桃叶珊瑚属植物的叶绿体基因组结构特征及系统发育分析

Chloroplast genome structure characteristics and phylogenic analysis of genus Aucuba

为确定桃叶珊瑚属(Aucuba)植物叶绿体基因组的结构及其序列变异,揭示其属下种间亲缘关系,该研究对桃叶珊瑚(A.chinensis)、花叶青木(A.japonica var.variegata)等6种桃叶珊瑚属植物和丝缨花属植物黄杨叶丝缨花(Garrya buxifolia)进行二代测序,利用生物信息学软件对其叶绿体基因组序列进行组装和注释,并进行基本特征分析、序列比较以及系统发育分析。结果表明:(1)桃叶珊瑚属植物叶绿体基因组具典型的环状四分体结构,6条序列全长157891~158325 bp,均编码114个基因,包括80个蛋白质编码基因、30个tRNA基因和4个rRNA基因。(2)6种植物叶绿体基因组高频密码子数均为29个,偏好以A/U结尾,确定了这6条序列的最优密码子共100个,包含12个共有的最优密码子。(3)6条叶绿体基因组序列共检测到270条散在重复序列,133条串联重复序列以及412个SSR位点。(4)比较基因组学分析结果表明,该属植物叶绿体基因组序列高度保守。(5)从叶绿体基因组中筛选出10个高变片段。(6)系统发育分析结果显示支持桃叶珊瑚属为一个支持率较高的单系,与丝缨花属关系较近。该研究中的5种桃叶珊瑚属植物以及1种丝缨花属植物的叶绿体基因组均为首次测序组装,揭示了桃叶珊瑚属及其属下种间的系统发育关系,为桃叶珊瑚属植物的分类鉴定和系统发育提供了参考资料。

To determine the structure and sequence variation of the chloroplast genome of genus Aucuba and to reveal their interspecies relationship,the chloroplast genomes of six Aucuba species including A.chinensis and A.japonica var.variegata as well as Garrya buxifolia were sequenced using next-generation sequencing technology.The chloroplast genomes were assembled and annotated using bioinformatics software.The genome characteristics,sequence comparison and phylogeny were analyzed based on the chloroplast genomes.The results were as follows:(1)Six Aucuba species chloroplast genomes exhibited typical quadripartite circular structure(i.e.,LSC,SSC,IRB and IRA)and were between 157891-158325 bp in length.A total of 114 genes were annotated(except the duplicate genes on IRs),including 80 protein-coding genes(CDS),30 tRNA genes and 4 rRNA genes.(2)A total of 29 high-frequency codons prefer ending in A/U,and a total of 100 optimal codons of these six sequences were filtered out,including 12 were shared by six Aucuba species.(3)A total of 270 interspersed repeats,133 tandem repeats and 412 SSR loci were detected in the six Aucuba chloroplast genomes.(4)Comparative analysis result of six Aucuba species revealed a highly conserved chloroplast genome sequence.(5)Ten highly divergent regions were identified based on nucleotide diversity analysis.(6)The phylogenetic trees were constructed using maximum likelihood(ML)and Bayesian(BI)showing a similar topology.The results supported that genus Aucuba was monophyletic with high support rate,as a sister to genus Garrya.The complete chloroplast genomes of these five Aucuba species and one Garrya species is firstly sequenced in the study.The results reveal the interspecies relationships and the taxonomic status of genus Aucuba,and provide references for the classification,identification and phylogeny of the genus Aucuba.