Characteristics and phylogenetic analysis of the complete chloroplast genome of Cupressus tonkinensis (Cupressaceae)

Cupressus tonkinensis Silba (1994), locally known as “Hoàng Đàn Hữu Liên,” is a critically endangered conifer endemic to the limestone karst of Huu Lien Nature Reserve in Lang Son Province of northern Vietnam. Despite its high ecological, cultural, and economic value, this species faces severe threats from overexploitation and habitat degradation, and its taxonomic identity remains controversial. To address these issues, we reported the complete chloroplast (cp) genome of C. tonkinensis, which was assembled using highthroughput sequencing data and annotated against the closely related Cupressus plastome. The cp genome was 128,000 bp in length and encodes 119 genes, consisting of 82 proteincoding genes, 33 tRNA genes, and 4 rRNA genes. The genome exhibited the typical composition of large single-copy regions, small single-copy regions, and a pair of inverted repeat regions of 91,607bp, 35,945bp, and 224bp, respectively. A comparative analysis revealed high structural conservation among the Cupressus plastome, while phylogenetic reconstruction based on 82 concatenated protein-coding genes resolved C. tonkinensis as one of the earliest diverging lineages within the genus. This robust phylogenetic placement helps clarify long-standing taxonomic ambiguities and reinforces the recognition of a distinct clade of Tonkinensis. This study provides the first complete cp genome of C. tonkinensis from it s type locality in northern Vietnam. These genomic resources serve as a critical foundation for further evolutionary studies, species identification, and conservation planning, supporting urgent efforts to safeguard this unique and irreplaceable conifer lineage.