Chloroplast Genome Variation and Phylogenetic Relationships of Lavandula angustifolia and Lavandula × intermedia

Plant chloroplast genomes are characterized by high conservatism and a well-described organization, making them a convenient basis for analyzing evolutionary dynamics and constructing phylogenetic hypotheses. In this study, we performed de novo assembly and complete annotation of six chloroplast genomes from the genus Lavandula: four accessions of L. angustifolia and two hybrid samples of Lavandula × intermedia. The assembled genomes ranged from 151,431 to 151,480 bp, which is consistent with the expected chloroplast genome organization and indicates high structural stability within the genus. All six genomes exhibited the typical quadripartite structure of angiosperm chloroplast genomes, with a large single-copy (LSC) region of 82,682–82,837 bp, a small single-copy (SSC) region of 17,579–17,580 bp, and two inverted repeats (IRa and IRb) of 25,532–25,586 bp each. They contained 113 genes in total, including 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Nucleotide diversity analysis revealed several variable intergenic regions that could serve as potential candidate molecular markers. Each sample harboured 56–57 simple sequence repeat (SSR) loci, unevenly distributed across the genome. Phylogenetic analysis based on whole chloroplast genome alignments confirmed the placement of the newly assembled Lavandula sequences within the family Lamiaceae. The six chloroplast genomes obtained in this work provide a robust reference set for future comparative genomic, phylogenetic and population-level studies in Lavandula.