新疆野苹果叶绿体基因组特征及其进化历史

doi:10.13866/j.azr.2024.12.12

干旱区研究 ›› 2024, Vol. 41 ›› Issue (12): 2110-2119.doi: 10.13866/j.azr.2024.12.12 cstr: 32277.14.AZR.20241212

新疆野苹果叶绿体基因组特征及其进化历史

张健¹^,²(), 张宏祥¹^,³^,⁴()

1.中国科学院新疆生态与地理研究所，荒漠与绿洲生态国家重点实验室，干旱区生态安全与可持续发展重点实验室，新疆乌鲁木齐 830011
2.中国科学院大学，北京 100093
3.新疆抗逆植物基因资源保育与利用重点实验室，新疆乌鲁木齐 830011
4.中国科学院新疆生态与地理研究所标本馆，新疆乌鲁木齐 830011

收稿日期:2024-01-04 修回日期:2024-10-06 出版日期:2024-12-15 发布日期:2024-12-20
通讯作者: 张宏祥. E-mail: zhanghx561@ms.xjb.ac.cn
作者简介:张健（1999-），男，硕士研究生，主要从事干旱区植物保护遗传学研究. E-mail: zj13201654032@163.com
基金资助:
国家自然科学基金(32170391);中国科学院战略生物资源计划(KFJ-BRP-007-008);中国科学院“西部青年学者”项目(2022-XBQNXZ-007)

Characteristics and evolutionary history of the chloroplast genome in Malus sieversii

ZHANG Jian¹^,²(), ZHANG Hongxiang¹^,³^,⁴()

1. State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, Xinjiang, China
2. University of Chinese Academy of Science, Beijing 100093, China
3. Xinjiang Key Lab of Conservation and Utilization of Gene Resources, Urumqi 830011, Xinjiang, China
4. Specimen Museum of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, Xinjiang, China

Received:2024-01-04 Revised:2024-10-06 Published:2024-12-15 Online:2024-12-20

摘要/Abstract

摘要：

新疆野苹果是苹果属重要的种质资源，属国家二级保护植物，同时也是栽培苹果的祖先之一。通过比较新疆野苹果不同种群的叶绿体基因组结构特征差异，来阐明新疆野苹果谱系分化格局与物种演化历史。利用Illumina NovaSeq平台对来自16个不同地区的种群进行了全基因组测序，每个种群选取了一个代表性个体。测序数据经过质量控制后，进行了基因组组装和功能注释。随后，对组装得到的基因组进行了深入的结构分析和谱系分化研究。结果显示：新疆野苹果叶绿体基因组序列全长160195~160279 bp，具有典型的四分结构。叶绿体基因组共注释到131个基因；检测出长重复序列48~58个，简单重复序列93~101个。新疆野苹果与苹果属其他物种的叶绿体基因组在IR（反向重复）区域的变异程度较低，而检测到的变异主要发生在非编码区域。系统发育方面，新疆野苹果最终分成了三个谱系，谱系Ⅰ主要分布在东部，谱系Ⅱ与谱系Ⅲ主要分布在西部。谱系Ⅰ与谱系Ⅱ的分化时间为1.74 Ma，谱系Ⅰ、谱系Ⅱ与谱系Ⅲ的分化时间为2.28 Ma。新疆野苹果遗传分化受到了第四纪气候变化的影响。相较于国外分布的新疆野苹果，中国分布的新疆野苹果遗传多样性较低，对于分布在中国的新疆野苹果需分别采取不同的方式保护，并着重关注遗传多样性较高的塔城区域。

关键词: 新疆野苹果, 叶绿体基因组, 系统发育, 分化时间, 保护遗传

Abstract:

