Plastid genome data provide new insights into the phylogeny and evolution of the Subtribe Swertiinae

Abstract Background Subtribe Swertiinae, belonging to Gentianaceae, is one of the most taxonomically difficult representatives. The intergeneric and infrageneric classification and phylogenetic relationships within Subtribe Swertiinae are controversial and unresolved. Methods With the aim of clarifying the circumscription of taxa within the Subtribe Swertiinae, comparative and phylogenetic analyses were conducted using 34 Subtribe Swertiinae chloroplast genomes (4 newly sequenced) representing 9 genera. Results The results showed that 34 chloroplast genomes of Subtribe Swertiinae were smaller and ranged in size from 149,036 to 154,365 bp, each comprising two inverted repeat regions (size range 25,069 − 26,126 bp) that separated large single-copy (80,432 − 84,153 bp) and small single-copy (17,887 − 18,47 bp) regions, and all chloroplast genomes showed similar gene order, content, and structure. These chloroplast genomes contained 129–134 genes each, including 84–89 protein-coding genes, 30 tRNAs, and 4 rRNAs. The chloroplast genomes of Subtribe Swertiinae appeared to lose some genes, such as the rpl33, rpl2 and ycf15 genes. Nineteen hypervariable regions, including trnC-GCA-petN, trnS-GCU-trnR-UCU, ndhC-trnV-UAC, trnC-GCA-petN, psbM-trnD-GUC, trnG-GCC-trnfM-CAU, trnS-GGA-rps4, ndhC-trnV-UAC, accD-psaI, psbH-petB, rpl36-infA, rps15-ycf1, ycf3, petD, ndhF, petL, rpl20, rpl15 and ycf1, were screened, and 36–63 SSRs were identified as potential molecular markers. Positive selection analyses showed that two genes (ccsA and psbB) were proven to have high Ka/Ks ratios, indicating that chloroplast genes may have undergone positive selection in evolutionary history. Phylogenetic analysis showed that 34 Subtribe Swertiinae species formed a monophyletic clade including two evident subbranches, and Swertia was paraphyly with other related genera, which were distributed in different clades. Conclusion These results provide valuable information to elucidate the phylogeny, divergence time and evolution process of Subtribe Swertiinae.