怀玉山产三叶青叶绿体基因组特征及其系统进化关系

Phylogenetic relationship and characterization of chloroplast genome of Tetrastigma hemsleyanumfrom Huaiyu Mountain

目的解析怀玉山产三叶青Tetrastigmahemsleyanum叶绿体基因组信息序列特征和确定其在崖爬藤属的系统位置。方法用Illumina高通量测序平台Nova Seq6000进行测序获得怀玉山产三叶青叶绿体基因组序列,借助Ge Seq、t RNAscan-SE、MISA、VISTA tools、DNADna SP6.0、JSHYCloud、CodonW1.4.2、Pasteur Galaxy、mafft 7.0、fasttree 2.1.10等生物信息学工具进行序列分析、密码子偏好分析、崖爬藤属基因组比较分析和系统发育研究。结果怀玉山产三叶青Tetrastigma hemsleyanum叶绿体基因组为共价闭合双链环状分子,长160165 bp,包含1个大单拷贝区(large single copy region,LSC)、1个反向重复区a(inverted repeat region a,IRa)、1个反向重复区b(inverted repeat region b,IRb)和1个小单拷贝区(small single copy region,SSC);怀玉山产三叶青叶绿体基因组注释到光合作用基因、自我复制基因、其他基因和未知功能基因4类共133个基因,包括88个CDS基因、37个t RNA基因和8个r RNA基因;怀玉山产三叶青叶绿体基因组检测到63个SSR位点,其中单碱基重复56个,双碱基重复7个;怀玉山产三叶青叶绿体基因组核苷酸多样性的变化范围为0~0.23418,基因间隔区trn S-GCU-trn G-UCC、rps16-trnG-UCC以及基因ycf1变异率最高。怀玉山产三叶青叶绿体基因组密码子偏好以A或U结尾,具有较强的偏好性。突变对密码子偏好性的影响较强,而其他因素如自然选择对密码子的偏好性影响较小。怀玉山产三叶青叶绿体基因组有31个高频密码子,16个以U结尾,13个以A结尾,2个以G结尾,其中13个为最优密码子。怀玉山产三叶青与福建产三叶青(MW375708)和广西产三叶青(MW375709)亲缘关系较近,与浙江产三叶青(MT827073)、浙江产三叶青(MW375707)、浙江产三叶青KT033563(NC_029339)、四川产三叶青(MW375710)和浙江产三叶青(MW375711)亲缘关系较远。结论三叶青之间的亲缘关系与地理位置相关性不大。首次采用生物信息学分析方法对怀玉山产三叶青叶绿体基因组进行了全面、深度解析,结果将为崖爬藤属药用植物的遗传多样性分析以及新品系的遗传育种研究等提供理论依据。

ObjectiveTo analyze the genomic information sequence characteristics of the chloroplast of Tetrastigma hemsleyanumfrom Huaiyu Mountainand determine its systematic position in the genus of Tetrastigma.MethodsThe chloroplast genome sequence of T.hemsleyanumfrom Huaiyu Mountainwas obtained by sequencing with Illumina high throughput sequencing platform NovaSeq6000,and bioinformatics tools such as GeSeq,tRNAscan SE,MISA,VISTA tools,DNADnaSP6.0,JSHYCloud,CodonW1.4.2,Pasteur Galaxy,Mafft 7.0,fasttree 2.1.10 were used for sequence analysis,codon preference analysis,genome comparative analysis and phylogenetic research of Tetrastigma.ResultsThe chloroplast genome of T.hemsleyanumfrom Huaiyu Mountain is a covalently closed double stranded ring molecule with a length of 160165 bp,including 1 LSC,1 IRa,1 IRb and 1 SSC;the chloroplast genome of T.hemsleyanumfrom Huaiyu Mountain has been annotated with 133 genes in four categories:photosynthesis genes,self-replication genes,other genes and unknown functional genes,including 88 CDS genes,37tRNA genes and eight rRNA genes;Sixty three SSR loci were detected in the chloroplast genome of T.hemsleyanumfrom Huaiyu Mountain,including 56 single base repeats and seven double base repeats;The variation range of nucleotide diversity of the chloroplast genome of T.hemsleyanumfrom Huaiyu Mountain was 0-0.23418,and the variation rates oftrnS-GCU-trnG UCC,rps16-trnG UCC and gene ycf1were the highest.The codon of chloroplast genome of T.hemsleyanumfrom Huaiyu Mountain had a strong preference for ending in A or U.Mutation had a strong impact on codon preference,while other factors such as natural selection had a small impact on codon preference.The chloroplast genome of T.hemsleyanumfrom Huaiyu Mountain had 31 high-frequency codons,16 ending in U,13 ending in A,and two ending in G,of which 13 were the optimal ones.T.hemsleyanumfrom Huaiyu Mountain was close to T.hemsleyanumfrom Fujian MW375708 and T.hemsleyanumfrom Guangxi MW375709,and far from T.hemsleyanumfrom Zhejiang MT827073,T.hemsleyanumfrom Zhejiang MW375707,T.hemsleyanumfrom Zhejiang KT033563(NC_029339),T.hemsleyanumfrom Sichuan MW375710 and T.hemsleyanumfrom Zhejiang MW375711,which showed that there was little correlation between the genetic relationship and the geographical location.ConclusionThe genetic relationship between T.hemsleyanumis not closely related to its geographical location.In this study,the chloroplast genome of T.hemsleyanumfrom Huaiyu Mountainis analyzed comprehensively and deeply for the first time by using bioinformatics analysis method,which will provide theoretical basis for genetic diversity analysis of medicinal plants and genetic breeding research of new strains ofTetrastigma.