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Analyzing and Characterizing the Chloroplast Genome of Salix wilsonii

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 obt...

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Autores principales: Chen, Yingnan, Hu, Nan, Wu, Huaitong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6662467/
https://www.ncbi.nlm.nih.gov/pubmed/31380427
http://dx.doi.org/10.1155/2019/5190425
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author Chen, Yingnan
Hu, Nan
Wu, Huaitong
author_facet Chen, Yingnan
Hu, Nan
Wu, Huaitong
author_sort Chen, Yingnan
collection PubMed
description 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.
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spelling pubmed-66624672019-08-04 Analyzing and Characterizing the Chloroplast Genome of Salix wilsonii Chen, Yingnan Hu, Nan Wu, Huaitong Biomed Res Int Research Article 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. Hindawi 2019-07-15 /pmc/articles/PMC6662467/ /pubmed/31380427 http://dx.doi.org/10.1155/2019/5190425 Text en Copyright © 2019 Yingnan Chen et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Chen, Yingnan
Hu, Nan
Wu, Huaitong
Analyzing and Characterizing the Chloroplast Genome of Salix wilsonii
title Analyzing and Characterizing the Chloroplast Genome of Salix wilsonii
title_full Analyzing and Characterizing the Chloroplast Genome of Salix wilsonii
title_fullStr Analyzing and Characterizing the Chloroplast Genome of Salix wilsonii
title_full_unstemmed Analyzing and Characterizing the Chloroplast Genome of Salix wilsonii
title_short Analyzing and Characterizing the Chloroplast Genome of Salix wilsonii
title_sort analyzing and characterizing the chloroplast genome of salix wilsonii
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6662467/
https://www.ncbi.nlm.nih.gov/pubmed/31380427
http://dx.doi.org/10.1155/2019/5190425
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