西藏吉隆沟地区开花植物叶绿体基因组数据集

doi:10.17520/biods.2025270

生物多样性 ›› 2025, Vol. 33 ›› Issue (9): 25270. DOI: 10.17520/biods.2025270 cstr: 32101.14.biods.2025270

西藏吉隆沟地区开花植物叶绿体基因组数据集

旦增尼玛¹^,^#(), 孙伟²^,^#(), 李聪²(), 张纾意²(), 赵竹楠²(), 许永强¹(), 普布卓玛¹(), 罗诗琦²(), 达娃¹^,^*()(), 周欣²^,^*()()

1.西藏自治区高原生物研究所, 吉隆沟生物多样性观测研究站, 拉萨 850001
2.农林生物安全全国重点实验室, 农业农村部作物有害生物监测与绿色防控重点实验室, 中国农业大学植物保护学院, 北京 100193

收稿日期:2025-07-14 接受日期:2025-08-20 出版日期:2025-09-20 发布日期:2025-10-31
通讯作者: *E-mail: tsea2@163.com; xinzhoucaddis@icloud.com
作者简介:^#共同第一作者
基金资助:
中央引导地方项目(XZ202301YD0007C)

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

Tenzin Nyima¹^,^#(), Wei Sun²^,^#(), Cong Li²(), Shuyi Zhang²(), Zhunan Zhao²(), Yongqiang Xu¹(), Zhuoma Pubu¹(), Shiqi Luo²(), Wa Da¹^,^*()(), Xin Zhou²^,^*()()

1 Institute of Plateau Biology of Xizang Autonomous Region, Jilong Valley Biodiversity Observation and Research Station, Lhasa 850001, China
2 State Key Laboratory of Agricultural and Forestry Biosecurity, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agriculture University, Beijing 100193, China

Received:2025-07-14 Accepted:2025-08-20 Online:2025-09-20 Published:2025-10-31
Contact: *E-mail: tsea2@163.com; xinzhoucaddis@icloud.com
About author:^#Co-first authors
Supported by:
Central-Guided Local Projects(XZ202301YD0007C)

1. 附录.pdf(518KB)

摘要/Abstract

摘要：

西藏吉隆沟生物多样性丰富, 其中以传粉昆虫为主要媒介的传粉网络在维护生态系统的稳定性中发挥了重要作用。为了更高效地对当地传粉网络的组成和变化、以及关键传粉昆虫的食性组成等开展监测研究, 本研究拟构建西藏吉隆沟的开花植物叶绿体数据库以用于花粉植物种类的分子鉴定。首先, 我们基于中国数字植物标本馆数据, 整理了吉隆沟6-11月份开花植物名录。通过NCBI公共数据库下载吉隆沟名录物种中已发表的叶绿体基因组数据, 并基于高通量测序数据新组装和注释了9种植物的叶绿体基因组, 其中包括3种在我国仅分布于西藏地区的植物物种: 美丽唐松草(Thalictrum reniforme)、尼泊尔锦鸡儿(Caragana sukiensis)以及耳叶象牙参(Roscoea auriculata) (近危)。随后, 我们对每种植物的64个蛋白质编码基因(protein coding genes, PCGs)进行提取拼接以作为数据库参考序列。阶段性的吉隆沟开花植物叶绿体基因组数据库包含了419个开花植物物种。该数据库的建立将为吉隆沟传粉昆虫食物多样性组成和传粉偏好的分子鉴定提供重要的数据基础。

数据库(集)基本信息简介

数据库(集)名称	西藏吉隆沟地区开花植物叶绿体基因组数据集
作者	旦增尼玛, 孙伟, 李聪, 张纾意, 赵竹楠, 许永强, 普布卓玛, 罗诗琦, 达娃, 周欣
通讯作者	达娃(tsea2@163.com); 周欣(xinzhoucaddis@icloud.com)
时间范围	2023-2024年
地理区域	西藏日喀则市吉隆县(28°16′-29°18′ N, 80°20′-86°09′ E)
文件大小	25.63 MB
数据格式	.fasta; .xlsx; *.txt
数据链接	https://doi.org/10.57760/sciencedb.j00152.00042 https://www.biodiversity-science.net/fileup/1005-0094/DATA/2025270.zip
数据库(集)组成	数据集共包括1个序列数据文件, 1个数据库样本信息文件, 1个吉隆沟所有开花植物信息记录文件, 9种植物叶绿体基因组注释信息文件。

关键词: 数据库, 叶绿体基因组, 花粉, 吉隆沟

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

旦增尼玛, 孙伟, 李聪, 张纾意, 赵竹楠, 许永强, 普布卓玛, 罗诗琦, 达娃, 周欣 (2025) 西藏吉隆沟地区开花植物叶绿体基因组数据集. 生物多样性, 33, 25270. DOI: 10.17520/biods.2025270.

Tenzin Nyima, Wei Sun, Cong Li, Shuyi Zhang, Zhunan Zhao, Yongqiang Xu, Zhuoma Pubu, Shiqi Luo, Wa Da, Xin Zhou (2025) The chloroplast genome dataset of flowering plants from the Jilong Valley region in Xizang. Biodiversity Science, 33, 25270. DOI: 10.17520/biods.2025270.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2025270

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

图/表 4

图1 西藏吉隆镇帮兴村开花植物采集地点的样带分布

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

图2 尼泊尔锦鸡儿(A)、泉卷耳(B)、小米草(C)、百脉根(D)、鳞腺杜鹃(E)、耳叶象牙参(F)、纤花千里光(G)、尼泊尔蝇子草(H)和美丽唐松草(I)的叶绿体基因组结构图。外圈显示叶绿体基因组中的基因及其排列和方向; 内圈显示的是不同基因CG含量和调控区。

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.

图3 吉隆沟叶绿体基因组数据库中每种植物蛋白质编码基因(PCGs)的数目分布

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

表1 用于构建数据库的叶绿体蛋白编码基因名单

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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西藏吉隆沟地区开花植物叶绿体基因组数据集

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

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