the northern and southern population of Parrotia subaequalis [40]; and 1663 polymorphic EST-SSRs were identified by comparing the transcriptomes of tea plant and 19 Camellia species [48]. The identified SSRs in these studies were relatively small.…”