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

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.