辽东丁香完整叶绿体基因组的结构与特征

Complete Chloroplast Genome Structure and Characterization of Syringa villosa subsp.wolfii

为获得辽东丁香(Syringa villosa subsp.wolfii)叶绿体全基因组的基本特征,采用高通量测序技术分析了其叶绿体基因组序列信息,并讨论其系统演化位置。结果表明:(1)辽东丁香叶绿体基因组全长156517 bp,具有典型的四分体结构;具有131个功能基因,包括36个tRNA基因、8个rRNA基因和87个蛋白质编码基因。(2)该叶绿体基因组蛋白编码区的总密码子偏好性(RSCU)分析显示,RSCU值>1的密码子有31个,其中以A/U碱基结尾的有21个;RSCU值<1的密码子有34个,其中以G/C碱基结尾的密码子有22个。(3)在辽东丁香的叶绿体基因组中,检测出334个散在重复序列,包括170个正向重复序列和164个回文重复序列;检测到227个SSR位点,其中226个位点成功设计出PCR引物。(4)最大似然法构建系统进化树分析显示,辽东丁香与云南丁香(S.yunnanensis)亲缘关系最近。本研究通过对辽东丁香叶绿体基因组重复序列、IR边界、系统发育等进行分析,为辽东丁香后续的分子标记开发、系统发育分析、物种资源鉴定评价、DNA条形码开发等提供参考。

To clarify the basic characteristics of the complete chloroplast genome of Syringa villosa subsp.wolfii,the sequence information of chloroplast genome was analyzed by high-throughput sequencing technology,and its systematic evolution position was discussed.The results showed that:(1)The total length of the S.villosa subsp.wolfii chloroplast genome was 156517 bp,which had a typical tetrad structure and had 131functional genes,including 36 tRNA genes,8 r RNA genes and 87 protein-coding genes respectively.(2)The relative synonymous codon usage(RSCU)analysis of the protein-coding region of the chloroplast genome showed that there were 31 codons with RSCU>1,of which 21 ended with A/U base;and there were 34 codons with RSCU<1,including 22 codons ending with G/C base.(3)In the chloroplast genome of S.villosa subsp.wolfii,334 scattered repeats were detected,including 170 forward repeats and 164 palindromic repeats,and227 SSR loci were discovered,and PCR primers were designed successfully for 226 of these loci.(4)Phylogenetic tree analysis based on the maximum likelihood method showed that S.villosa subsp.wolfii was the most closely to the S.yunnanensis.In this study,repeated sequences,IR boundaries and phylogeny of chloroplast genome of S.villosa subsp.wolfii were analyzed to provide reference data for molecular markers,phylogenetic classification,species identification and evaluation and DNA barcode development.