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丽江铁杉和云南铁杉叶绿体基因组序列特征及系统发育分析

Chloroplast genome characteristics and phylogenic analysis of Tsuga forrestii Downie and Tsuga dumosa Eichler

  • 摘要: 本研究采用二代测序技术获得了丽江铁杉(Tsuga forrestii Downie)和云南铁杉(T. dumosa Eichler)的叶绿体全基因组序列,并对它们的序列特征进行了分析。结果显示,丽江铁杉和云南铁杉叶绿体全基因组大小分别为120 520 bp和121 010 bp,GC含量分别为38.10%和38.19%,均注释到104个基因,其中包括71个蛋白编码基因,29个tRNA基因和4个rRNA基因。丽江铁杉和云南铁杉叶绿体基因组中分别鉴定到23个和27个简单重复序列,44个和32个串联重复序列单元。密码子偏好性分析结果表明,云南铁杉与丽江铁杉中共有30个高频密码子,同义密码子使用度最高的为编码精氨酸(Arg)的AGA,最低的是编码丙氨酸(Ala)的GCG。基于21种松科植物和2个外类群的叶绿体系统发育基因组学分析结果,显示松科被分为两大分支,与铁杉属(Tsuga)亲缘关系最近的为长苞铁杉属(Nothotsuga),所有铁杉属植物构成了一个单系群,丽江铁杉与日本铁杉(T. sieboldii Carrière)亲缘关系最近。最后,本研究还发现铁杉属与长苞铁杉属accD基因中部区域出现了很多串联重复序列单元。研究结果说明叶绿体基因组序列可以用于重建铁杉属的系统发育关系。

     

    Abstract: Tsuga species, known for their excellent wood properties and high economic value, encompass several endangered plants. In this study, the complete chloroplast genomes of T. forrestii Downie and T. dumosa Eichler were sequenced using next-generation sequencing. The assembled genomes were 120 520 bp and 121 010 bp in length, with GC contents of 38.10% and 38.19%, respectively. Both genomes encoded 104 genes, including 71 protein-coding genes, 29 tRNA genes, and four rRNA genes. A total of 23 and 27 simple sequence repeats, as well as 44 and 32 tandem repeat sequences, were identified in T. forrestii and T. dumosa, respectively. Codon usage analysis revealed 30 high-frequency codons shared by both species, with AGA encoding arginine being the most frequent and GCG encoding alanine being the least. Phylogenomic analysis based on chloroplast genome data from 21 Pinaceae species and two outgroups resolved two major clades, with all Tsuga taxa forming a monophyletic group closely related to Nothotsuga. Among Tsuga, T. forrestii exhibited the closest relationship to T. sieboldii Carriere. Notably, multiple tandem repeats were detected in the central region of the accD gene in both Tsuga and Nothotsuga. These results support the utility of chloroplast genomes in reconstructing phylogenetic relationships within Tsuga.

     

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