Characterization and Phylogenetic Analysis of the Chloroplast Genomes of var. and var. .

This study sequenced the complete chloroplast genomes of var. and var. using the Illumina NovaSeq and PacBio RSII platforms. Following sequencing, the genomes were assembled, annotated, comparatively analyzed, and used to construct a phylogenetic tree to explore their phylogenetic positions. Results indicated that the chloroplast genomes of var. and var. both displayed a typical double-stranded circular tetrameric structure, measuring 157,609 and 157,748 bp in length, respectively. Each genome contained 130 annotated genes, with similar total GC content and relative codon usage patterns, showing a distinct preference for A/U at the third codon position. Simple sequence repeat analysis identified 207 and 211 repeats in var. and var. , respectively, primarily the A/T type. Boundary condition analysis indicated no significant expansion or contraction in the inverted repeat regions with consistent gene types and locations across both varieties. Nucleotide polymorphism analysis highlighted greater variation in the intergenic regions than in the coding sequences of chloroplast genomes. Phylogenetic analyses demonstrated that the species clustered into a distinct, well-supported clade. Notably, , along with var. and var. , established a monophyletic lineage. Within this lineage, and var. were closely related, with var. serving as their sister taxon.