Abstract
Salix wilsonii is an important ornamental willow tree widely distributed in China. In this study, an integrated circular chloroplast genome was reconstructed for S. wilsonii 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 S. wilsonii 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 S. wilsonii 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 S. wilsonii was most closely related to S. chaenomeloides and revealed the monophyly of the genus Salix. The complete S. wilsonii chloroplast genome provides an additional sequence-based resource for studying the evolution of organelle genomes in woody plants.
Highlights
In plant, chloroplast is an essential organelle with its own genome and servers as the metabolic center involved in photosynthesis and other cellular functions, including the synthesis of starch, fatty acids, pigments, and amino acids [1]
The gene content and order are highly conserved among land plants, with most genes involved in photosynthesis, transcription, and translation [1, 2]
By mapping the highquality reads to the land plant cp genomes available in the NCBI Organelle Genome Resources database, S. wilsonii chloroplast reads were extracted with a BLASTN algorithm (e-value of 1e−5)
Summary
Chloroplast is an essential organelle with its own genome and servers as the metabolic center involved in photosynthesis and other cellular functions, including the synthesis of starch, fatty acids, pigments, and amino acids [1]. Despite the overall conservation, during evolution, cp genomes have undergone extensive rearrangements within and between plant species, including gene/intron gains and losses, expansion and contraction of the IRs, and inversions [2, 3]. This information, which is revealed by comparisons of cp genomes, has been especially valuable for plant phylogenetic and evolutionary studies. The uniparental inheritance of the cp genome (usually maternal in angiosperms and paternal in gymnosperms), accompanied by the general lack of heteroplasmy and recombination, has enabled researchers to evaluate the relative influences of seed and pollen dispersal on total gene flow [4]
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