款冬叶绿体基因组序列特征及其系统发育分析

Phylogenetic analysis of chloroplast genome of Tussilago farfara L.

款冬Tussilago farfara L.为菊科植物Compositae款冬属Tussilago多年生草本植物,其干燥花蕾及叶具有良好的生物活性成分,在我国及欧洲地区药用历史悠久。本文对款冬全叶绿体基因组特征、序列重复、结构变异和系统发育进行了研究,利用Illumination技术对款冬叶绿体基因组进行测序后,进一步通过组装、注释获得了完整的款冬叶绿体基因组,随后开展了反向重复-大单拷贝/小单拷贝区的收缩和扩张分析、基因组序列变异等一系列的特征分析,并利用从NCBI下载的13种同科植物序列构建了邻接系统发育树。结果表明,款冬叶绿体基因组总GC含量为37.4%,长度为150300bp;共注释得到125个基因,其中包括82个蛋白编码基因、35个tRNA和8个rRNA;共检测出148个简单重复序列(simple sequence repeats,SSR)位点,相对同义密码子使用度显示,在64种密码子中,有31种密码子的使用度>1,密码子偏好A/U结尾;边界分析显示款冬在内的7种菊科植物叶绿体基因组均高度保守大单拷贝(large single-copy,LSC)区和一个小单拷贝(small single-copy,SSC)区序列变异高于反向重复(inverted repeat,IR)区;系统发育分析中,样品款冬与已报道的榆林产款冬叶绿体基因组支持率呈100%,聚为一小支,并与橐吾属植物复序橐吾、全缘橐吾等构成一个单系分支。本研究获得了高质量的款冬叶绿体全基因组,并对其基因组特征、密码子偏好性、简单重复序列SSR特性、SC/IR边界、序列变异和系统发育等进行了全面的分析,可为该药用植物的物种鉴定、遗传多样性分析及资源开发提供依据。

Tussilago farfara L.is a perennial herb of Tussilago genus in the Compositae family.Its dried buds and leaves have good biological activities and have a long history of medicinal use in China and Europe.In this paper,we investigated the whole chloroplast genome characteristics,sequence duplication,structural variation and phylogeny of the Tussilago farfara L.After sequencing the Tussilago farfara L.chloroplast genome using Illumination technology,the complete Tussilago farfara L.chloroplast genome was further obtained by assembly and annotation,followed by a series of inverted repeat-large single copy/small single copy region contraction and expansion analysis,genome sequence variation,etc.The sequences of 13 homologous plants downloaded from NCBI were used to construct a neighbor-joining phylogenetic tree.The results showed that the total GC content of the chloroplast genome was 37.4%and the length was 150300 bp;125 genes were annotated,including 82 proteincoding genes,35 tRNAs and 8 rRNAs;148(simple sequence repeats,SSR)loci were detected,and the relative synonymous codon usage showed that 31 codons out of 64 codons had a usage of>1.In the phylogenetic analysis,the chloroplast genomes of the seven species of Asteraceae,including the Yulin Tussilago farfara L.,were highly conserved,and the sequence variation of the(large single-copy,LSC)and(small single-copy,SSC)regions was higher than that of the(inverted repeat,IR)region.This is in general agreement with the reported phylogeny of Yulin Tussilago farfara L.In this study,we obtained a high quality chloroplast genome and analyzed its genome characteristics,codon preference,SSR characteristics,SC/IR boundary,sequence variation and phylogeny,which can provide a basis for species identification,genetic diversity analysis and resource development of this medicinal plant.