Comparative and phylogenetic analyses of eleven complete chloroplast genomes of Dipterocarpoideae

Abstract Background In South-east Asia, Dipterocarpoideae is predominant in most mature forest communities, comprising around 20% of all trees. As large quantity and high quality wood are produced in many species, Dipterocarpoideae plants are the most important and valuable source in the timber mark...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Yang Yu, Yuwei Han, Yingmei Peng, Zunzhe Tian, Peng Zeng, Hang Zong, Tinggan Zhou, Jing Cai
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Dipterocarpoideae Chloroplast genomes Comparative genomics Selected selection Phylogenetics DNA barcoding Other systems of medicine RZ201-999
Acceso en línea:	https://doaj.org/article/d84b95d08afb4f2bb368bb6d08fa59db
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:d84b95d08afb4f2bb368bb6d08fa59db
record_format	dspace
spelling	oai:doaj.org-article:d84b95d08afb4f2bb368bb6d08fa59db2021-11-28T12:08:19ZComparative and phylogenetic analyses of eleven complete chloroplast genomes of Dipterocarpoideae10.1186/s13020-021-00538-81749-8546https://doaj.org/article/d84b95d08afb4f2bb368bb6d08fa59db2021-11-01T00:00:00Zhttps://doi.org/10.1186/s13020-021-00538-8https://doaj.org/toc/1749-8546Abstract Background In South-east Asia, Dipterocarpoideae is predominant in most mature forest communities, comprising around 20% of all trees. As large quantity and high quality wood are produced in many species, Dipterocarpoideae plants are the most important and valuable source in the timber market. The d-borneol is one of the essential oil components from Dipterocarpoideae (for example, Dryobalanops aromatica or Dipterocarpus turbinatus) and it is also an important traditional Chinese medicine (TCM) formulation known as “Bingpian” in Chinese, with antibacterial, analgesic and anti-inflammatory effects and can enhance anticancer efficiency. Methods In this study, we analyzed 20 chloroplast (cp) genomes characteristics of Dipterocarpoideae, including eleven newly reported genomes and nine cp genomes previously published elsewhere, then we explored the chloroplast genomic features, inverted repeats contraction and expansion, codon usage, amino acid frequency, the repeat sequences and selective pressure analyses. At last, we constructed phylogenetic relationships of Dipterocarpoideae and found the potential barcoding loci. Results The cp genome of this subfamily has a typical quadripartite structure and maintains a high degree of consistency among species. There were slightly more tandem repeats in cp genomes of Dipterocarpus and Vatica, and the psbH gene was subjected to positive selection in the common ancestor of all the 20 species of Dipterocarpoideae compared with three outgroups. Phylogenetic tree showed that genus Shorea was not a monophyletic group, some Shorea species and genus Parashorea are placed in one clade. In addition, the rpoC2 gene can be used as a potential marker to achieve accurate and rapid species identification in subfamily Dipterocarpoideae. Conclusions Dipterocarpoideae had similar cp genomic features and psbM, rbcL, psbH may function in the growth of Dipterocarpoideae. Phylogenetic analysis suggested new taxon treatment is needed for this subfamily indentification. In addition, rpoC2 is potential to be a barcoding gene to TCM distinguish.Yang YuYuwei HanYingmei PengZunzhe TianPeng ZengHang ZongTinggan ZhouJing CaiBMCarticleDipterocarpoideaeChloroplast genomesComparative genomicsSelected selectionPhylogeneticsDNA barcodingOther systems of medicineRZ201-999ENChinese Medicine, Vol 16, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Dipterocarpoideae Chloroplast genomes Comparative genomics Selected selection Phylogenetics DNA barcoding Other systems of medicine RZ201-999
spellingShingle	Dipterocarpoideae Chloroplast genomes Comparative genomics Selected selection Phylogenetics DNA barcoding Other systems of medicine RZ201-999 Yang Yu Yuwei Han Yingmei Peng Zunzhe Tian Peng Zeng Hang Zong Tinggan Zhou Jing Cai Comparative and phylogenetic analyses of eleven complete chloroplast genomes of Dipterocarpoideae
