新疆吐鲁番和哈密地区梭梭种群遗传多样性和遗传结构

doi:10.17521/cjpe.2024.0214

摘要/Abstract

摘要：

该研究以新疆吐鲁番和哈密两个地区(以下简称吐哈地区)的9个梭梭(Haloxylon ammodendron)种群为研究对象, 结合准噶尔盆地东南缘昌吉州奇台县和木垒县2个种群, 以及甘肃省2个种群, 使用基因组重测序获得的单核苷酸多态性(SNP)数据和叶绿体基因组数据, 分析其遗传多样性及遗传结构。SNP数据分析表明, 新疆昌吉州奇台县的梭梭种群核苷酸多样性较高, 而其东部哈密市巴里坤哈萨克自治县以及伊州区北部西山乡、沁城乡等地的梭梭种群核苷酸多样性相对较低; 吐哈地区的9个梭梭种群可分为4个类群, 其中哈密市巴里坤县和镜儿泉的梭梭种群与准噶尔盆地东南缘种群和甘肃种群具有相似的遗传成分; 吐鲁番高昌区、哈密市西山乡分布的2个类群保留有独特的遗传成分。13个种群共有39个叶绿体单倍型, 其中新疆昌吉州奇台县单倍型最多且最古老, 多样性最高; 吐哈地区和甘肃种群中均含有奇台单倍型。综合核基因组和叶绿体基因组种群遗传格局研究结果, 支持研究区域梭梭种群由准噶尔盆地东南缘的奇台种群向东传播的趋势判断, 提出了吐哈地区梭梭保护建议。

关键词: 梭梭, 基因组重测序, 种群遗传结构, 叶绿体基因组单倍型, 核苷酸多样性

Abstract:

Aims In this study, we analyzed the genetic diversity and structure of Haloxylon ammodendron populations in the Turpan-Hami area, Xinjiang. The objective is to reveal the genetic diversity and genetic structure of the Haloxylon ammodendron population in the region, so as to provide a scientific basis for the conservation of Haloxylon resources in these areas.

Methods We sampled 154 individuals from 13 natural populations of H. ammodendron. Based on single nucleotide polymorphism (SNP) and chloroplast sequences genome data obtained by population resequencing, nucleotide diversity, haplotype diversity and genetic differentiation coefficient were calculated. The genetic structure was assessed by conducting ADMIXTURE, principal components analysis (PCA), phylogenetic tree and chloroplast haplotype network analyses.

Important findings The SNPs variations indicated that population Qitai exhibited higher nucleotide diversity compared to Barikun, Xishan and Qincheng Township in Hami City. Haloxylon ammodendron populations in the Turpan-Hami area can be divided into four groups. Populations in the Barkol County of Hami City has similar genetic composition with populations in the southeast of Junggar Basin and Gansu Province, and unique genetic compositions were retained in the Gaochang District and Xishan Township. The chloroplast genome analyses results showed that 39 haplotypes were detected, and Qitai region had the most diverse haplotypes and the highest genetic diversity. The haplotypes from Qitai were found in both Turpan-Hami and Gansu populations. This may suggest that H. ammodendron populations in the Turpan-Hami region originated from Qitai and dispersed eastward.

Key words: Haloxylon ammodendron, genome resequencing, population genetic structure, chloroplast genome haplotype, nucleotide diversity

张望, 谭思仪, 涂文琴, 娄安如. 新疆吐鲁番和哈密地区梭梭种群遗传多样性和遗传结构. 植物生态学报, 2025, 49(11): 1858-1868. DOI: 10.17521/cjpe.2024.0214

ZHANG Wang, TAN Si-Yi, TU Wen-Qin, LOU An-Ru. Genetic diversity and genetic structure of Haloxylon ammodendron in the Turpan and Hami area, Xinjiang, China. Chinese Journal of Plant Ecology, 2025, 49(11): 1858-1868. DOI: 10.17521/cjpe.2024.0214

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链接本文: https://www.plant-ecology.com/CN/10.17521/cjpe.2024.0214

https://www.plant-ecology.com/CN/Y2025/V49/I11/1858

图/表 8

表1 本研究中13个梭梭种群采样位置和遗传多样性信息

Table 1 Sampling information and genetic diversity of the 13 Haloxylon ammodendron populations

序号 ID	地点 Locality	编号 Code	经度 Longitude (E)	纬度 Latitude (N)	样本量 Sample size	单倍型 Haplotypes	核苷酸多样性 Nucleotide diversity (π)
新疆昌吉回族自治州 Changji Hui Autonomous Prefecture, Xinjiang
1	奇台 Qitai	QT	89.63°	44.19°	12	H3(3), H4(1), H5(2), H6(1), H14(1), H15(1), H34(1), H35(1), 36(1)	0.004	-0.604	0.929
2	木垒 Mori	ML	90.78°	44.03°	12	H11(10), H29(1), H30(1)	0.003	-0.050	0.318
新疆吐鲁番和哈密地区 Turpan and Hami area, Xinjiang
3	星星峡 Xingxingxia	XXX	95.17°	41.72°	12	H20(10)	0.003	0.440	0.000
4	镜儿泉 Jing’erquan	JEQ	95.34°	42.35°	12	H7(1), H8(9), H28(1)	0.004	0.194	0.345
5	沁城 Qincheng	QCN	94.61°	42.60°	12	H6(3), H12(2), H13(2), H14(1), H31(1), H32(1), H33(1)	0.003	-0.748	0.909
6	西山乡 Xishan Township	XSN	93.35°	43.06°	12	H5(1), H18(8), H19(1), H20(1)	0.003	0.419	0.491
7	亚勒曼 Yaleman	YLM	95.70°	43.05°	12	H8(7), H40(5)	0.003	-0.010	0.530
8	三塘湖 Santanghu	STH	93.21°	44.11°	12	H6(7), H15(1), H16(1), H37(1), H38(1), 39(1)	0.003	-0.771	0.682
9	老爷庙 Laoyemiao	LYM	93.93°	44.66°	12	H9(7), H10(5)	0.003	-0.164	0.530
10	汉水泉 Hanshuiquan	HSQ	92.05°	44.52°	12	H6(4), H24(4), H25(1), H26(1), H27(1)	0.002	-0.843	0.782
11	吐鲁番 Turpan	TLF	88.86°	43.28°	12	H17(11), H18(1)	0.004	0.493	0.167
甘肃 Gansu
12	敦煌 Dunhuang	DH	94.70°	40.11°	12	H3(3), H4(4), H5(4)	0.004	-0.292	0.727
13	阿克塞 Aksay	AKS	94.36°	39.72°	12	H1(8), H2(2), H22(1), H23(1)	0.003	-0.630	0.561

