Sequencing, Characterization, and Comparative Analyses of the Plastome of Caragana rosea var. rosea

Abstract

To exploit the drought-resistant <i>Caragana</i> species, we performed a comparative study of the plastomes from four species: <i>Caragana rosea</i>, <i>C. microphylla</i>, <i>C. kozlowii</i>, and <i>C. Korshinskii</i>. The complete plastome sequence of the <i>C. rosea</i> was obtained using the next generation DNA sequencing technology. The genome is a circular structure of 133,122 bases and it lacks inverted repeat. It contains 111 unique genes, including 76 protein-coding, 30 tRNA, and four rRNA genes. Repeat analyses obtained 239, 244, 258, and 246 simple sequence repeats in <i>C. rosea</i>, <i>C. microphylla</i>, <i>C. kozlowii</i>, and <i>C. korshinskii</i>, respectively. Analyses of sequence divergence found two intergenic regions: <i>trnI</i>-<i>CAU</i>-<i>ycf2</i> and <i>trnN</i>-<i>GUU</i>-<i>ycf1</i>, exhibiting a high degree of variations. Phylogenetic analyses showed that the four <i>Caragana</i> species belong to a monophyletic clade. Analyses of Ka/Ks ratios revealed that five genes: <i>rpl16</i>, <i>rpl20</i>, <i>rps11</i>, <i>rps7,</i> and <i>ycf1</i> and several sites having undergone strong positive selection in the <i>Caragana</i> branch. The results lay the foundation for the development of molecular markers and the understanding of the evolutionary process for drought-resistant characteristics.