TeaPGDB: Tea Plant Genome Database

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 type	Counts	Data size
Tea plant cultivars	6	−
Nuclear genomes¹	7	21.5 Gb
Organellar genomes²	17	3.8 Mb
Coding sequences	271,430	352 Mb
Proteins	271,430	150 Mb
Gene family identification	4,460	25 M
GO term	71,996	59 M
KEGG	90,893	1.2 G
Signal peptide	19,156	13 M
SSR	2,363,168	152 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.

Database	Count	Species	Assembly scale	Di	Tri	Tetra	Penta	Hexa
TPGDB	7	CSS 'Biyun'	Chromosome	200 688	106 538	31 272	32 222	22 695
		CSS 'Shuchazao'¹	Chromosome	202 217	108 561	32 822	33 629	23 712
		CSS 'Shuchazao'²	Chromosome	163 949	82 721	28 356	31 275	21 408
		CSS 'Huangdan'	Chromosome	190 146	106 242	31 604	32 562	23 956
		CSS 'Longjing 43'	Chromosome	195 729	109 900	31 620	32 195	21 882
		CSA 'Yunkang 10'	Scaffold	118 758	49 111	17 059	22 058	15 878
		Wild tea plant³	Chromosome	190 468	104 621	30 014	31 930	22 488
TeaMiD	3	CSS 'Shuchazao'⁴	Scaffold	118 777	21 352	17 096	5 183	4 585
		CSA 'Yunkang 10'	Scaffold	163 982	33 223	28 426	7 289	6 091
		CA 'TV-1'⁵	Scaffold	138 689	25 392	18 829	5 720	5 281
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.