丽江云杉叶绿体基因组序列特征及系统发育分析

Chloroplast genome characteristics and phylogenetic analysis of Picea likiangensis

关键词:  丽江云杉, 叶绿体基因组, 密码子偏好性, 重复序列, 系统发育基因组学

Key words:  Picea likiangensis, chloroplast genome, codon bias, repeat sequence, phylogenomics

摘要:

云杉属植物形态高度相似,其属内系统发育关系复杂,基于叶绿体基因组序列可以解析该属的系统发育关系,并为谱系地理学及细胞器基因组多样性的研究提供依据。丽江云杉(Picea likiangensis)隶属于松科云杉属,具生长迅速、材质优良的特点,是重要的用材与造林树种,有重要经济和生态价值。迄今为止,其叶绿体基因组序列尚未被解析。因此,该研究采用Illumina NovaSeq 6000平台对丽江云杉叶绿体全基因组进行测序,使用GetOrganelle软件进行组装,并利用MISA和Tandem repeat finder软件分析重复序列,CodonW 软件分析密码子使用偏性,以及利用PhyloSuite软件重建了17种云杉属植物的系统发育关系。结果表明:(1)丽江云杉叶绿体基因组总长124 207 bp,GC含量为38.74%,共编码113个基因,包含74个蛋白质编码基因、35个tRNA基因和4个rRNA基因。(2)共检测到29个简单重复序列和29个串联重复序列,其中简单重复序列以单核苷酸重复为主(22个),另有7个为双核苷酸重复。(3)共鉴定出30个高频密码子(RSCU>1),其中密码子AGA(编码精氨酸)的使用度最高。(4)系统发育基因组学分析显示,巨云杉(P. sitchensis)位于该属基部类群,剩余云杉属植物被分为两大类群,丽江云杉与麦吊云杉(P. brachytyla)亲缘关系最近。该研究结果解析了丽江云杉的叶绿体基因组特征,并重建了云杉属的系统发育关系,为后续研究该属植物的遗传多样性及良种选育工作提供了数据基础。

Abstract:

The phylogenetic relationships among Picea species are highly complex due to their morphological similarity. Chloroplast genome sequences can be utilized to resolve the phylogenetic relationships within Picea and provide a foundation for studies on phylogeography and organellar genome diversity. Picea likiangensis, a species in the genus Picea of Pinaceae family, is characterized by rapid growth and high-quality timber. It is widely used as an industrial timber and reforestation species, holding significant economic and ecological value. To date, the complete chloroplast genome sequence of P. likiangensis has not been determined. In this study, the complete chloroplast genome of P. likiangensis was sequenced using Illumina NovaSeq 6000 platform and assembled by GetOrganelle. Repeat sequences within the chloroplast genome were identified using MISA and Tandem repeat finder, while codon usage bias was analyzed by CodonW. Furthermore, phylogenetic relationships among 17 Picea species were reconstructed using PhyloSuite software. The results were as follows:(1)The chloroplast genome of P. likiangensis was 124 207 bp in length with a GC content of 38.74%. It contained 113 genes, including 74 protein-coding genes, 35 transfer RNA(tRNA)genes, and 4 ribosome RNA(rRNA)genes.(2)A total of 29 simple sequence repeats(SSRs)and 29 tandem repeat sequences were identified. Mononucleotide repeats(22)were the predominant SSRs, followed by 7 dinucleotide repeats.(3)In codon usage bias analysis, 30 codons were identified with a relative synonymous codon usage(RSCU)>1, among which the AGA codon(encoding arginine)showed the highest usage.(4)Phylogenomic analysis revealed that P. sitchensis was the basal taxon of Picea, while the remaining Picea species were divided into two major clades. P. likiangensis was most closely related to P. brachytyla. This study clarified the chloroplast genome features of P. likiangensis and reconstructed the phylogenetic relationships of Picea, thereby providing valuable data for future research on genetic diversity and the breeding of superior varieties in this genus.