Analyzing and Characterizing the Chloroplast Genome of<i> Salix wilsonii</i>

Abstract

<i>Salix wilsonii</i> is an important ornamental willow tree widely distributed in China. In this study, an integrated circular chloroplast genome was reconstructed for <i>S. wilsonii</i> based on the chloroplast reads screened from the whole-genome sequencing data generated with the PacBio RSII platform. The obtained pseudomolecule was 155,750 bp long and had a typical quadripartite structure, comprising a large single copy region (LSC, 84,638 bp) and a small single copy region (SSC, 16,282 bp) separated by two inverted repeat regions (IR, 27,415 bp). The <i>S. wilsonii</i> chloroplast genome encoded 115 unique genes, including four rRNA genes, 30 tRNA genes, 78 protein-coding genes, and three pseudogenes. Repetitive sequence analysis identified 32 tandem repeats, 22 forward repeats, two reverse repeats, and five palindromic repeats. Additionally, a total of 118 perfect microsatellites were detected, with mononucleotide repeats being the most common (89.83%). By comparing the <i>S. wilsonii</i> chloroplast genome with those of other rosid plant species, significant contractions or expansions were identified at the IR-LSC/SSC borders. Phylogenetic analysis of 17 willow species confirmed that <i>S. wilsonii</i> was most closely related to <i>S. chaenomeloides</i> and revealed the monophyly of the genus <i>Salix</i>. The complete <i>S. wilsonii</i> chloroplast genome provides an additional sequence-based resource for studying the evolution of organelle genomes in woody plants.