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Complete chloroplast genome of a rare and endangered plant species Phalaenopsis zhejiangensis: genomic features and phylogenetic relationship within Orchidaceae

Phalaenopsis zhejiangensis is a rare and endangered plant species with extremely small populations. The complete chloroplast (cp) genome of P. zhejiangensis was assembled, its structural organization was described and comparative genomic analyses was carried out. The cp genome of P. zhejiangensis is...

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Autores principales: Jiang, Ming, Zhu, Yan, Wu, Qian, Zhang, Huijuan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Taylor & Francis 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8439234/
https://www.ncbi.nlm.nih.gov/pubmed/34532575
http://dx.doi.org/10.1080/23802359.2021.1972049
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author Jiang, Ming
Zhu, Yan
Wu, Qian
Zhang, Huijuan
author_facet Jiang, Ming
Zhu, Yan
Wu, Qian
Zhang, Huijuan
author_sort Jiang, Ming
collection PubMed
description Phalaenopsis zhejiangensis is a rare and endangered plant species with extremely small populations. The complete chloroplast (cp) genome of P. zhejiangensis was assembled, its structural organization was described and comparative genomic analyses was carried out. The cp genome of P. zhejiangensis is 143,547 bp in length, with a GC content of 37.2%, which includes a pair of inverted repeats (IRs) of 24,464 bp separated by a small single-copy region of 10,764 bp and a large single-copy region of 83,856 bp. The cp genome contains 126 genes, consisting of 80 protein-coding genes, 38 transfer RNAs, and eight ribosomal RNAs. Six protein-coding genes, including ψndhB (two copies), ψndhD, ψndhG, ψndhK, and ψndhI, are identified as pseudogenes. Another six ndh genes, ndhA, ndhC, ndhE, ndhF, ndhH, and ndhJ, are missing from the plastid genome. A total of 41 cp simple sequence repeats (SSRs) were identified, including 40 mono-nucleotides and one di-nucleotides. Phylogenic analysis revealed P. zhejiangensis was nested inside the Phalaenopsis species and sister to P. wilsonii. The assembly and analysis of P. zhejiangensis cp genome will provide essential data for further study of taxonomy and systematics of Orchidaceae.
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spelling pubmed-84392342021-09-15 Complete chloroplast genome of a rare and endangered plant species Phalaenopsis zhejiangensis: genomic features and phylogenetic relationship within Orchidaceae Jiang, Ming Zhu, Yan Wu, Qian Zhang, Huijuan Mitochondrial DNA B Resour Rapid Communication Phalaenopsis zhejiangensis is a rare and endangered plant species with extremely small populations. The complete chloroplast (cp) genome of P. zhejiangensis was assembled, its structural organization was described and comparative genomic analyses was carried out. The cp genome of P. zhejiangensis is 143,547 bp in length, with a GC content of 37.2%, which includes a pair of inverted repeats (IRs) of 24,464 bp separated by a small single-copy region of 10,764 bp and a large single-copy region of 83,856 bp. The cp genome contains 126 genes, consisting of 80 protein-coding genes, 38 transfer RNAs, and eight ribosomal RNAs. Six protein-coding genes, including ψndhB (two copies), ψndhD, ψndhG, ψndhK, and ψndhI, are identified as pseudogenes. Another six ndh genes, ndhA, ndhC, ndhE, ndhF, ndhH, and ndhJ, are missing from the plastid genome. A total of 41 cp simple sequence repeats (SSRs) were identified, including 40 mono-nucleotides and one di-nucleotides. Phylogenic analysis revealed P. zhejiangensis was nested inside the Phalaenopsis species and sister to P. wilsonii. The assembly and analysis of P. zhejiangensis cp genome will provide essential data for further study of taxonomy and systematics of Orchidaceae. Taylor & Francis 2021-09-09 /pmc/articles/PMC8439234/ /pubmed/34532575 http://dx.doi.org/10.1080/23802359.2021.1972049 Text en © 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Rapid Communication
Jiang, Ming
Zhu, Yan
Wu, Qian
Zhang, Huijuan
Complete chloroplast genome of a rare and endangered plant species Phalaenopsis zhejiangensis: genomic features and phylogenetic relationship within Orchidaceae
title Complete chloroplast genome of a rare and endangered plant species Phalaenopsis zhejiangensis: genomic features and phylogenetic relationship within Orchidaceae
title_full Complete chloroplast genome of a rare and endangered plant species Phalaenopsis zhejiangensis: genomic features and phylogenetic relationship within Orchidaceae
title_fullStr Complete chloroplast genome of a rare and endangered plant species Phalaenopsis zhejiangensis: genomic features and phylogenetic relationship within Orchidaceae
title_full_unstemmed Complete chloroplast genome of a rare and endangered plant species Phalaenopsis zhejiangensis: genomic features and phylogenetic relationship within Orchidaceae
title_short Complete chloroplast genome of a rare and endangered plant species Phalaenopsis zhejiangensis: genomic features and phylogenetic relationship within Orchidaceae
title_sort complete chloroplast genome of a rare and endangered plant species phalaenopsis zhejiangensis: genomic features and phylogenetic relationship within orchidaceae
topic Rapid Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8439234/
https://www.ncbi.nlm.nih.gov/pubmed/34532575
http://dx.doi.org/10.1080/23802359.2021.1972049
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