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Complete chloroplast genome of Boesenbergia rotunda and a comparative analysis with members of the family Zingiberaceae

Boesenbergia rotunda (L.) Mansf. is a medically important ginger species of the family Zingiberaceae but its genomic information on molecular phylogeny and identification is scarce. In this work, the chloroplast genome of B. rotunda was sequenced, characterized and compared to the other Zingiberacea...

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Autores principales: Liew, Yvonne Jing Mei, Chua, Kah-Ooi, Yong, Hoi-Sen, Song, Sze-Looi, Chan, Kok-Gan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9607705/
https://www.ncbi.nlm.nih.gov/pubmed/36320930
http://dx.doi.org/10.1007/s40415-022-00845-w
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author Liew, Yvonne Jing Mei
Chua, Kah-Ooi
Yong, Hoi-Sen
Song, Sze-Looi
Chan, Kok-Gan
author_facet Liew, Yvonne Jing Mei
Chua, Kah-Ooi
Yong, Hoi-Sen
Song, Sze-Looi
Chan, Kok-Gan
author_sort Liew, Yvonne Jing Mei
collection PubMed
description Boesenbergia rotunda (L.) Mansf. is a medically important ginger species of the family Zingiberaceae but its genomic information on molecular phylogeny and identification is scarce. In this work, the chloroplast genome of B. rotunda was sequenced, characterized and compared to the other Zingiberaceae species to provide chloroplast genetic resources and to determine its phylogenetic position in the family. The chloroplast genome of B. rotunda was 163,817 bp in length and consisted of a large single-copy (LSC) region of 88,302 bp, a small single-copy (SSC) region of 16,023 bp and a pair of inverted repeats (IRA and IRB) of 29,746 bp each. The chloroplast genome contained 113 unique genes, including 79 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. Several genes had atypical start codons, while most amino acids exhibited biased usage of synonymous codons. Comparative analyses with various chloroplast genomes of Zingiberaceae taxa revealed several highly variable regions (psbK-psbI, trnT-GGU-psbD, rbcL-accD, ndhF-rpl32, and ycf1) in the LSC and SSC regions in the chloroplast genome of B. rotunda that could be utilized as molecular markers for DNA barcoding and species delimitation. Phylogenetic analyses based on shared protein-coding genes revealed that B. rotunda formed a distinct lineage with B. kingii Mood & L.M.Prince, in a subclade that also contained the genera Kaempferia and Zingiber. These findings constitute the first chloroplast genome information of B. rotunda that could be a reference for phylogenetic analysis and identification of genus Boesenbergia within the Zingiberaceae family. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s40415-022-00845-w.
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spelling pubmed-96077052022-10-28 Complete chloroplast genome of Boesenbergia rotunda and a comparative analysis with members of the family Zingiberaceae Liew, Yvonne Jing Mei Chua, Kah-Ooi Yong, Hoi-Sen Song, Sze-Looi Chan, Kok-Gan Rev Bras Bot Genetics & Evolutionary Biology - Original Article Boesenbergia rotunda (L.) Mansf. is a medically important ginger species of the family Zingiberaceae but its genomic information on molecular phylogeny and identification is scarce. In this work, the chloroplast genome of B. rotunda was sequenced, characterized and compared to the other Zingiberaceae species to provide chloroplast genetic resources and to determine its phylogenetic position in the family. The chloroplast genome of B. rotunda was 163,817 bp in length and consisted of a large single-copy (LSC) region of 88,302 bp, a small single-copy (SSC) region of 16,023 bp and a pair of inverted repeats (IRA and IRB) of 29,746 bp each. The chloroplast genome contained 113 unique genes, including 79 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. Several genes had atypical start codons, while most amino acids exhibited biased usage of synonymous codons. Comparative analyses with various chloroplast genomes of Zingiberaceae taxa revealed several highly variable regions (psbK-psbI, trnT-GGU-psbD, rbcL-accD, ndhF-rpl32, and ycf1) in the LSC and SSC regions in the chloroplast genome of B. rotunda that could be utilized as molecular markers for DNA barcoding and species delimitation. Phylogenetic analyses based on shared protein-coding genes revealed that B. rotunda formed a distinct lineage with B. kingii Mood & L.M.Prince, in a subclade that also contained the genera Kaempferia and Zingiber. These findings constitute the first chloroplast genome information of B. rotunda that could be a reference for phylogenetic analysis and identification of genus Boesenbergia within the Zingiberaceae family. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s40415-022-00845-w. Springer International Publishing 2022-10-26 2022 /pmc/articles/PMC9607705/ /pubmed/36320930 http://dx.doi.org/10.1007/s40415-022-00845-w Text en © The Author(s), under exclusive licence to Botanical Society of Sao Paulo 2022, Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.
spellingShingle Genetics & Evolutionary Biology - Original Article
Liew, Yvonne Jing Mei
Chua, Kah-Ooi
Yong, Hoi-Sen
Song, Sze-Looi
Chan, Kok-Gan
Complete chloroplast genome of Boesenbergia rotunda and a comparative analysis with members of the family Zingiberaceae
title Complete chloroplast genome of Boesenbergia rotunda and a comparative analysis with members of the family Zingiberaceae
title_full Complete chloroplast genome of Boesenbergia rotunda and a comparative analysis with members of the family Zingiberaceae
title_fullStr Complete chloroplast genome of Boesenbergia rotunda and a comparative analysis with members of the family Zingiberaceae
title_full_unstemmed Complete chloroplast genome of Boesenbergia rotunda and a comparative analysis with members of the family Zingiberaceae
title_short Complete chloroplast genome of Boesenbergia rotunda and a comparative analysis with members of the family Zingiberaceae
title_sort complete chloroplast genome of boesenbergia rotunda and a comparative analysis with members of the family zingiberaceae
topic Genetics & Evolutionary Biology - Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9607705/
https://www.ncbi.nlm.nih.gov/pubmed/36320930
http://dx.doi.org/10.1007/s40415-022-00845-w
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