Figures (6)  Tables (2)
    • Figure 1.  Overview of the TeaPGDB server. (a) Genomic data, (b) middleware on the server, (c) application layer for public users.

    • Figure 2.  Homepage of Tea Plant Genome Database (TeaPGDB). The homepage consists of five main parts: (a) species gallery, (b) carousel diagram, (c) toolkit, (d) a brief introduction, (e) news, citation and introduction information, (f) user access map.

    • Figure 3.  The pathways and genes responsible for tea flavor in TeaPGDB. Tea plant quality components catechins, caffeine and theanine synthesis genes. (a) Compound synthesis route, (b) related genes.

    • Figure 4.  An example of gene search and the returned results. Using Gene ID to search for gene annotation results. (a) Search box and drop-down options, (b) search results page containing detailed annotation information.

    • Figure 5.  JBrowse tools. Users can visualize the location of the query gene in the genome with the help of JBrowse. (a) JBrowse Genome Data Selection Page, (b) visual interface of genetic data on the chromosome, (c) details of the genetic data.

    • Figure 6.  The integrated BLAST tool. Users could search tea plant homologous genes by using the BLAST function. (a) Sequence input box, (b) optional parameters for sequence alignment, (c) sequence alignment database, (d) sequence alignment results.

    • Data typeCountsData size
      Tea plant cultivars6
      Nuclear genomes1 7 21.5 Gb
      Organellar genomes2173.8 Mb
      Coding sequences271,430352 Mb
      Proteins271,430150 Mb
      Gene family identification4,46025 M
      GO term71,99659 M
      KEGG90,8931.2 G
      Signal peptide19,15613 M
      SSR2,363,168152 M
      1 C. sinensis var. sinensis 'Shuchazao' has two nuclear genome sequences.
      2 C. sinensis var. assamica 'Yunkang 10' has two mitochondrion genome sequences.

      Table 1.  The dataset integrated in TeaPGDB.

    • DatabaseCountSpeciesAssembly scaleDiTriTetraPentaHexa
      TPGDB7CSS 'Biyun'Chromosome200 688106 53831 27232 22222 695
      CSS 'Shuchazao'1Chromosome202 217108 56132 82233 62923 712
      CSS 'Shuchazao'2Chromosome163 94982 72128 35631 27521 408
      CSS 'Huangdan'Chromosome190 146106 24231 60432 56223 956
      CSS 'Longjing 43'Chromosome195 729109 90031 62032 19521 882
      CSA 'Yunkang 10'Scaffold118 75849 11117 05922 05815 878
      Wild tea plant3Chromosome190 468104 62130 01431 93022 488
      TeaMiD3CSS 'Shuchazao'4Scaffold118 77721 35217 0965 1834 585
      CSA 'Yunkang 10'Scaffold163 98233 22328 4267 2896 091
      CA 'TV-1'5Scaffold138 68925 39218 8295 7205 281
      1 C. sinensis var. sinensis 'Shuchazao' was released by AHAU in 2020.
      2 C. sinensis var. sinensis 'Shuchazao' was released by TRI in 2020.
      3 Wild tea plant (DASZ) was released by HZAU in 2020.
      4 C. sinensis var. sinensis 'Shuchazao' was released by AHAU in 2018.
      5 C. assamica L (O). Kuntze 'TV-1' was released by IARI.

      Table 2.  SSRs integrated in TPGDB and TeaMiD.