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Comparison of the complete plastomes and the phylogenetic analysis of Paulownia species
Paulownia species are important ecological, economic and ornamental species, but their phylogenetic relationship remains unclear, which seriously affects the development and utilization of these important resources. The complete chloroplast genomes of six Paulownia species were assembled by next-gen...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Nature Publishing Group UK
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7010769/ https://www.ncbi.nlm.nih.gov/pubmed/32042041 http://dx.doi.org/10.1038/s41598-020-59204-y |
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author | Li, Pingping Lou, Gongli Cai, Xiaoran Zhang, Bin Cheng, Yueqin Wang, Hongwei |
author_facet | Li, Pingping Lou, Gongli Cai, Xiaoran Zhang, Bin Cheng, Yueqin Wang, Hongwei |
author_sort | Li, Pingping |
collection | PubMed |
description | Paulownia species are important ecological, economic and ornamental species, but their phylogenetic relationship remains unclear, which seriously affects the development and utilization of these important resources. The complete chloroplast genomes of six Paulownia species were assembled by next-generation sequencing data. By adding two known Paulownia chloroplast genomes to these six assembled genomes, we performed the comparative analysis and phylogenetic tree reconstruction of Paulownia. The results indicated that the chloroplast genomes of Paulownia species ranged in size from 154,107 to 154,694 bp. These chloroplast genomes contained 117 unique functional genes, including 80 protein-coding genes, four rRNA genes, and 33 tRNA genes. Twelve hotspot regions, five protein-coding genes and seven noncoding regions, were identified in the chloroplast genomes that showed high levels of sequence variation. Additionally, positive selection was observed in three genes, rps2, rbcL and ndhG. The maximum likelihood (ML) and Bayesian (BI) analysis strongly supported the monophyletic origin of Paulownia species, which clustered into two major clades: One clade included P. coreana, P. tomentosa and P. kawakamii, while the other clade comprised the 5 other species including P. fargesii and P. australis. This study provides useful genetic information for phylogenetic reconstruction, taxonomic discrepancies, and studying species evolution and phylogeography in Paulownia. |
format | Online Article Text |
id | pubmed-7010769 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-70107692020-02-21 Comparison of the complete plastomes and the phylogenetic analysis of Paulownia species Li, Pingping Lou, Gongli Cai, Xiaoran Zhang, Bin Cheng, Yueqin Wang, Hongwei Sci Rep Article Paulownia species are important ecological, economic and ornamental species, but their phylogenetic relationship remains unclear, which seriously affects the development and utilization of these important resources. The complete chloroplast genomes of six Paulownia species were assembled by next-generation sequencing data. By adding two known Paulownia chloroplast genomes to these six assembled genomes, we performed the comparative analysis and phylogenetic tree reconstruction of Paulownia. The results indicated that the chloroplast genomes of Paulownia species ranged in size from 154,107 to 154,694 bp. These chloroplast genomes contained 117 unique functional genes, including 80 protein-coding genes, four rRNA genes, and 33 tRNA genes. Twelve hotspot regions, five protein-coding genes and seven noncoding regions, were identified in the chloroplast genomes that showed high levels of sequence variation. Additionally, positive selection was observed in three genes, rps2, rbcL and ndhG. The maximum likelihood (ML) and Bayesian (BI) analysis strongly supported the monophyletic origin of Paulownia species, which clustered into two major clades: One clade included P. coreana, P. tomentosa and P. kawakamii, while the other clade comprised the 5 other species including P. fargesii and P. australis. This study provides useful genetic information for phylogenetic reconstruction, taxonomic discrepancies, and studying species evolution and phylogeography in Paulownia. Nature Publishing Group UK 2020-02-10 /pmc/articles/PMC7010769/ /pubmed/32042041 http://dx.doi.org/10.1038/s41598-020-59204-y Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Li, Pingping Lou, Gongli Cai, Xiaoran Zhang, Bin Cheng, Yueqin Wang, Hongwei Comparison of the complete plastomes and the phylogenetic analysis of Paulownia species |
title | Comparison of the complete plastomes and the phylogenetic analysis of Paulownia species |
title_full | Comparison of the complete plastomes and the phylogenetic analysis of Paulownia species |
title_fullStr | Comparison of the complete plastomes and the phylogenetic analysis of Paulownia species |
title_full_unstemmed | Comparison of the complete plastomes and the phylogenetic analysis of Paulownia species |
title_short | Comparison of the complete plastomes and the phylogenetic analysis of Paulownia species |
title_sort | comparison of the complete plastomes and the phylogenetic analysis of paulownia species |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7010769/ https://www.ncbi.nlm.nih.gov/pubmed/32042041 http://dx.doi.org/10.1038/s41598-020-59204-y |
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