Comparative chloroplast genome analyses of 23 species in Swertia L. (Gentianaceae) with implications for its phylogeny

Abstract

<i>Swertia</i> L. is a large genus in the family Gentianaceae. Different chloroplast gene segments have been used to study systematic evolutionary relationships between species of <i>Swertia</i> L. However, as gene fragment-based phylogenies lack sufficient resolution, the systematic evolutionary relationships between <i>Swertia</i> L. species have remained unclear. We sequenced and annotated the complete chloroplast genomes of four <i>Swertia</i> species, namely, <i>S. bifolia</i>, <i>S. tetraptera</i>, <i>S. franchetian</i>, and <i>S. przewalskii</i>, using next generation sequencing and the plastid genome annotator tool. The chloroplast genome sequences of 19 additional species of <i>Swertia</i> L. were downloaded from the NCBI database and also assessed. We found that all 23 <i>Swertia</i> L. species had a similar genetic structure, that is, a ring tetrad structure, but with some clear differences. The chloroplast genomes of the 23 <i>Swertia</i> L. species were 149036-153691 bp long, averaging 152385 bp; the genomes contained 134 functional genes: 38 tRNA, eight rRNA, and 88 protein-encoding genes. A comparative analysis showed that chloroplasts genome of <i>Swertia</i> was conserved in terms of genome structure, codon preference, and repeat sequences, but it differed in terms of genome sizes, gene contents, and SC/IR boundary. Using <i>Swertia wolfangiana</i> as a reference, we found clear divergences in most of the non-coding and intergenic regions of the complete chloroplast genomes of these species; we also found that <i>rpoC1</i>, <i>ccsA</i>, <i>ndhI</i>, <i>ndhA</i>, and <i>rps15</i> protein-coding genes had large variations. These highly variable hotspots will be useful for future phylogenetic and population genetic studies. Phylogenetic analysis with high bootstrap support showed that <i>Swertia</i> L. was not monophyletic. The classification of subgen. <i>Swertia</i> and subgen. <i>Ophelia</i> was supported by molecular data, which also partly supported the division of sect. <i>Ophelia</i>, sect. <i>Platynema</i>, sect. <i>Poephila,</i> sect<i>. Swertia</i>, and sect. <i>Macranthos</i>. However, the systematic positions of other groups and species require further exploration. The <i>Swertia</i> L formed at 29.60 Ma. Speciation of 10 species occurred in succession after 12 Ma and 13 species occurred in succession after 2.5 Ma. Our analysis provides insight into the unresolved evolutionary relationships of <i>Swertia</i> L. species.