黄槽毛竹叶绿体基因组及毛竹种下分类群的叶绿体基因组序列比较

Chloroplast genome of Phyllostachys edulis f.luteosulcata and comparison of chloroplast genome sequence of subspecies of Ph.edulis

【目的】对黄槽毛竹Phyllostachys edulis f.luteosulcata叶绿体基因组进行组装、注释和分析,并与其他毛竹Ph.edulis种下分类群比较叶绿体遗传信息差异和系统进化关系。【方法】利用高通量二代测序数据组装了黄槽毛竹的叶绿体基因组序列并进行了基因结构注释,通过生物信息学分析软件进行其组成、密码子偏好性、重复序列等分析。通过序列比对和系统进化分析,比较不同毛竹种下分类群的系统进化关系和基因组序列差异。【结果】黄槽毛竹的叶绿体基因组是长度为139678 bp,包含132个基因的双环DNA;包含蛋白质编码基因85个、核糖体RNA(rRNA)8个和转运RNA(tRNA)39个。该基因组的最优密码子偏好使用以A/U碱基结尾,包含49个重复序列、55个简单重复序列(SSR)位点,其中简单重复序列最多的类型为A/T。利用叶绿体基因组序列构建的系统发育分析显示:黄槽毛竹与其他毛竹种下分类群共同组成单系分支,且与毛竹原变种Ph.edulis var.pubescens亲缘关系最近。基于7个毛竹种下分类群的叶绿体基因组序列和编码基因特征分析显示:毛竹种下分类群之间存在着编码基因数量和结构差异,编码区和非编码区存在较低程度序列变异。【结论】首次对毛竹种下分类群的叶绿体基因组进行比较分析,并揭示了这些种下分类群存在着一定程度的序列差异。这些变异资料可以用于毛竹种下分类群的鉴定比较。图5表2参27.

[Objective]This study aims to sequence,assemble,annotate,and analyze the chloroplast genome of Phyllostachys edulis f.luteosulcata.The research also involves comparing its chloroplast genetic information and phylogenetic relationships with those of other subspecies of Ph.edulis(moso bamboo).[Method]High-throughput sequencing data were used to assemble and annotate the complete chloroplast genome of Ph.edulis f.luteosulcata.Subsequently,we analyze the composition,codon preference,and repetitive sequences of the genome.Furthermore,sequence comparison and phylogenetic analysis were conducted to compare the phylogenetic relationships and genome sequence differences among different subspecies of moso bamboo.[Result]The chloroplast genome of Ph.edulis f.luteosulcata is a double-loop DNA of 139678 bp in length containing 132 genes,including 85 protein-coding genes,eight ribosomal RNAs(rRNAs),and 39 transfer RNAs(tRNAs).The codon preference for this genome has an A/U base at the end.There are 49 repetitive sequences with the most common type being A/T and 55 Simple Sequence Repeat(SSR)sites.Phylogenetic analyses constructed using the chloroplast genome sequences showed that Ph.edulis f.luteulosulcata is in a monophyletic branch together with other subspecies of Ph.edulis and is closely related to the original variety of Ph.edulis var.pubescens.The analysis of chloroplast genome sequence and coding gene characteristics showed that there were differences in the number and structure of coding genes and low degree of sequence variation among the subspecies of Ph.edulis.[Conclusion]This study is the first to comparatively analyze the chloroplast genomes of subspecies of Ph.edulis and reveals a degree of sequence variation in these subspecies of Ph.edulis.This variation information would be available for the identification and comparison of subspecies of Ph.edulis.[Ch,5 fig.2 tab.27 ref.]