Malus sieversii, a state-protected species and the progenitor of cultivated apples, is an important germplasm resource within the genus Malus. In this study, we aimed to compare the structural characteristics of chloroplast genomes across various populations of M. sieversii, clarify the lineage divergence pattern, and trace the evolutionary history of this species. We used the Illumina NovaSeq platform to conduct whole-genome sequencing of individuals from 16 different populations, with one sample representing each population. After conducting quality control on the sequencing data, we conducted genome assembly and functional annotation. Subsequently, we conducted a comprehensive structural analysis and lineage differentiation studies on the assembled genomes. The chloroplast genome length in M. sieversii ranged from 160195 to 160279 base pairs (bp), exhibiting a typical tetrad structure. In total, 131 genes were identified within the chloroplast genome, along with 48-58 long repeats and 93-101 simple sequence repeats. Notably, variations in the IR region between M. sieversii and other species in the genus were minimal, predominantly occurring in noncoding regions. Phylogenetic analysis revealed that M. sieversii clusters into three distinct lineages: lineage I, primarily occupying the eastern part of the distribution range, and lineages II and III, predominantly found in the west. The divergence time between lineages I and II was approximately 1.74 million years ago (Ma), while the divergence between lineages I, II, and III was around 2.28 Ma. These findings indicate that the lineage divergences of M. sieversii were significantly influenced by climate changes during the Quaternary period. Compared to internationally distributed populations, M. sieversii in China shows relatively low genetic diversity. Therefore, tailored conservation strategies should be implemented for M. sieversii across different regions, with particular emphasis on protecting genetically diverse populations in the Tacheng area.

Key words: Malus sieversii, chloroplast genome, phylogeny, divergence time, conservation genetics

张健, 张宏祥. 新疆野苹果叶绿体基因组特征及其进化历史[J]. 干旱区研究, 2024, 41(12): 2110-2119.

ZHANG Jian, ZHANG Hongxiang. Characteristics and evolutionary history of the chloroplast genome in Malus sieversii[J]. Arid Zone Research, 2024, 41(12): 2110-2119.

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种群编号	国家来源	经度	纬度
EM	中国	84.00°E	46.36°N
GL	中国	82.86°E	43.26°N
HC	中国	80.78°E	44.43°N
JEJ2	吉尔吉斯斯坦	71.95°E	41.84°N
JEJ3	吉尔吉斯斯坦	72.96°E	41.36°N
JEJ5	吉尔吉斯斯坦	72.75°E	40.45°N
JEJ6	吉尔吉斯斯坦	73.34°E	41.21°N
NHZ	哈萨克斯坦	70.26°E	42.67°N
QMKT	哈萨克斯坦	69.95°E	41.94°N
TJK1	塔吉克斯坦	68.82°E	38.81°N
TJK2	塔吉克斯坦	69.68°E	38.72°N
TL	中国	83.54°E	46.13°N
XY	中国	83.61°E	43.38°N
YLALT	哈萨克斯坦	77.67°E	43.37°N
YN	中国	81.62°E	44.12°N
ZGR	哈萨克斯坦	80.96°E	45.64°N

基因名称	基因数量/个	内含子数量/个	基因组
ndhA	1	1	NADH脱氢酶的亚基
ndhB	2	1	NADH脱氢酶的亚基
petB	1	1	细胞色素b/f复合体的亚基
petD	1	1	细胞色素b/f复合体的亚基
atpF	1	1	ATP合酶的亚基
rpl16	1	1	大核糖体亚基的蛋白质
rpl2	2	1	大核糖体亚基的蛋白质
rps12	2	2	小核糖体亚基的蛋白质
rps16	1	1	小核糖体亚基的蛋白质
rpoC1	1	1	RNA聚合酶的亚基
trnA-UGC	2	1	转运RNA
trnG-GCC	1	1	转运RNA
trnG-UCC	1	1	转运RNA
trnK-UUU	1	1	转运RNA
trnL-UAA	1	1	转运RNA
trnT-UGU	1	1	转运RNA
trnV-UAC	1	1	转运RNA
trnS-GCU	1	1	转运RNA
clpP	1	2	蛋白酶
ycf3	1	2	保守的假设性叶绿体开放阅读框

新疆野苹果叶绿体基因组特征及其进化历史

Characteristics and evolutionary history of the chloroplast genome in Malus sieversii

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