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

Abstract

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

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

Figures/Tables 8

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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

Characteristics and evolutionary history of the chloroplast genome in Malus sieversii

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