Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae)

Abstract Background Zingiberoideae is a large and diverse subfamily of the family Zingiberaceae. Four genera in subfamily Zingiberoideae each possess 50 or more species, including Globba (100), Hedychium (> 80), Kaempferia (50) and Zingiber (150). Despite the agricultural, medicinal and horticult...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Dong-Mei Li, Jie Li, Dai-Rong Wang, Ye-Chun Xu, Gen-Fa Zhu
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Zingiberaceae Zingiberoideae Chloroplast genome Phylogeny Divergent hotspots Genome evolution Botany QK1-989
Acceso en línea:	https://doaj.org/article/0b578c3607824895807a93a16cc6f83c
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:0b578c3607824895807a93a16cc6f83c
record_format	dspace
spelling	oai:doaj.org-article:0b578c3607824895807a93a16cc6f83c2021-11-28T12:07:22ZMolecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae)10.1186/s12870-021-03315-91471-2229https://doaj.org/article/0b578c3607824895807a93a16cc6f83c2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12870-021-03315-9https://doaj.org/toc/1471-2229Abstract Background Zingiberoideae is a large and diverse subfamily of the family Zingiberaceae. Four genera in subfamily Zingiberoideae each possess 50 or more species, including Globba (100), Hedychium (> 80), Kaempferia (50) and Zingiber (150). Despite the agricultural, medicinal and horticultural importance of these species, genomic resources and suitable molecular markers for them are currently sparse. Results Here, we have sequenced, assembled and analyzed ten complete chloroplast genomes from nine species of subfamily Zingiberoideae: Globba lancangensis, Globba marantina, Globba multiflora, Globba schomburgkii, Globba schomburgkii var. angustata, Hedychium coccineum, Hedychium neocarneum, Kaempferia rotunda ‘Red Leaf’, Kaempferia rotunda ‘Silver Diamonds’ and Zingiber recurvatum. These ten chloroplast genomes (size range 162,630–163,968 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 87,172–88,632 bp), a small single copy (SSC, 15,393–15,917 bp) and a pair of inverted repeats (IRs, 29,673–29,833 bp). The genomes contain 111–113 different genes, including 79 protein coding genes, 28–30 tRNAs and 4 rRNA genes. The dynamics of the genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats and long repeats exhibit similarities, with slight differences observed among the ten genomes. Further comparative analysis of seventeen related Zingiberoideae species, 12 divergent hotspots are identified. Positive selection is observed in 14 protein coding genes, including accD, ccsA, ndhA, ndhB, psbJ, rbcL, rpl20, rpoC1, rpoC2, rps12, rps18, ycf1, ycf2 and ycf4. Phylogenetic analyses, based on the complete chloroplast-derived single-nucleotide polymorphism data, strongly support that Globba, Hedychium, and Curcuma I + “the Kaempferia clade” consisting of Curcuma II, Kaempferia and Zingiber, form a nested evolutionary relationship in subfamily Zingiberoideae. Conclusions Our study provides detailed information on ten complete Zingiberoideae chloroplast genomes, representing a valuable resource for future studies that seek to understand the molecular evolutionary dynamics in family Zingiberaceae. The identified divergent hotspots can be used for development of molecular markers for phylogenetic inference and species identification among closely related species within four genera of Globba, Hedychium, Kaempferia and Zingiber in subfamily Zingiberoideae.Dong-Mei LiJie LiDai-Rong WangYe-Chun XuGen-Fa ZhuBMCarticleZingiberaceaeZingiberoideaeChloroplast genomePhylogenyDivergent hotspotsGenome evolutionBotanyQK1-989ENBMC Plant Biology, Vol 21, Iss 1, Pp 1-24 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Zingiberaceae Zingiberoideae Chloroplast genome Phylogeny Divergent hotspots Genome evolution Botany QK1-989
spellingShingle	Zingiberaceae Zingiberoideae Chloroplast genome Phylogeny Divergent hotspots Genome evolution Botany QK1-989 Dong-Mei Li Jie Li Dai-Rong Wang Ye-Chun Xu Gen-Fa Zhu Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae)
description	Abstract Background Zingiberoideae is a large and diverse subfamily of the family Zingiberaceae. Four genera in subfamily Zingiberoideae each possess 50 or more species, including Globba (100), Hedychium (> 80), Kaempferia (50) and Zingiber (150). Despite the agricultural, medicinal and horticultural importance of these species, genomic resources and suitable molecular markers for them are currently sparse. Results Here, we have sequenced, assembled and analyzed ten complete chloroplast genomes from nine species of subfamily Zingiberoideae: Globba lancangensis, Globba marantina, Globba multiflora, Globba schomburgkii, Globba schomburgkii var. angustata, Hedychium coccineum, Hedychium neocarneum, Kaempferia rotunda ‘Red Leaf’, Kaempferia rotunda ‘Silver Diamonds’ and Zingiber recurvatum. These ten chloroplast genomes (size range 162,630–163,968 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 87,172–88,632 bp), a small single copy (SSC, 15,393–15,917 bp) and a pair of inverted repeats (IRs, 29,673–29,833 bp). The genomes contain 111–113 different genes, including 79 protein coding genes, 28–30 tRNAs and 4 rRNA genes. The dynamics of the genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats and long repeats exhibit similarities, with slight differences observed among the ten genomes. Further comparative analysis of seventeen related Zingiberoideae species, 12 divergent hotspots are identified. Positive selection is observed in 14 protein coding genes, including accD, ccsA, ndhA, ndhB, psbJ, rbcL, rpl20, rpoC1, rpoC2, rps12, rps18, ycf1, ycf2 and ycf4. Phylogenetic analyses, based on the complete chloroplast-derived single-nucleotide polymorphism data, strongly support that Globba, Hedychium, and Curcuma I + “the Kaempferia clade” consisting of Curcuma II, Kaempferia and Zingiber, form a nested evolutionary relationship in subfamily Zingiberoideae. Conclusions Our study provides detailed information on ten complete Zingiberoideae chloroplast genomes, representing a valuable resource for future studies that seek to understand the molecular evolutionary dynamics in family Zingiberaceae. The identified divergent hotspots can be used for development of molecular markers for phylogenetic inference and species identification among closely related species within four genera of Globba, Hedychium, Kaempferia and Zingiber in subfamily Zingiberoideae.
format	article
author	Dong-Mei Li Jie Li Dai-Rong Wang Ye-Chun Xu Gen-Fa Zhu
author_facet	Dong-Mei Li Jie Li Dai-Rong Wang Ye-Chun Xu Gen-Fa Zhu
author_sort	Dong-Mei Li
title	Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae)
title_short	Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae)
title_full	Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae)
title_fullStr	Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae)
title_full_unstemmed	Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae)
title_sort	molecular evolution of chloroplast genomes in subfamily zingiberoideae (zingiberaceae)
publisher	BMC
publishDate	2021
url	https://doaj.org/article/0b578c3607824895807a93a16cc6f83c
work_keys_str_mv	AT dongmeili molecularevolutionofchloroplastgenomesinsubfamilyzingiberoideaezingiberaceae AT jieli molecularevolutionofchloroplastgenomesinsubfamilyzingiberoideaezingiberaceae AT dairongwang molecularevolutionofchloroplastgenomesinsubfamilyzingiberoideaezingiberaceae AT yechunxu molecularevolutionofchloroplastgenomesinsubfamilyzingiberoideaezingiberaceae AT genfazhu molecularevolutionofchloroplastgenomesinsubfamilyzingiberoideaezingiberaceae
_version_	1718408180943290368

Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae)

Ejemplares similares