半边旗叶绿体基因组及其结构分析

Analysis on Chloroplast Genome and Its Structure of Pteris semipinnata L.

目的获得半边旗Pteris semipinnata L.叶绿体基因组序列信息,明确其叶绿体基因组的结构特点和系统进化关系。方法通过高通量测序技术进行半边旗叶绿体基因组的测序,使用生物信息学方法对其进行组装和注释,分析其密码子偏好性、简单重复序列,比较其与近缘物种的序列变异,并构建系统进化树。结果半边旗叶绿体基因组大小为162270 bp,为环状双链四分体结构,包括81963 bp的大单拷贝区,21125 bp的小单拷贝区,以及两个29591 bp的反向重复区。半边旗叶绿体基因组共注释到131个基因,其中蛋白编码基因88个,rRNA基因8个,tRNA基因35个。半边旗叶绿体基因组偏好使用以A/T碱基结尾的密码子,且检测到的59个简单重复序列中,以A或T碱基的单核苷酸重复为主。序列比对和系统进化分析显示半边旗与同属植物井栏边草、蜈蚣草同源性最高。结论该研究丰富了蕨类药用植物的叶绿体基因组资料,也为半边旗的物种鉴别、遗传多样性和进化发育等可持续性研究奠定了基础。

Objective To acquire the sequence of chloroplast genome from Pteris semipinnata L.,and to clarify its structural characteristics and phylogenetic relationship.Methods The sequencing of chloroplast genome from Pteris semipinnata L.was fulflled using high-throughput technology.The acquired chloroplast genome was annotated and assembled by bioinformatics approaches.Next,codon preference and simple sequence repeat were analyzed.The sequence variation between Pteris semipinnata L.and related species was compared to construct a phylogenetic tree.Results The chloroplast genome of P.semipinnata was characterized as a circular double chain-stranded tetrad structure with a length of 162270 bp,which comprises a large single copy region of 81963 bp,a small single copy region of 21125 bp and two inverted repeat regions of 29591 bp.A total of 131 genes were annotated from the chloroplast genome,including 88 protein-coding genes,8 rRNA genes and 35 tRNA genes.The codon in the chloroplast genome tended to end with A or T base.Totally,59 simple sequence repeats were identified in the chloroplast genome,and the single nucleotide repeats were mostly composed of A or T base.Sequence alignment and phylogenetic analysis revealed that P.semipinnata shared a closer relationship with P.multifidia and P.vittate.Conclusion The study enriched the data of chloroplast genome in medicinal fern and provided a firm foundation for the research on species identification,genetic diversity,evolution and phylogeny of Pteris semipinnata L.