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两种物种(鳞叶蕨科: )的完整线粒体基因组:特征、比较分析及系统发育意义

Complete Mitochondrial Genome of Two Species (Lepidoideae: : ): Characterization, Comparative Analyses, and Phylogenetic Implications.

作者信息

Shi Qinghui, Wang Xinyue, Xing Jianhong, Xu Xiaoyun, Sun Gang, Zhang Juncheng

机构信息

Fujian Provincial Key Laboratory of Resources and Environment Monitoring & Sustainable Management and Utilization, Sanming University, Sanming 365004, China.

Medical Plant Exploitation and Utilization Engineering Research Center, Sanming University, Sanming 365004, China.

出版信息

Genes (Basel). 2025 Apr 12;16(4):447. doi: 10.3390/genes16040447.

Abstract

: The subfamily represents a taxonomically critical group within , characterized by its remarkable species diversity. Despite its evolutionary significance, the phylogenetic relationships among tribal and subtribal lineages remain poorly resolved. Although mitochondrial genomes have become crucial molecular markers in Lepidoptera phylogenetics, their potential remains underutilized in the systematics of . Notably, exhibits a particular paucity, with only two congeneric representatives having been comprehensively sequenced to date. : We employed high-throughput sequencing to assemble the complete mitochondrial genomes of two species, and . Our study revealed novel evolutionary insights through comparative genomics, which encompassed all available mitochondrial genomes. Additionally, we conducted phylogenetic reconstruction using maximum likelihood and Bayesian inference approaches, utilizing the most extensive dataset to date. : The closed, circular mitochondrial genomes measure 15,333 bp for and 15,423 bp for , maintaining the ancestral lepidopteran architecture: 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and an AT-rich control region. Comparative analyses of 71 mitochondrial genomes revealed strong evolutionary conservation across multiple parameters: nucleotide composition (AT content range: 77.9-81.8%), codon usage bias (ENC = 30.83-37.55), tRNA secondary structures, and control region organization. All PCGs showed purifying selection signals (Ka/Ks < 1.0), with exhibiting the highest evolutionary rate (Ka/Ks = 0.277). Phylogenetic reconstructions yielded congruent tribal-level topologies with strong nodal support: (( + ) + ( + ) + ), confirming a sister relationship between and . Within , five subtribes formed monophyletic groups: , , , , and , arranged as (( + ( + )) + ( + )). , , and comprised a well-supported clade (BS = 100%; PP = 1.0), though internal relationships required further resolution due to 's polyphyly. : This study provides novel insights into mitochondrial genomic evolution within the subfamily while elucidating the efficacy of mitogenomic data for resolving deep phylogenetic relationships within this ecologically significant subfamily. Our findings establish critical genome baselines for further systematic research and underscore essential pathways for refining subtribal-level taxonomy through integrative molecular approaches.

摘要

该亚科是[某分类单元]内一个在分类学上至关重要的类群,以其显著的物种多样性为特征。尽管具有进化意义,但族级和亚族级谱系之间的系统发育关系仍未得到很好的解析。虽然线粒体基因组已成为鳞翅目系统发育学中至关重要的分子标记,但其在[该分类单元]系统学中的潜力仍未得到充分利用。值得注意的是,[该分类单元]表现出特别的匮乏,迄今为止仅有两个同属代表物种进行了全面测序。

我们采用高通量测序技术组装了两个[该分类单元]物种[物种名称1]和[物种名称2]的完整线粒体基因组。我们的研究通过比较基因组学揭示了新的进化见解,比较基因组学涵盖了所有可用的[该分类单元]线粒体基因组。此外,我们使用最大似然法和贝叶斯推断方法进行系统发育重建,利用了迄今为止最广泛的数据集。

闭合的环状线粒体基因组,[物种名称1]为15333 bp,[物种名称2]为15423 bp,保持了鳞翅目祖先的结构:13个蛋白质编码基因(PCGs)、22个tRNA、2个rRNA和一个富含AT的控制区。对71个线粒体基因组的比较分析揭示了多个参数上的强烈进化保守性:核苷酸组成(AT含量范围:77.9 - 81.8%)、密码子使用偏好(ENC = 30.83 - 37.55)、tRNA二级结构和控制区组织。所有PCGs都显示出纯化选择信号(Ka/Ks < 1.0),[某基因名称]表现出最高的进化速率(Ka/Ks = 0.277)。系统发育重建产生了具有强节点支持的一致的族级拓扑结构:(([类群名称1] + [类群名称2]) + ([类群名称3] + [类群名称4]) + [类群名称5]),证实了[类群名称1]和[类群名称2]之间的姐妹关系。在[该分类单元]内,五个亚族形成了单系类群:[亚族名称1]、[亚族名称2]、[亚族名称3]、[亚族名称4]和[亚族名称5],排列为(([亚族名称1] + ([亚族名称2] + [亚族名称3])) + ([亚族名称4] + [亚族名称5]))。[亚族名称1]、[亚族名称2]和[亚族名称3]组成了一个得到充分支持的分支(BS = 100%;PP = 1.0),不过由于[某亚族名称]的多系性,其内部关系需要进一步解析。

本研究为[该亚科]内的线粒体基因组进化提供了新的见解,同时阐明了线粒体基因组数据在解决这个具有生态重要性的亚科内深层系统发育关系方面的有效性。我们的发现为进一步的系统研究建立了关键的基因组基线,并强调了通过综合分子方法完善亚族级分类学的重要途径。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1929/12026527/252586a53391/genes-16-00447-g001.jpg

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