蒿属植物叶绿体基因组特征及进化

Characteristics of Chloroplast Genomes and Phylogenetic Analysis of Artemisia Species

蒿属植物具有重要的药用和经济价值,开展蒿属物种叶绿体基因组研究,为我国蒿属植物的分类鉴定和资源利用提供借鉴。基于29个蒿属物种叶绿体基因组序列,采用REPuter、MISA、DNASP和IQ-TREE等生物信息学软件,比较叶绿体基因组特征、序列重复和结构变异,并对蒿属物种系统发育进行分析。结果表明,蒿属叶绿体基因组均由大单拷贝(LSC)区、小单拷贝(SSC)区和1对反向重复(IRs)区构成,基因组序列长度150 858~151 318 bp, GC含量相近。所有蒿属叶绿体基因组均注释到114个unique基因,包含80个蛋白编码基因、30个tRNA基因和4个rRNA基因。蒿属叶绿体基因组长重复序列主要由正向重复和回文重复构成,长度30~49 bp。简单重复序列(SSR)主要由A/T碱基构成,其中单碱基重复最多,其次为四碱基重复。RSCU(相对同义密码子使用度)值大于1的30个高频密码子中,13个以A结尾,16个以T结尾。蒿属植物叶绿体基因组结构高度相似,未检测到基因重排或倒置事件。检测到11个核苷酸变异值Pi>0.007的高变区,其中8个位于LSC区,3个位于SSC区,单拷贝区核苷酸多态性高于IR区。系统发育分析显示,蒿属物种分为4个聚类组,分支结构支持了植物的蒿亚属和龙蒿亚属分类。蒿属物种叶绿体基因组结构保守,鉴定的重复序列和核苷酸多态性区域可用作蒿属物种分类鉴定和遗传多样性研究的分子标记,为后续蒿属物种群体遗传学研究和资源开发利用提供科学依据。

Artemisia species have important medicinal and economic values.The research on the chloroplast genome will provide references for the classification,identification and resource utilization of Artemisia species in China.Based on the chloroplast genome sequences of 29 Artemisia species,the characteristics,repeats and structural variation of chloroplast genome were compared by using bioinformatics software such as REPuter,MISA and DNASP.The phylogeny of Artemisia species was analyzed by IQ-TREE.The results showed that chloroplast genomes of Artemisia species were composed of a large single copy(LSC)region,a small single copy(SSC)region and a pair of inverted repeats(IRs),and the length ranges of 29 chloroplast genomes were from 150858 bp to 151318 bp with similar GC content.All Artemisia chloroplast genomes were annotated with 114 unique genes,including 80 protein coding genes,30 tRNA genes and four rRNA genes.The long repeats of Artemisia chloroplast genomes were mainly composed of forward repeats and palindromic repeats,and the length of repeats was mainly from 30 bp to 49 bp.SSR was mainly composed of A/T bases,in which mononucleotide repeats were the most,followed by tetranucleotide repeats.Among the 30 high frequency codons with RSCU value greater than 1,13 codons ended with A and 16 codons ended with T.Chloroplast genome structures of Artemisia species were highly similar,and no gene rearrangement or inversion events were detected.Eleven nucleotide variation hotspots with P i>0.007 were detected,including eight in LSC region and three in SSC region.The nucleotide polymorphisms in single copy regions were higher than those in IR regions.Phylogenetic analysis demonstrated that Artemisia species were divided into four clades,and the branching structure supported the classification of subgenera Artemisia and Dracunculus.The chloroplast genome structure of Artemisia species is conservative,and the identified repeats and nucleotide polymorphism hotspots can be used as molecular markers for the classification,identification and the study of genetic diversity of Artemisia species.The study provides a scientific basis for the population genetics research,resource development and utilization of Artemisia species.