Comparison of Chloroplast Genomes Reveals the Evolution of Salix

As the most diverse genus of Salicaceae, Salix is mainly distributed in the temperate zone of the northern hemisphere, with about 350 to 500 species worldwide. The evolutionary history of this genus is complicated because of the high genetic differentiation. Chloroplast genes are highly conserved, which makes it an effective tool for studying uniparental inheritance evolution. In this study, we sequenced and assembled five chloroplast genomes of representative species of Salix. The phylogenetic relationships of Salix were constructed using the chloroplast genome, and the differences in chloroplast structure among different lineages were compared. The chloroplast genomes of Salix exhibited a typical quadripartite structure, with lengths ranging from 154,444 to 155,725 bp. A total of 131 genes were successfully annotated, including 88 protein-coding genes, 35 tRNA genes, and 8 rRNA genes. Clade I had higher variability regions in the SSC region, identifying 7 highly variable regions, namely ndhD, ndhF-trnL, trnL, ccsA-ndhD, ycf1, aptF, and aptF-rps14. The rapidly evolving clpP gene was identified. The deletion site of Clade I was 169 to 269 bp in length, and the insertion site was 183 to 283 bp in length. Clade II had higher variability regions in the LSC region, with four highly variable regions identified: ndhC-trnV, psdE-petL, clpP, and ccsA. The rapidly evolving rps18 and infA genes were identified. The deletion site of Clade II was 1703 to 2984 bp in length, and the insertion site was 1556 to 2837 bp in length. This study elucidated the evolution of chloroplast genomes across different lineages of Salix, offering deeper insights into the relationships within the genus.