生物多样性 ›› 2026, Vol. 34 ›› Issue (5): 25475.  DOI: 10.17520/biods.2025475  cstr: 32101.14.biods.2025475

• 研究报告: 遗传多样性 • 上一篇    下一篇

基于叶绿体基因组构建的系统发育关系应慎用于物种鉴定和生物地理学研究: 以枫杨属为例

王姗姗1,2, 刘琦2,3, 李玉2, 王天瑞2, 戴锡玲3, Gregor Kozlowski2,4,5, 许瑾1*, 宋以刚2*   

  1. 1. 上海应用技术大学城市建设与生态技术学部, 上海 201418, 中国; 2. 上海辰山植物园华东植物迁地保护与利用国家林业和草原局重点实验室, 上海 201602, 中国; 3. 上海师范大学生命科学学院, 上海 200234, 中国; 4. Department of Biology and Botanic Garden, University of Fribourg, Fribourg 1700, Switzerland; 5. Natural History Museum Fribourg, Fribourg 1700, Switzerland
  • 收稿日期:2025-11-25 修回日期:2026-02-20 接受日期:2026-04-17 出版日期:2026-05-20 发布日期:2026-07-01
  • 通讯作者: 许瑾, 宋以刚
  • 基金资助:
    上海市绿化和市容管理局科研专项(G212406); 上海市绿化和市容管理局科研专项(G242414); 上海市绿化和市容管理局科研专项(G242416); 上海应用技术大学中青年教师科技人才发展基金(ZQ2022-17)

Cautions on using chloroplast genome-based phylogeny for species identification and biogeography: A case study of Pterocarya

Shanshan Wang1,2, Qi Liu2,3, Yu Li2, Tianrui Wang2, Xiling Dai3, Gregor Kozlowski2,4,5, Jin Xu1*, Yigang Song2*   

  1. 1 School of Urban Construction and Ecological Technology, Shanghai Institute of Technology, Shanghai 201418, China 

    2 Key Laboratory of National Forestry and Grassland Administration on East China Plant Conservation and Utilization, Shanghai Chenshan Botanical Garden, Shanghai 201602, China 

    3 College of Life Sciences, Shanghai Normal University, Shanghai 200234, China 

    4 Department of Biology and Botanic Garden, University of Fribourg, Fribourg 1700, Switzerland 

    5 Natural History Museum Fribourg, Fribourg 1700, Switzerland

  • Received:2025-11-25 Revised:2026-02-20 Accepted:2026-04-17 Online:2026-05-20 Published:2026-07-01
  • Contact: Jin Xu, Yigang Song

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摘要： 叶绿体基因组因其结构保守、母系单亲遗传以及拷贝数高等特点, 曾被广泛应用于植物物种的识别、界定以及系统发育关系的重建。然而, 叶绿体基因组无法有效反映花粉介导的基因流, 对遗传漂变较为敏感, 且容易受到不完全谱系分选和杂交事件的影响。因此, 在植物鉴定和种群演化历史研究中, 如果仅依赖叶绿体基因组证据, 可能导致结论存在偏差或不够全面。本研究对枫杨属(Pterocarya)的7个个体进行了叶绿体全基因组测序、组装与注释, 并结合已发表数据开展了比较基因组与系统发育分析。结果显示, 叶绿体基因组长度介于160,176–160,318 bp, 均具典型四分体结构, 编码131个基因(86个蛋白编码基因、8个rRNA和37个tRNA)。简单重复序列(SSRs)位点数量为87–96个, 以单核苷酸重复为主。比较基因组分析结果表明, 枫杨属物种间的叶绿体基因组整体呈现高度保守性, 其中, 反向重复区和编码区的序列保守性高于单拷贝区和非编码区。值得注意的是, 在编码区中, ndhF基因的序列变异程度显著高于其他蛋白编码基因。系统发育分析结果显示, 基于不同数据分区(全基因组、蛋白质编码序列、高变区与滑窗)构建的系统树呈现2–5分支的多种拓扑结构。枫杨(P. stenoptera)、甘肃枫杨(P. macroptera var. macroptera)和华西枫杨(P. insignis)等物种个体在不同分析中均出现谱系混杂与跨分支分布现象。这些结果表明, 叶绿体基因组在解析枫杨属物种鉴定及生物地理历史方面存在明显局限, 单纯依赖其数据易导致系统性偏差。因此, 未来的植物系统发育研究有必要整合核基因组数据并采用多物种溯祖分析方法, 以实现更准确的物种鉴定与演化关系重建。

关键词: 叶绿体基因组, 枫杨属, 系统发育分析, 生物地理学

Abstract

Aim: The chloroplast genome has been widely used for plant species identification, delimitation, and phylogenetic reconstruction due to its structural conservation, maternal uniparental inheritance, and high copy number. However, the chloroplast genome cannot effectively reflect pollen-mediated gene flow, is sensitive to genetic drift, and is susceptible to incomplete lineage sorting and hybridization events. Therefore, in plant identification and population evolutionary history studies, relying solely on chloroplast genome evidence may lead to biased or incomplete conclusions. 

Methods: This study performed whole-chloroplast genome sequencing, assembly, and annotation for seven Pterocarya individuals, and conducted comparative genomic and phylogenetic analyses incorporating published data. 

Results: The chloroplast genome ranged in length from 160,176 to 160,318 bp and exhibited a typical quadripartite structure, encoding 131 genes (86 protein-coding genes, 8 rRNAs, and 37 tRNAs). The number of simple sequence repeats (SSRs) loci ranged from 87 to 96, dominated by mononucleotide repeats. Comparative genomic analysis indicated that chloroplast genomes among Pterocarya species were highly conserved overall. The sequence conservation of the inverted repeat regions and coding regions was higher than that of the single-copy regions and non-coding regions. Notably, within the coding regions, the ndhF gene exhibited significantly higher sequence variation than other protein-coding genes. The results of phylogenetic analysis showed that the phylogenetic trees constructed based on different data partitions (whole genome, protein-coding sequence, hypervariable regions, and sliding windows) exhibited various topological structures with two to five major clades. Individuals of species such as P. stenoptera, P. macroptera var. macroptera, and P. insignis consistently showed lineage admixture and cross-clade distribution across different analyses. 

Conclusion: The chloroplast genome exhibits significant limitations in resolving species identification and biogeographic history within the genus Pterocarya, and relying solely on its data may lead to systematic bias. Therefore, future studies on plant phylogenetics should integrate nuclear genomic data and employ multispecies coalescent methods to achieve more accurate species identification and evolutionary relationship reconstruction.

Key words: chloroplast genome, Pterocarya, phylogenetic analysis, biogeography

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