桫椤叶绿体基因组特征及其系统发育分析  

Chloroplast Genome Characteristics and Phylogenetic Analysis of Alsophila spinulosa

作　　者：陈健虹 龙方 刘操 梁圣华 和秋兰 黄红宝 黄耀恒[1] 朱泽宽 CHEN JianHong;LONG Fang;LIU Cao;LIANG ShengHua;HE QiuLan;HUANG HongBao;HUANG YaoHeng;ZHU ZeKuan(Guangxi Key Laboratory of Special Non-Wood Forest Cultivation&Utilization,Guangxi Laboratory of Forestry,Guangxi Forestry Research Institute,Nanning,Guangxi 530002,China;Engineering Construction Management Branch of the China Southern Power Grid Peak and Frequency Modulation Power Generation Co.,Ltd.,Guangzhou,Guangdong 510510,China)

机构地区：[1]广西壮族自治区林业科学研究院/广西特色经济林培育与利用重点实验室/广西林业实验室,广西南宁530002 [2]南方电网调峰调频发电有限公司工程建设管理分公司,广西南宁530002

出　　处：《农业研究与应用》2024年第5期391-401,共11页Agricultural Research and Application

基　　金：广西南宁抽水蓄能电站保护植物迁地保护项目(029500202203030100900022);广西林草种质资源普查与收集项目(桂林科字[2021]第34号)。

摘　　要：【目的】研究桫椤叶绿体基因组的结构特征与功能基因,探索其基因组的进化特征,并基于叶绿体基因组数据揭示桫椤及其近缘物种的系统发育关系,为蕨类植物的系统分类学和进化研究提供依据。【方法】使用高通量测序技术获取桫椤完整的叶绿体基因组序列,并利用生物信息学工具对基因组进行注释和SSR分析。选择近缘物种作为参照,通过叶绿体蛋白编码基因构建系统发育树,分析物种间的进化关系。【结果】桫椤叶绿体基因组为典型的四分体结构,大小约为156196 bp,GC含量为40.44%;共注释到132个功能基因,包括89个蛋白编码基因、35个tRNA基因和8个rRNA基因。SSR分析检测到127个SSR,其中大多数为单核苷酸SSR,共94个,约占总数的74.02%。密码子偏好性分析显示RSCU值大于1的密码子有30个,其中碱基构成以A或U结尾的密码子28个,以G或C结尾的2个。系统发育分析表明,本研究的桫椤叶绿体基因组序列(PQ740943.1)与NCBI公开的桫椤叶绿体基因组序列(NC012818.1)聚在一个分支,并与白桫椤属亲缘关系密切;桫椤与小叶桫椤和锯齿桫椤亲缘关系较近。【结论】桫椤的叶绿体基因组具有保守的基因组结构和基因组成。研究结果为桫椤属植物的分类地位和进化历史提供了数据支持,同时为蕨类植物的进化研究、物种鉴定、遗传多样性分析奠定了基础。【Objective】This study aimed to investigate the structural characteristics and functional genes of the chloroplast genome in Alsophila spinulosa,explore its genomic evolutionary characteristics,and reveal the phylogenetic relationships of A.spinulosa with its related species based on chloroplast genome data,so as to provide a basis for the taxonomy and evolutionary studies of ferns.【Method】Using high-throughput sequencing technology,the complete chloroplast genome sequence was obtained,and bioinformatics tools were employed for genome annotation and SSR analysis.Related fern species were selected as references,and a phylogenetic tree was constructed based on chloroplast protein-coding genes to analyze evolutionary relationships among them.【Result】The chloroplast genome of A.spinulosa had a typical tetradic structure,with a total length of approximately 156196 bp and a GC content of 40.44%.A total of 132 functional genes were annotated,including 89 protein-coding genes,35 tRNA genes,and 8 rRNA genes.In the chloroplast genomes,127 SSRs were identified,and most of them(94,accounting for approximately 74.02%)were single nucleotide SSRs.Codon preference analysis revealed that among the 30 codons with RSCU values greater than 1,28 ended with A or U and 2 ended with G or C.Phylogenetic analysis demonstrated that the chloroplast genome(PQ740943.1)of A.spinulosa used in this study and the chloroplast genome of A.spinulosa published in NCBI(NC012818.1)were in the same cluster,both sharing close relationships with Sphaeropteris;and A.spinulosa had a close genetic relationship with A.podophylla and A.denticulata.[Conclusion]The chloroplast genome of A.spinulosa contains a conserved genomic structure and gene composition.The results provide data support for the taxonomic position and evolutionary history of Alsophila plants.Furthermore,this study lays a foundation for the evolutionary studies,species identification and genetic diversity analysis of ferns.

关 键 词：桫椤 叶绿体基因组 密码子偏好性 系统发育 

分 类 号：S184[农业科学—农业基础科学]