干旱区研究

Arid Zone Research >

2024 , Vol. 41 >Issue 12: 2110 - 2119

DOI: https://doi.org/10.13866/j.azr.2024.12.12

Plant Ecology

Characteristics and evolutionary history of the chloroplast genome in Malus sieversii

  • ZHANG Jian ,
  • ZHANG Hongxiang
Expand
  • 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 date: 2024-01-04

  Revised date: 2024-10-06

  Online published: 2024-12-20

Fold

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

Cite this article

ZHANG Jian , ZHANG Hongxiang . Characteristics and evolutionary history of the chloroplast genome in Malus sieversii[J]. Arid Zone Research, 2024 , 41(12) : 2110 -2119 . DOI: 10.13866/j.azr.2024.12.12

References

[1] Velasco R, Zharkikh A, Affourtit J, et al. The genome of the domesticated apple(Malus×domestica borkh.)[J]. Nature Genetics, 2010, 42(10): 833-839.
[2] 张新时. 伊犁野果林的生态地理特征和群落学问题[J]. 植物学报, 1973, 15(2): 239-253.
  [Zhang Xinshi. On the eco-geographical characters and the problems of classification of the wild fruit-tree forest in the Ili valley of Sinkiang[J]. Acta Botanica Sinica, 1973, 15(2): 239-253. ]
[3] Volk G M, Peace C P, Henk A D, et al. DNA profiling with the 20K apple SNP array reveals Malus domestica hybridization and admixture in M. sieversii, M. orientalis, and M. sylvestris genebank accessions[J]. Frontiers in Plant Science, 2022, 13: 1015658.
[4] 米尔卡米力·麦麦提, 刘忠权, 马晓东, 等. 新疆野苹果的生存现状、问题及保护策略[J]. 广西植物, 2021, 41(12): 2100-2109.
  [Maimaiti Maiti, Liu Zhongquan, Ma Xiaodong, et al. Survival status, problems and conservation strategies of Malus sieversii[J]. Guihaia, 2021, 41(12): 2100-2109. ]
[5] 张宏祥, 郑田勇. 生境片段化对新疆野苹果种群遗传结构的影响[J]. 干旱区研究, 2020, 37(3): 715-721.
  [Zhang Hongxiang, Zheng Tianyong. Effect of habitat fragmentation on the population genetic structure of Malus sieversii[J]. Arid Zone Research, 2020, 37(3): 715-721. ]
[6] Zhang H X, Li X S, Wang J C, et al. Insights into the aridification history of central Asian mountains and international conservation strategy from the endangered wild apple tree[J]. Journal of Biogeography, 2021, 48(2): 332-344.
[7] Zhang H X, Zhang M L, Wang L N. Genetic structure and historical demography of Malus sieversii in the Ili valley and the western mountains of the Junggar Basin, Xinjiang, China[J]. Journal of Arid Land, 2015, 7(2): 264-271.
[8] 赵玉芬. 叶绿体基因组在植物学研究中的应用进展[J]. 生物学教学, 2022, 47(3): 83-85.
  [Zhao Yufen. Application progress of chloroplast genome in botany research[J]. Biology Teaching, 2022, 47(3): 83-85. ]
[9] Vaughn J N, Chaluvadi S R, Tushar, et al. Whole plastome sequences from five ginger species facilitate marker development and define limits to barcode methodology[J]. PLoS One, 2014, 9(10): e108581.
[10] Naizaier R, Qu Z, Wu S, et al. The complete chloroplast genome of Malus sieversii (Rosaceae), a wild apple tree in Xinjiang, China[J]. Mitochondrial DNA Part B, 2019, 4(1): 983-984.
[11] Chen S F, Zhou Y Q, Chen Y R, et al. Fastp: An ultra-fast all-in-one fastq preprocessor[J]. Bioinformatics, 2018, 34(17): 884-890.
[12] Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform[J]. Bioinformatics, 2009, 25(14): 1754-1760.
[13] Qu X J, Moore M J, Li D Z, et al. PGA: A software package for rapid, accurate, and flexible batch annotation of plastomes[J]. Plant Methods, 2019, 15: 1-12.
[14] Geneious Prime[EB/OL]. https://www.geneious.com
[15] Kurtz S, Choudhuri J V, Ohlebusch E, et al. Reputer: The manifold applications of repeat analysis on a genomic scale[J]. Nucleic Acids Research, 2001, 29(22): 4633-4642.
[16] Beier S, Thiel T, Münch T, et al. MISA-web: A web server for microsatellite prediction[J]. Bioinformatics, 2017, 33(16): 2583-2585.
