Complete chloroplast genome of Cupressus funebris and comparative analyses within Cupressaceae

Abstract Cupressus funebris Endl., a widely cultivated evergreen species in China, plays an important ecological and economic role in afforestation, ecological restoration, and the production of essential oils and medicinal compounds. However, its taxonomic status within Cupressaceae has long been debated due to complex phylogenetic relationships. In this study, we sequenced and annotated the complete chloroplast genome of C. funebris and conducted comparative analyses with nine other Cupressaceae species. The genome of C. funebris is 127,816 bp in length, encoding 117 genes. Comparative analyses revealed a highly conserved genome structure across the ten species, with notable divergence concentrated in coding regions such as accD, ycf1, ycf2, and rpoC2. Codon usage analysis indicated a significant bias toward codons ending in A or U. A total of 709 simple sequence repeats (SSRs) and 170,475 single nucleotide polymorphisms (SNPs) were identified, providing valuable markers for genetic studies. The phylogenetic tree constructed from 63 complete chloroplast genomes revealed species relationships largely consistent with traditional taxonomy, indicating that chloroplast genomes can effectively reflect phenotypic variation within Cupressaceae and thus hold broad potential for systematic and evolutionary studies. Furthermore, variable regions within the rpoA and rpoC2 genes were identified as SNP-rich hotspots, enabling species-level discrimination across all ten species. These findings not only enhance our understanding of chloroplast genome evolution in Cupressaceae but also offer genomic resources for taxonomy, phylogenetics, and molecular breeding.