Comparative and phylogenetic analyses of the chloroplast genomes of species of Paeoniaceae

Abstract Plants belonging to family Paeoniaceae are not only economically important ornamental plants but also medicinal plants used as an important source of traditional Chinese medicine. Owing to the complex network evolution and polyploidy evolution of this family, its systematics and taxonomy ar...

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Autores principales:	Liwei Wu, Liping Nie, Qing Wang, Zhichao Xu, Yu Wang, Chunnian He, Jingyuan Song, Hui Yao
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e7d1e3bc34a54e50a51ca866b7fe4bab
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spelling	oai:doaj.org-article:e7d1e3bc34a54e50a51ca866b7fe4bab2021-12-02T16:17:33ZComparative and phylogenetic analyses of the chloroplast genomes of species of Paeoniaceae10.1038/s41598-021-94137-02045-2322https://doaj.org/article/e7d1e3bc34a54e50a51ca866b7fe4bab2021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-94137-0https://doaj.org/toc/2045-2322Abstract Plants belonging to family Paeoniaceae are not only economically important ornamental plants but also medicinal plants used as an important source of traditional Chinese medicine. Owing to the complex network evolution and polyploidy evolution of this family, its systematics and taxonomy are controversial and require a detailed investigation. In this study, three complete chloroplast genomes of sect. Paeonia, one of the sections of Paeonia, were sequenced and then analysed together with 16 other published chloroplast genomes of Paeoniaceae species. The total lengths of the chloroplast genomes of these species were 152,153–154,405 bp. A total of 82–87 protein-coding genes, 31–40 tRNA genes and 8 rRNA genes were annotated. Bioinformatics analysis revealed 61–74 simple sequence repeats (SSRs) in the chloroplast genomes, most of which have A/T base preference. Codon usage analysis showed that A/U-ending codons were more positive than C/G-ending codons, and a slight bias in codon usage was observed in these species. A comparative analysis of these 19 species of Paeoniaceae was then conducted. Fourteen highly variable regions were selected for species relationship study. Phylogenetic analysis revealed that the species of sect. Paeonia gathered in one branch and then divided into different small branches. P. lactiflora, P. anomala, P. anomala subsp. veitchii and P. mairei clustered together. P. intermedia was related to P. obovata and P. obovata subsp. willmottiae. P. emodi was the sister to all other species in the sect. Paeonia.Liwei WuLiping NieQing WangZhichao XuYu WangChunnian HeJingyuan SongHui YaoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-16 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Liwei Wu Liping Nie Qing Wang Zhichao Xu Yu Wang Chunnian He Jingyuan Song Hui Yao Comparative and phylogenetic analyses of the chloroplast genomes of species of Paeoniaceae
description	Abstract Plants belonging to family Paeoniaceae are not only economically important ornamental plants but also medicinal plants used as an important source of traditional Chinese medicine. Owing to the complex network evolution and polyploidy evolution of this family, its systematics and taxonomy are controversial and require a detailed investigation. In this study, three complete chloroplast genomes of sect. Paeonia, one of the sections of Paeonia, were sequenced and then analysed together with 16 other published chloroplast genomes of Paeoniaceae species. The total lengths of the chloroplast genomes of these species were 152,153–154,405 bp. A total of 82–87 protein-coding genes, 31–40 tRNA genes and 8 rRNA genes were annotated. Bioinformatics analysis revealed 61–74 simple sequence repeats (SSRs) in the chloroplast genomes, most of which have A/T base preference. Codon usage analysis showed that A/U-ending codons were more positive than C/G-ending codons, and a slight bias in codon usage was observed in these species. A comparative analysis of these 19 species of Paeoniaceae was then conducted. Fourteen highly variable regions were selected for species relationship study. Phylogenetic analysis revealed that the species of sect. Paeonia gathered in one branch and then divided into different small branches. P. lactiflora, P. anomala, P. anomala subsp. veitchii and P. mairei clustered together. P. intermedia was related to P. obovata and P. obovata subsp. willmottiae. P. emodi was the sister to all other species in the sect. Paeonia.
format	article
author	Liwei Wu Liping Nie Qing Wang Zhichao Xu Yu Wang Chunnian He Jingyuan Song Hui Yao
author_facet	Liwei Wu Liping Nie Qing Wang Zhichao Xu Yu Wang Chunnian He Jingyuan Song Hui Yao
author_sort	Liwei Wu
title	Comparative and phylogenetic analyses of the chloroplast genomes of species of Paeoniaceae
title_short	Comparative and phylogenetic analyses of the chloroplast genomes of species of Paeoniaceae
title_full	Comparative and phylogenetic analyses of the chloroplast genomes of species of Paeoniaceae
title_fullStr	Comparative and phylogenetic analyses of the chloroplast genomes of species of Paeoniaceae
title_full_unstemmed	Comparative and phylogenetic analyses of the chloroplast genomes of species of Paeoniaceae
title_sort	comparative and phylogenetic analyses of the chloroplast genomes of species of paeoniaceae
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/e7d1e3bc34a54e50a51ca866b7fe4bab
work_keys_str_mv	AT liweiwu comparativeandphylogeneticanalysesofthechloroplastgenomesofspeciesofpaeoniaceae AT lipingnie comparativeandphylogeneticanalysesofthechloroplastgenomesofspeciesofpaeoniaceae AT qingwang comparativeandphylogeneticanalysesofthechloroplastgenomesofspeciesofpaeoniaceae AT zhichaoxu comparativeandphylogeneticanalysesofthechloroplastgenomesofspeciesofpaeoniaceae AT yuwang comparativeandphylogeneticanalysesofthechloroplastgenomesofspeciesofpaeoniaceae AT chunnianhe comparativeandphylogeneticanalysesofthechloroplastgenomesofspeciesofpaeoniaceae AT jingyuansong comparativeandphylogeneticanalysesofthechloroplastgenomesofspeciesofpaeoniaceae AT huiyao comparativeandphylogeneticanalysesofthechloroplastgenomesofspeciesofpaeoniaceae
_version_	1718384265385738240

Comparative and phylogenetic analyses of the chloroplast genomes of species of Paeoniaceae

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