description	Abstract Background In South-east Asia, Dipterocarpoideae is predominant in most mature forest communities, comprising around 20% of all trees. As large quantity and high quality wood are produced in many species, Dipterocarpoideae plants are the most important and valuable source in the timber market. The d-borneol is one of the essential oil components from Dipterocarpoideae (for example, Dryobalanops aromatica or Dipterocarpus turbinatus) and it is also an important traditional Chinese medicine (TCM) formulation known as “Bingpian” in Chinese, with antibacterial, analgesic and anti-inflammatory effects and can enhance anticancer efficiency. Methods In this study, we analyzed 20 chloroplast (cp) genomes characteristics of Dipterocarpoideae, including eleven newly reported genomes and nine cp genomes previously published elsewhere, then we explored the chloroplast genomic features, inverted repeats contraction and expansion, codon usage, amino acid frequency, the repeat sequences and selective pressure analyses. At last, we constructed phylogenetic relationships of Dipterocarpoideae and found the potential barcoding loci. Results The cp genome of this subfamily has a typical quadripartite structure and maintains a high degree of consistency among species. There were slightly more tandem repeats in cp genomes of Dipterocarpus and Vatica, and the psbH gene was subjected to positive selection in the common ancestor of all the 20 species of Dipterocarpoideae compared with three outgroups. Phylogenetic tree showed that genus Shorea was not a monophyletic group, some Shorea species and genus Parashorea are placed in one clade. In addition, the rpoC2 gene can be used as a potential marker to achieve accurate and rapid species identification in subfamily Dipterocarpoideae. Conclusions Dipterocarpoideae had similar cp genomic features and psbM, rbcL, psbH may function in the growth of Dipterocarpoideae. Phylogenetic analysis suggested new taxon treatment is needed for this subfamily indentification. In addition, rpoC2 is potential to be a barcoding gene to TCM distinguish.
format	article
author	Yang Yu Yuwei Han Yingmei Peng Zunzhe Tian Peng Zeng Hang Zong Tinggan Zhou Jing Cai
author_facet	Yang Yu Yuwei Han Yingmei Peng Zunzhe Tian Peng Zeng Hang Zong Tinggan Zhou Jing Cai
author_sort	Yang Yu
title	Comparative and phylogenetic analyses of eleven complete chloroplast genomes of Dipterocarpoideae
title_short	Comparative and phylogenetic analyses of eleven complete chloroplast genomes of Dipterocarpoideae
title_full	Comparative and phylogenetic analyses of eleven complete chloroplast genomes of Dipterocarpoideae
title_fullStr	Comparative and phylogenetic analyses of eleven complete chloroplast genomes of Dipterocarpoideae
title_full_unstemmed	Comparative and phylogenetic analyses of eleven complete chloroplast genomes of Dipterocarpoideae
title_sort	comparative and phylogenetic analyses of eleven complete chloroplast genomes of dipterocarpoideae
publisher	BMC
publishDate	2021
url	https://doaj.org/article/d84b95d08afb4f2bb368bb6d08fa59db
work_keys_str_mv	AT yangyu comparativeandphylogeneticanalysesofelevencompletechloroplastgenomesofdipterocarpoideae AT yuweihan comparativeandphylogeneticanalysesofelevencompletechloroplastgenomesofdipterocarpoideae AT yingmeipeng comparativeandphylogeneticanalysesofelevencompletechloroplastgenomesofdipterocarpoideae AT zunzhetian comparativeandphylogeneticanalysesofelevencompletechloroplastgenomesofdipterocarpoideae AT pengzeng comparativeandphylogeneticanalysesofelevencompletechloroplastgenomesofdipterocarpoideae AT hangzong comparativeandphylogeneticanalysesofelevencompletechloroplastgenomesofdipterocarpoideae AT tingganzhou comparativeandphylogeneticanalysesofelevencompletechloroplastgenomesofdipterocarpoideae AT jingcai comparativeandphylogeneticanalysesofelevencompletechloroplastgenomesofdipterocarpoideae
_version_	1718408228020158464

Comparative and phylogenetic analyses of eleven complete chloroplast genomes of Dipterocarpoideae

Ejemplares similares