图1 13个梭梭种群K值为1-6时交叉验证错误值(CV error)。

Fig. 1 Estimation of cross-validation errors (CV error) for K values ranging from 1 to 6 of the13 Haloxylon ammodendron populations.

图2 基于单核苷酸多态性(SNP)分子标记的梭梭种群的遗传结构和地理分布。A, 13个梭梭种群的151个样本在K = 4时的ADMIXTURE结果图。B, 基于K = 4的13个梭梭种群的遗传结构地理分布图, 图中缩写为种群编号, 同表1。

Fig. 2 Results of population genetic structure and geographical distribution of Haloxylon ammodendron obtained based on single nucleotide polymerphism (SNP) markers. A, ADMIXTURE results for 151 samples from 13 populations at K = 4. B, Geographical distribution of the genetic structure of 13 H. ammodendron populations with ADMIXTURE at K = 4. The abbreviations indicate population codes, as shown in Table 1.

图3 基于单核苷酸多态性分子标记使用邻接法构建13个梭梭种群聚类树(A)和主成分分析(PCA)结果(B)。G-I-G-IV表示按照ADMIXTURE结果划分的四个类群。种群编号同表1。

Fig. 3 Neighbor-Joining tree (A) and principal components analysis (PCA) (B) of 13 Haloxylon ammodendron populations obtained based on single nucleotide polymorphism markers. G-I-G-IV represents the four groups divided according to the ADMIXTURE result. The abbreviations indicate population codes, as shown in Table 1.

表2 4个梭梭类群间遗传分化(Fst)

Table 2 Pairwise genetic differentiation (Fst) of the four groups in this study

类群 Inferred group	G-I	G-II	G-III	G-IV
G-I	-	0.048	0.110	0.038
G-II		-	0.136	0.059
G-III			-	0.118
G-IV				-

图4 梭梭13个种群的39个叶绿体单倍型的地理分布。图中缩写为13个采样种群编号, 详见表1。扇形图中不同颜色表示不同单倍型, 扇形大小表示该种群中某种单倍型的占比。Clade I-IV表示使用叶绿体基因组划分的4个类群。

Fig. 4 Geographical distribution of 39 haplotypes of 13 Haloxylon ammodendron populations. The abbreviations indicate population codes, as shown in Table 1. In the fan chart, the color represents different haplotypes, and the size of the fan represents the proportion of haplotypes in the population. Clade I-IV represent four clades divided according to chloroplast genomes.

图5 基于cpDNA使用最大似然法构建149个梭梭个体最大似然系统发育树。每个枝条末端表示13个梭梭种群中149个个体, 奇台种群为红色, 吐鲁番种群为浅蓝色, 汉水泉、三塘湖、沁城乡种群为紫色, 老爷庙种群为橙色, 西山乡种群为黑色, 木垒种群为绿色, 镜儿泉、亚勒曼、星星峡种群为深蓝色, 阿克塞、敦煌种群为黄色, 各种群信息同表1。外围彩色条带(Clade I-IV)表示使用叶绿体基因将149个梭梭个体分为4个类群。

Fig. 5 A maximum likelihood phylogenetic tree of the 149 Haloxylon ammodendron based on chloroplast genomes. The end of each branch represents 149 individuals in 13 H. ammodendron populations, QT is red, TLF is light blue, HSQ, STH, QCN is purple, LYM is orange, XSN is brown, ML is green, JEQ, YLM, XXX is dark blue, AKS, DH is yellow. The information of populations is shown in Table 1. The outmost colored strips (Clade I-IV) indicate four clades divided according to chloroplast genomes.

图6 基于cpDNA的单倍型(Hap)网络连接图。圆圈表示一种单倍型, 圆圈大小表示拥有该单倍型的个体数量, 不同颜色表示不同种群, 种群名称详见表1, 黑色圆圈表示未采样或已灭绝单倍型, 白色圆圈表示外类群白梭梭单倍型。扇形大小表示拥有某种单倍型的个体来自不同种群的占比。Clade I-IV表示使用叶绿体基因组划分的4个类群。

Fig. 6 Haplotype (Hap) network for the 39 haplotypes of Haloxylon ammodendron based on chloroplast genomes. The circles represent haplotypes, the size of the circle represents the number of individuals with the haplotype, and different colors represent different populations. The abbreviations indicate population codes, as shown in Table 1. The black circle represents the unsampled or extinct haplotypes, and the white circle represents the haplotype of Haloxylon persicum. The fan size indicates the proportion of individuals from different populations with a certain haplotype. Clade I-IV represent four clades divided according to chloroplast genomes.

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