[17] Li H, Guo Q, Xu L, et al. CPJSdraw: Analysis and visualization of junction sites of chloroplast genomes[J]. PeerJ, 2023, 11: e15326.
[18] Frazer K A, Pachter L, Poliakov A, et al. VISTA: Computational tools for comparative genomics[J]. Nucleic Acids Research, 2004, 32(Suppl_2): W273-W279.
[19] Katoh K, Standley D M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability[J]. Molecular Biology and Evolution, 2013, 30(4): 772-780.
[20] Suchard M A, Lemey P, BaeleA G, et al. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10[J]. Virus Evolution, 2018, 4(1): vey016.
[21] Ma X, Cai Z, Liu W, et al. Identification, genealogical structure and population genetics of salleles in Malus sieversii, the wild ancestor of domesticated apple[J]. Heredity, 2017, 119(3): 185-196.
[22] Nikiforova S V, Cavalieri D, Velasco R, et al. Phylogenetic analysis of 47 chloroplast genomes clarifies the contribution of wild species to the domesticated apple maternal line[J]. Molecular Biology and Evolution, 2013, 30(8): 1751-1760.
[23] Xiang Y Z, Huang C H, Hu Y, et al. Evolution of Rosaceae fruit types based on nuclear phylogeny in the context of geological times and genome duplication[J]. Molecular Biology and Evolution, 2017, 34(2): 262-281.
[24] Minh B Q, Schmidt H A, Chernomor O, et al. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era[J]. Molecular Biology and Evolution, 2020, 37(5): 1530-1534.
[25] Ya N L, Yan L L, Chao X, et al. The complete chloroplast genome sequence of Malus toringo (Rosaceae)[J]. Mitochondrial DNA Part B, 2020, 5(3): 2832-2833.
[26] Galtier N, Piganeau G, Mouchiroud D, et al. GC-content evolution in mammalian genomes: The biased gene conversion hypothesis[J]. Genetics, 2001, 159(2): 907-911.
[27] Liu B B, Ren C, Kwak M, et al. Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere[J]. Journal of Integrative Plant Biology, 2022, 64(5): 1020-1043.
[28] 崔大方, 廖文波, 羊海军, 等. 中国伊犁天山野果林区系表征地理成分及区系发生的研究[J]. 林业科学研究, 2006, 19(5): 555-560.
  [Cui Dafang, Liao Wenbo, Yang Haijun, et al. Studies on the floristic composition and genesis of the wild fruit forest in Tianshan Mountains in China[J]. Forest Research, 2006, 19(5): 555-560. ]
[29] 刘兴诗, 林培钧, 钟骏平. 伊犁野果林生境分析和发生探讨[J]. 干旱区研究, 1993, 10(3): 28-33.
  [Liu Xinshi, Lin Peijun, Zhong Junpin. An analysis and inquiry into the wild apple trees in Ili[J]. Arid Zone Research, 1993, 10(3): 28-33. ]
[30] 张宏祥, 闻志彬, 王茜. 新疆野苹果种群遗传结构及其环境适应性[J]. 植物生态学报, 2022, 46(9): 1098-1108.
  [Zhang Hongxiang, Wen Zhibing, Wang Qian. Population genetic structure of Malus sieversii and environmental adaptations[J]. Chinese Journal of Plant Ecology, 2022, 46(9): 1098-1108. ]
[31] 周小东, 常顺利, 王冠正, 等. 天山北坡中段雪岭云杉径向生长对气候变化的响应[J]. 干旱区研究, 2023, 40(8): 1215-1228.
  [Zhou Xiaodong, Chang Shunli, Wang Guanzheng, et al. Radial growth response of Picea schrenkiana to climate change in the middle section of the northern slope of the Tianshan Mountains[J]. Arid Zone Research, 2023, 40(8): 1215-1228. ]
[32] 赵卓怡, 郝兴明. 基于Priestley-Taylor方法的中亚干旱区实际蒸散特征及归因[J]. 干旱区研究, 2023, 40(7): 1085-1093.
  [Zhao Zhuoyi, Hao Xingming. Actual evapotranspiration characteristics and attribution in arid Central Asia based on the Priestley-Taylor method[J]. Arid Zone Research, 2023, 40(7): 1085-1093. ]
[33] 褚佳瑶, 冯琳骄, 侯毅兴, 等. 新疆野苹果种群受损现状[J]. 经济林研究, 2022, 40(1): 265-273.
  [Chu Jiayao, Feng Lingjiao, Hou Yixing, et al. Analysis on population damage of Malus sieversii[J]. Non-wood Forest Research, 2022, 40(1): 265-273. ]
[34] 董翰林, 王文婷, 谢云, 等. 新疆气候干湿变化特征及其影响因素[J]. 干旱区研究, 2023, 40(12): 1875-1884.
  [Dong Hanlin, Wang Wenting, Xie Yun, et al. Climate dry-wet conditions, changes, and their driving factors in Xinjiang[J]. Arid Zone Research, 2023, 40(12): 1875-1884. ]
Options
Outlines

/

〈 〉