Characterization of the complete chloroplast genomes of five <i>Populus</i> species from the western Sichuan plateau, southwest China: comparative and phylogenetic analyses

Abstract

Species of the genus <i>Populus</i>, which is widely distributed in the northern hemisphere from subtropical to boreal forests, are among the most commercially exploited groups of forest trees. In this study, the complete chloroplast genomes of five <i>Populus</i> species (<i>Populus cathayana</i>, <i>P. kangdingensis</i>, <i>P. pseudoglauca</i>, <i>P. schneideri</i>, and <i>P. xiangchengensis</i>) were compared. The chloroplast genomes of the five <i>Populus</i> species are very similar. The total chloroplast genome sequence lengths for the five plastomes were 156,789, 156,523, 156,512, 156,513, and 156,465 bp, respectively. A total of 130 genes were identified in each genome, including 85 protein-coding genes, 37 tRNA genes and eight rRNA genes. Seven genes were duplicated in the protein-coding genes, whereas 11 genes were duplicated in the RNA genes. The GC content was 36.7% for all plastomes. We analyzed nucleotide substitutions, small inversions, simple sequence repeats and long repeats in the chloroplast genomes and found nine divergence hotspots (<i>ccsA</i>+<i>ccsA-ndhD, ndhC-trnV</i>, <i>psbZ-trnfM</i>, <i>trnG-atpA</i>, <i>trnL-ndhJ</i>, <i>trnR-trnN</i>, <i>ycf4-cemA</i>, <i>ycf1</i>, and <i>trnR-trnN</i>), which could be useful molecular genetic markers for future population genetic and phylogenetic studies. We also observed that two genes (<i>rpoC2</i> and <i>rbcL</i>) were subject to positive selection. Phylogenetic analysis based on whole cp genomes showed that <i>P. schneideri</i> had a close relationship with <i>P. kangdingensis</i> and <i>P. pseudoglauca</i>, while <i>P. xiangchengensis</i> was a sister to <i>P. cathayana.</i>