Comparative chloroplast genome analyses of Oxytropis DC. species: new insights into genome evolution and phylogenomic implications

The genus <i>Oxytropis</i> DC. comprises about 310 species distributed in Asia, Europe, and North America. Previous studies based on evidences from morphology or a few molecular markers are helpful for understanding the classification and systematic evolution of <i>Oxytropis</i>. However, a scarcity of chloroplast genomic resources for <i>Oxytropis</i> has hindered the understanding of the genus's systematic classification and chloroplast genome evolution. Here comparative genomic analyses were conducted on chloroplast genomes of 24 <i>Oxytropis</i> species. Chloroplast genomes of <i>Oxytropis</i> species showed the triad structure due to the loss of one copy of the IR, with the size range from 121854 bp to 125271 bp. The <i>Oxytropis</i> cp genomes encoded a total of 110 genes, including 76 protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. It was found that the <i>atpF</i> intron, one <i>clpP</i> intron, one <i>rps12</i> intron, <i>rpl22</i> gene, <i>rps16</i> gene, and <i>infA</i> gene were lost in the <i>Oxytropis</i> cp genomes. Seven regions (<i>5'-rps12-clpP, clpP</i> intron<i>, psbM-petN</i>, <i>rpl23-trnI-CAU</i>, <i>ndhJ-trnF-GAA,trnQ-UUG-accD</i>, <i>trnL-UAA-trnT-UGU</i>) were chosen as potential molecular markers, which will contribute to species identification, population genetics and phylogenetic studies of <i>Oxytropis.</i> The phylogenetic relationships among <i>Oxytropis</i> species provided some implications for the classification of <i>Oxytropis</i>. Congruent with studies based on the morphological evidence, the close relationships between <i>O. neimonggolica</i> and <i>O. diversifolia</i>, as well as <i>O. filiformis</i> and <i>O. coerulea</i> were revealed. The results supported the treatment of <i>O. daqingshanica</i> as a separate species and refuted the inclusion of <i>O. daqingshanica</i> in <i>O. ochrantha</i> as conspecific taxa. In addition, it was suggested that <i>O. chiliophylla</i> should be considered as a separate species rather than its inclusion in <i>O. microphylla</i>. The 16 positively selected genes (<i>rps3</i>, <i>rps4</i>, <i>rps7</i>, <i>rps11</i>, <i>rps12</i>, <i>rpl2</i>, <i>rpl20</i>, <i>rpl32</i>, <i>rpoC2, psbC</i>, <i>rbcL</i>, <i>atpF, clpP</i>, <i>accD, ycf1</i>, <i>ycf2</i>) are related to important biological processes for instance self-replication, photosynthesis and metabolite biosynthesis, which may contribute to the adaptation of <i>Oxytropis</i> to its habitats. This study will lay a solid foundation for further studies on species identification, taxonomy, and systematic evolution of <i>Oxytropis</i>.