Objective To characterize the chloroplast genomes and phylogenetic relationships of four medicinal species of Disporopsis, namely Disporopsis aspersa, D. fuscopicta, D. longifolia, and D. pernyi, and to identify potential regions for species discrimination, thereby providing a molecular and theoretical basis for species identification, germplasm resource conservation, quality control of medicinal materials, and resource development and utilization of this genus. Methods Young leaves of the four medicinal Disporopsis species were subjected to high-throughput sequencing. The chloroplast genomes were assembled and annotated, followed by bioinformatic analyses of repeat sequences, inverted repeat (IR) boundaries, codon usage bias, nucleotide diversity, selection pressure, and phylogenetic relationships. Results The chloroplast genomes of the four medicinal Disporopsis species exhibited a typical quadripartite circular structure, with genome sizes ranging from 155 975 to 156 109 bp and an overall GC content of 37.68%. A total of 131 genes were annotated in each genome, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Simple sequence repeats (SSRs) were dominated by mononucleotide repeats, whereas long sequence repeats (LSRs) were dominated by palindromic repeats. The IR boundaries were generally conserved among the four species. Their codon usage patterns were highly similar, with a preference for codons ending in A or T. Nucleotide diversity analysis showed that rrn23S and trnT-UGU had relatively high Pi values among the genic regions, whereas rrn4.5S–rrn5S, ccsA–ndhD, rps11–rpl36, and rps15–ycf1 were highly variable intergenic regions. Selection pressure analysis showed that most protein-coding genes had Ka/Ks values below 1 and were predominantly constrained by purifying selection. However, ycf1, ycf4, psaI, and cemA had Ka/Ks values above 1 in some species comparisons, suggesting possible signals associated with adaptive evolution. Phylogenetic analysis showed that the four Disporopsis species clustered within the same well-supported branch and formed a sister group with Polygonatum. Conclusion The chloroplast genomes of the four Disporopsis species are generally conserved in genome structure and gene composition, although local sequence variation is present. The candidate highly variable regions identified in this study may provide useful references for species identification and molecular marker development in Disporopsis. The phylogenetic results also provide chloroplast genomic evidence for investigating the classification and relationships of this genus.

Disporopsis  /  Disporopsis aspersa (Hua) Engl. ex K. Krause  /  Disporopsis fuscopicta Hance  /  Disporopsis longifolia Craib  /  Disporopsis pernyi (Hua) Diels  /  chloroplast genome  /  germplasm resources  /  interspecific variation  /  selection pressure  /  phylogenetic analysis