The chloroplast genome dataset of flowering plants from the Jilong Valley region in Xizang

doi:10.17520/biods.2025270

Abstract

Abstract:

The Jilong Valley in Tibet harbors rich biodiversity, with pollination networks primarily mediated by pollinators playing a crucial role in maintaining the stability of local ecosystems. To more efficiently monitor the composition and dynamics of pollination networks in this region, as well as the dietary composition of key pollinator species, this study aims to construct a chloroplast genome database of flowering plants in Jilong Valley for molecular identification of pollen plant species. First, based on data from the Chinese Virtual Herbarium, we compiled a checklist of flowering plant species in Jilong Valley during the blooming season from June to November. Chloroplast genome sequences for species on this checklist were retrieved from the NCBI public database when available, and de novo assembly and annotation were performed for nine additional plant species using high-throughput sequencing data. Among these, three species are endemic to Xizang, including Thalictrum reniforme, Caragana sukiensis, Roscoea auriculata (Near Threatened). Subsequently, 64 protein coding genes (PCGs) from each species were extracted and concatenated to serve as reference sequences for the database. The preliminary chloroplast genome database for flowering plants comprises 419 species. The establishment of this database will provide crucial reference data to support molecular identification of the dietary diversity and pollination preferences of pollinating insects in Jilong Valley.

Database/Dataset Profile

Title	The chloroplast genome dataset of flowering plants from the Jilong Valley region in Xizang
Data author(s)	Tenzin Nyima, Wei Sun, Cong Li, Shuyi Zhang, Zhunan Zhao, Yongqiang Xu, Zhuoma Pubu, Shiqi Luo, Wa Da, Xin Zhou
Data corresponding author	Wa Da (tsea2@163.com); Xin Zhou (xinzhoucaddis@icloud.com)
Time range	2023-2024
Geographical scope	Jilong County, Shigatse City, Xizang (28°16′-29°18′ N, 80°20′-86°09′ E)
File size	25.63 MB
Data format	.fasta; .xlsx; *.txt
Data link	https://doi.org/10.57760/sciencedb.j00152.00042 https://www.biodiversity-science.net/fileup/1005-0094/DATA/2025270.zip
Database/Dataset composition	The dataset includes a total of a sequence data file, a database sample information file, a complete dataset documenting all flowering plant species recorded in Jilong Valley and nine chloroplast genome annotation files of different plant species.

Key words: database, chloroplast genome, pollen, Jilong Valley

Tenzin Nyima, Wei Sun, Cong Li, Shuyi Zhang, Zhunan Zhao, Yongqiang Xu, Zhuoma Pubu, Shiqi Luo, Wa Da, Xin Zhou. The chloroplast genome dataset of flowering plants from the Jilong Valley region in Xizang[J]. Biodiv Sci, 2025, 33(9): 25270.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2025270

https://www.biodiversity-science.net/EN/Y2025/V33/I9/25270

Figures/Tables 4

Fig. 1 Distribution of sampling sites for flowering plants in Bangxing Village, Jilong Town, Xizang

Fig. 2 Chloroplast genome circular maps of the Caragana sukiensis (A), Cerastium fontanum (B), Euphrasia pectinate (C), Lotus corniculatus (D), Rhododendron lepidotum (E), Roscoea auriculata (F), Senecio graciliflorus (G), Silene nepalensis (H) and Thalictrum reniforme (I). The outer circle of the chloroplast genome circular diagram displays the genes within the chloroplast genome along with their arrangement and orientation; the inner circle shows the CG content of different genes and regulatory regions.

Fig. 3 The distribution of the number of protein coding genes (PCGs) for each plant in the Jilong Valley chloroplast genome database

Table 1 List of chloroplast protein coding genes used for database construction

序号 ID	基因 Gene	序号 ID	基因 Gene	序号 ID	基因 Gene	序号 ID	基因 Gene
1	atpA	17	petL	33	psbL	49	rpoC2
2	atpB	18	petN	34	psbM	50	rps11
3	atpE	19	psaA	35	psbN	51	rps12
4	atpF	20	psaB	36	psbT	52	rps14
5	atpI	21	psaC	37	psbZ	53	rps15
6	ccsA	22	psaI	38	rbcL	54	rps16
7	cemA	23	psaJ	39	rpl14	55	rps18
8	clpP	24	psbA	40	rpl16	56	rps19
9	matK	25	psbB	41	rpl20	57	rps2
10	ndhD	26	psbC	42	rpl22	58	rps3
11	ndhF	27	psbD	43	rpl23	59	rps4
12	ndhJ	28	psbE	44	rpl32	60	rps7
13	ndhK	29	psbF	45	rpl36	61	rps8
14	petA	30	psbI	46	rpoA	62	ycf1
15	petB	31	psbJ	47	rpoB	63	ycf2
16	petD	32	psbK	48	rpoC1	64	ycf3

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