大花水蓑衣叶绿体基因组特征及系统发育分析

Characteristics of chloroplast genome and phylogenetic analysis of Hygrophila megaliths Merr.

关键词:  大花水蓑衣  广天仙子  叶绿体基因组  系统发育分析

Key words:  Hygrophila megalantha Merr.  the semen hygrophilae megalanthae  chloroplast genome  phylogenetic analysis

摘要:

[目的] 对大花水蓑衣及其同属近源物种Hygrophila sp.叶绿体基因组进行测序和分析，解析叶绿体基因组结构特征、探究系统发育位置和进化关系。[方法] 对大花水蓑衣及其同属近源物种Hygrophila sp.的叶绿体基因组进行测序，借助生物分析学方法及工具进行组装、注释和特征分析，并构建最大似然树进行系统发育分析。[结果] Hygrophila megalantha Merr.和Hygrophila sp.的叶绿体基因组序列长度分别为146 373 bp和146 698 bp，大单拷贝区（LSC）长度分别为90 414 bp和90 572 bp，小单拷贝区（SSC）长度分别为17 677 bp和17 720 bp，反向重复区（IR）长度分别为19 141 bp和19 203 bp；均编码130个基因，包括86个蛋白编码基因、36个tRNA基因和8个rRNA基因；Hygrophila megalantha和Hygrophila sp.分别有24 580和24 645个密码子，均倾向使用以碱基A/U结尾的密码子；微卫星序列（SSRs）分析分别检测出57、46个SSRs，以A/T碱基重复较多；以Hygrophila megalantha和Hygrophila sp.在内的17个芦莉草族的叶绿体基因组为内群，另选取3个爵床亚科下芦莉草族外的叶绿体基因组作为外类群，构建系统发育树，结果显示Hygrophila megalantha和Hygrophila sp.聚为一支，亲缘关系较近。[结论] 首次报道了大花水蓑衣的叶绿体基因组，对其序列变异及结构特征进行了深入解析，并基于叶绿体基因组构建了系统发育树，为以其种子入药的药材广天仙子的基原鉴定、资源开发利用提供了重要的研究基础。

Abstract:

[Objective] Sequence and analyze the chloroplast genomes of Hygrophila megalantha Merr. and its closely related species Hygrophila sp.，to analyze the structural characteristics of chloroplast genomes and explore their phylogenetic positions and evolution relationships. [Methods] The chloroplast genomes of Hygrophila megalantha and closely related species Hygrophila sp. were sequenced. Bioinformatics tools and methods were employed for assembly，annotation，and feature analysis. A maximum likelihood tree was constructed for phylogenetic analysis. [Results] The lengths of the complete chloroplast genomes of Hygrophila megalantha and Hygrophila sp. are 146 373 bp and 146 698 bp respectively，the LSC region lengths are 90 414 bp and 90 572 bpre respectively，the SSC region lengths are 17 677 bp and 17 720 bp respectively，and the IR region lengths are 19 141 bp and 19 203 bp respectively. Genome annotation of both genomes identified 130 genes，including 86 protein-coding genes，36 tRNA genes，and 8 rRNA genes. Hygrophila megalantha and Hygrophila sp. have 24 580 and 24 645 codons，respectively，and both tend to use codons ending with the base A/U. SSR analysis detected 57 and 46 microsatellite sequences respectively，with a predominance of A/T base repeats. Using 17 chloroplast genomes from the Acanthaceae Ruellieae，including Hygrophila megalantha and Hygrophila sp.，as the ingroup，and selecting 3 chloroplast genomes outside Ruellieae as the outgroup，a phylogenetic tree was constructed. The result showed Hygrophila megalantha and Hygrophila sp. clustering together，have a close genetic relationship. [Conclusion] This study reports on the chloroplast genome of Hygrophila megalantha for the first time，providing a detailed analysis of its sequence variation and structural features. Additionally，a phylogenetic tree based on the chloroplast genomes was constructed，laying an important research foundation for the identification of the semen hygrophilae megalanthae and the utilization of its resources.