Comparative analysis of chloroplast genomes of Loropetalum chinense and its purplish-red-flowered variety.

Loropetalum chinense var. rubrum is a highly favored ornamental plant in landscaping applications, where its vibrant purplish-red foliage and dense clusters of purplish-red flowers create a striking contrast to the green leaves and white blossoms of its parent species, L. chinense. Despite extensive horticultural utilization, chloroplast genome divergence between L. chinense and its red-leaved variety is poorly characterized. Here, we sequenced and analyzed complete chloroplast genomes of L. chinense and other two horticultural selections of L. chinense var. rubrum exhibiting distinct flower colors. Through comparative genomics, we aimed to identify sequence-level variations and detect potential selection signatures in chloroplast genes. The results showed that the chloroplast genomes ranged from 159,425 to 159,452 bp, with variations primarily driven by insertions and deletions (INDELs) within single-copy regions, while inverted repeat (IR) regions were highly conserved. Three hypervariable regions (trnH-GUG-psbA, ndhD, ycf1 ) enabled the differentiation between L. chinense and its horticultural variety rubrum, and six other regions (e.g., psbA, rps16-trnQ-UUG, atpF) exhibited intraspecific variation unique to the latter. Furthermore, we detected signals of positive selection in the rpoB gene, which contains a micro-inversion unique to the light red-flowered individual. This inversion resulted in five amino acid substitutions, suggesting potential functional consequences for the gene product. These findings enhance our understanding of chloroplast genome evolution in L. chinense and provide valuable genetic tools for phylogenetic and population genomic studies.