华山松叶绿体基因组特征分析

Characteristics Analysis of Chloroplast Genome of Pinus armandii

叶绿体基因组凭借稳定的结构、高度保守的序列在植物遗传结构、比较基因组学和系统发育进化等研究中发挥着重要作用。为明确南系华山松叶绿体基因组的大小、结构、基因组成及近缘种的关系和分类地位,本研究以南系华山松为研究对象,采用2×CTAB法提取南系华山松叶绿体基因组DNA,建立测序文库,进行浅层基因组测序、组装、SSR检测、序列对比、共线性分析以及系统发育树构建。结果表明,南系华山松叶绿体基因组全长116879 bp,GC含量为38.16%。南系华山松叶绿体基因组共编码136个基因。其中,蛋白编码基因77个,tRNA基因55个,rRNA基因4个,具有2~5份拷贝的基因共有14个(均属于tRNA基因),具有1个内含子的基因共有12个。经叶绿体基因组序列比对发现,南系华山松与新疆五针松的相似性最高,达98.852%;与欧洲云杉的相似性最低,仅为57.588%。运用最大似然法基于GTR+F+R2模型构建系统发育树,可将20种松科植物分为4类,其中,南系华山松与北系华山松虽聚为一类,但两者之间的支持率处于较低水平,仅为55%。此外,南系华山松与北系华山松叶绿体基因组序列存在碱基替换和插入缺失,编码基因数量和种类存在异同,说明南北系华山松间叶绿体基因组存在明显差异。本研究可为南系华山松遗传结构和华山松群体遗传研究提供理论依据。

With its stable structure and highly conserved sequence,chloroplast genome has played an important role in the research of plant genetic structure,comparative genomics,and phylogenetic evolution.In order to clarify the size,structure,gene composition of the chloroplast genome in Southern Pinus armandii and the relationship and classification status of related species.The Southern P.armandii was used as material and the 2×CTAB method was applied to extract the chloroplast genomic DNA in this study.Then the sequence library was constructed to perform shallow genome sequence,assembly,SSR detection,sequence comparison,collinearity analysis and construct phylogenetic tree.The results showed that the total length of the chloroplast genome of Southern P.armandii was 116879 bp,and the GC content was 38.16%.A total of 136 encoded genes which were in the chloroplast genome of Southern P.armandii,including 77 protein-coding genes,55 tRNA genes,4 rRNA genes,and 14 genes with 2 to 5 copies(all belonged to t RNA genes),and 12 genes have one intron.The sequence comparison result of chloroplast genome showed that Southern P.armandii had the highest similarity with P.sibirica,about 98.852%,and the lowest similarity with Picea abies,only 57.588%.A phylogenetic tree had constructed based on the GTR+F+R2 model,20 species of Pinaceae could be divided into 4 groups using the maximum likelihood method.Although the Southern and Northern P.armandii were clustered into one branch,but the bootstrap supported between the two at a low level,only 55%.Furthermore,the presence of base substitutions and indels,and then the similarities and differences were different in the number and types of encoding genes as well,in the genome sequences of the Southern and Northern P.armandii.It showed that there were obvious differences in the chloroplast genome among Southern and Northern P.armandii.The theoretical basis would be provided on the study of the genetic structure in Southern P.armandii and population genetic of P.armandii from the results of this research.