Comparative analysis of complete chloroplast genomes provides insights into phylogenetic relationships and screening of polymorphic markers in Dimocarpus and related species

BACKGROUND: Longan (Dimocarpus longan) is a highly nutritious subtropical perennial fruit tree that has been used as a traditional medicine since ancient times for its tonic properties. However, morphological variations and frequent hybridization events complicate cultivar identification and phylogenetic studies of this species. RESULTS: This study sequenced and assembled the chloroplast genomes of 12 longan varieties and assembled Dimocarpus confinis chloroplast genome using resequencing data, along with published chloroplast genomes of two Litchi species and three longan species, conducting comprehensive analyses to reveal structural variations in longan chloroplast genomes. A total of 490 long repeat sequences and 1,420 SSR loci were identified, mainly composed of A/T mononucleotide repeats located in the LSC region and intergenic spacers. Comparative analysis revealed low genomic divergence, with six highly variable regions and four polymorphic loci identified, offering potential for molecular marker development. Primers designed from the highly variable trnR (UCU)-atpA region showed preliminary discriminatory potential between D. longan and L. chinensis. IR boundary comparison showed expansion in Litchi species and slight contraction in D. confinis. Selection pressure analysis indicated most genes were under purifying selection, with only ccsA under positive selection. Phylogenetic analysis supported a close relationship between Dimocarpus and Litchi, with D. confinis forming an independent branch positioned between them, indicates that D. confinis might be a hybrid of lychee and longan. Primers based on the highly variable trnR (UCU)-atpA region enabled effective differentiation among longan and Litchi species. CONCLUSIONS: This study provides essential genetic resources for accurate species identification, resolving phylogenetic relationships, and assessing genetic diversity in Dimocarpus. Our findings establish a molecular foundation for germplasm conservation and breeding programs of this economically and medicinally important species.