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Analyzing and Characterizing the Chloroplast Genome of Salix wilsonii
- Source :
- BioMed Research International, Vol 2019 (2019), BioMed Research International
- Publication Year :
- 2019
- Publisher :
- Hindawi Limited, 2019.
-
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.
- Subjects :
- 0106 biological sciences
0301 basic medicine
Chloroplasts
Article Subject
Inverted repeat
Sequence analysis
Pseudogene
lcsh:Medicine
Biology
01 natural sciences
Genome
General Biochemistry, Genetics and Molecular Biology
Evolution, Molecular
03 medical and health sciences
RNA, Transfer
Tandem repeat
Genome, Chloroplast
Phylogeny
Genetics
Whole genome sequencing
Whole Genome Sequencing
General Immunology and Microbiology
Phylogenetic tree
lcsh:R
Molecular Sequence Annotation
Salix
Sequence Analysis, DNA
General Medicine
Ribosomal RNA
030104 developmental biology
Research Article
010606 plant biology & botany
Subjects
Details
- ISSN :
- 23146141 and 23146133
- Volume :
- 2019
- Database :
- OpenAIRE
- Journal :
- BioMed Research International
- Accession number :
- edsair.doi.dedup.....e4ffb87000e318bf2a552ca5769c1ba1