猴樟叶绿体基因组特征分析

Analysis on chloroplast genomic characteristics of Cinnamomum bodinieri

关键词:  猴樟, 叶绿体基因组, SSR, 密码子使用偏好性, 系统发育

Key words:  Cinnamomum bodinieri, chloroplast genome, SSR, codon usage bias, phylogeny

摘要:

猴樟(Cinnamomum bodinieri)枝叶含有丰富的精油,是重要的园林绿化树种和经济树种,但目前有关猴樟基因组学的研究报道不多。为揭示猴樟叶绿体基因组特征及系统发育关系,该文基于高通量测序平台进行测序,从头组装了完整的猴樟叶绿体基因组,并对其基因组结构、基因构成及序列重复、密码子使用偏好性以及系统发育进行分析,结合樟亚科主要属物种叶绿体基因组数据构建系统发育树。结果表明:(1)猴樟叶绿体基因组全长152 727 bp,包括一对20 132 bp的反向重复(IRs)区、93 605 bp的大单拷贝(LSC)区和18 858 bp的小单拷贝(SSC)区,总GC含量为39.13%。(2)该基因组共编码127个基因,包括83个蛋白质编码基因(PCGs)、36个转运RNA基因(tRNAs)和8个核糖体RNA基因(rRNAs); 共鉴定出92个SSR位点,其中大部分是A/T组成的单核苷酸重复序列; 密码子适应指数(CAI)为0.166,有效密码子数(ENc)为54.68; 猴樟与近缘种的叶绿体基因组主要在IR区和2个SC区边界上存在一定的差异。(3)24种樟亚科植物的系统发育树显示,猴樟与樟树亲缘关系最近,同时支持了樟属-甜樟属分支(Cinnamomum-Ocotea Clade)、月桂属-新木姜子属分支(Laurus-Neolitsea Clade)、润楠属-鳄梨属分支(Machilus-Persea Clade)的建立。该研究丰富了猴樟遗传资源信息,进一步确定了樟亚科主要属的系统发育地位。

Abstract:

Cinnamomum bodinieri is important landscaping and economic tree species, which is rich in essential oils in branches and leaves. However, there are few theoretical researches on the genomics of C. bodinieri. In order to reveal the chloroplast genomic characteristics and phylogenetic relationship of C. bodinieri, the complete chloroplast genome was sequenced based on Illumina platform and assembled through de novo. The genome structure, gene composition, sequence repeats, codon usage bias and phylogeny were analyzed subsequently. Furthermore, the phylogenetic tree was constructed with the chloroplast genome data of the main species of Subfam. Lauroideae. The results were as follows:(1)The complete chloroplast genome of C. bodinieri was 152 727 bp in length including two inverted repeats(IRs)of 20 132 bp, which were separated by large single copy(LSC)of 93 605 bp and short single copy(SSC)of 18 858 bp, respectively, and the GC content was 39.13%.(2)The genome encoded 127 functional genes, including 83 protein-coding genes(PCGs), 36 tRNA genes, and 8 rRNA genes. A total of 92 SSR loci were detected in the chloroplast genome, and most of them were composed of nucleobase A and T. The codon adaptation index(CAI)and effective number of codons(ENc)were 0.166 and 54.68, respectively. There were some differences in IR region and the boundary of two SC regions of the chloroplast genomes between C. bodinieri and related species.(3)Phylogenetic tree based on 24 species of Subfam. Lauroideae showed that the C. bodinieri was most closely related to C. camphora. The phylogeny strongly supported the establishment of the three clades, Cinnamomum-Ocotea, Laurus-Neolitsea, and Machilus-Persea. This study enriched the information on the genetic resources of C. bodinieri, and further clarified the phylogenetic status of the main genera of Subfam. Lauroideae.