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Characterization and Comparative Analysis of Chloroplast Genomes in Five Uncaria Species Endemic to China

Uncaria, a perennial vine from the Rubiaceae family, is a typical Chinese traditional medicine. Currently, uncertainty exists over the Uncaria genus’ evolutionary relationships and germplasm identification. The complete chloroplast genomes of four Uncaria species mentioned in the Chinese Pharmacopoe...

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Autores principales: Chen, Min-Min, Zhang, Miao, Liang, Zong-Suo, He, Qiu-Ling
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9569570/
https://www.ncbi.nlm.nih.gov/pubmed/36232915
http://dx.doi.org/10.3390/ijms231911617
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author Chen, Min-Min
Zhang, Miao
Liang, Zong-Suo
He, Qiu-Ling
author_facet Chen, Min-Min
Zhang, Miao
Liang, Zong-Suo
He, Qiu-Ling
author_sort Chen, Min-Min
collection PubMed
description Uncaria, a perennial vine from the Rubiaceae family, is a typical Chinese traditional medicine. Currently, uncertainty exists over the Uncaria genus’ evolutionary relationships and germplasm identification. The complete chloroplast genomes of four Uncaria species mentioned in the Chinese Pharmacopoeia and Uncaria scandens (an easily confused counterfeit) were sequenced and annotated. The findings demonstrated that the whole chloroplast genome of Uncaria genus is 153,780–155,138 bp in full length, encoding a total of 128–131 genes, containing 83–86 protein-coding genes, eight rRNAs and 37 tRNAs. These regions, which include eleven highly variable loci and 31–49 SSRs, can be used to create significant molecular markers for the Uncaria genus. The phylogenetic tree was constructed according to protein-coding genes and the whole chloroplast genome sequences of five Uncaria species using four methods. The topology of the two phylogenetic trees showed no difference. The sequences of U. rhynchophylla and U. scandens are clustered in one group, while the U. hirsuta and U. macrophylla are clustered in another group. U. sessilifructus is clustered together with the above two small clades. New insights on the relationship were revealed via phylogenetic research in five Uncaria species. This study will provide a theoretical basis for identifying U. rhynchophylla and its counterfeits, as well as the species of the Uncaria genus. This research provides the initial chloroplast genome report of Uncaria, contributes to elucidating the chloroplast genome evolution of Uncaria in China.
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spelling pubmed-95695702022-10-17 Characterization and Comparative Analysis of Chloroplast Genomes in Five Uncaria Species Endemic to China Chen, Min-Min Zhang, Miao Liang, Zong-Suo He, Qiu-Ling Int J Mol Sci Article Uncaria, a perennial vine from the Rubiaceae family, is a typical Chinese traditional medicine. Currently, uncertainty exists over the Uncaria genus’ evolutionary relationships and germplasm identification. The complete chloroplast genomes of four Uncaria species mentioned in the Chinese Pharmacopoeia and Uncaria scandens (an easily confused counterfeit) were sequenced and annotated. The findings demonstrated that the whole chloroplast genome of Uncaria genus is 153,780–155,138 bp in full length, encoding a total of 128–131 genes, containing 83–86 protein-coding genes, eight rRNAs and 37 tRNAs. These regions, which include eleven highly variable loci and 31–49 SSRs, can be used to create significant molecular markers for the Uncaria genus. The phylogenetic tree was constructed according to protein-coding genes and the whole chloroplast genome sequences of five Uncaria species using four methods. The topology of the two phylogenetic trees showed no difference. The sequences of U. rhynchophylla and U. scandens are clustered in one group, while the U. hirsuta and U. macrophylla are clustered in another group. U. sessilifructus is clustered together with the above two small clades. New insights on the relationship were revealed via phylogenetic research in five Uncaria species. This study will provide a theoretical basis for identifying U. rhynchophylla and its counterfeits, as well as the species of the Uncaria genus. This research provides the initial chloroplast genome report of Uncaria, contributes to elucidating the chloroplast genome evolution of Uncaria in China. MDPI 2022-10-01 /pmc/articles/PMC9569570/ /pubmed/36232915 http://dx.doi.org/10.3390/ijms231911617 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Chen, Min-Min
Zhang, Miao
Liang, Zong-Suo
He, Qiu-Ling
Characterization and Comparative Analysis of Chloroplast Genomes in Five Uncaria Species Endemic to China
title Characterization and Comparative Analysis of Chloroplast Genomes in Five Uncaria Species Endemic to China
title_full Characterization and Comparative Analysis of Chloroplast Genomes in Five Uncaria Species Endemic to China
title_fullStr Characterization and Comparative Analysis of Chloroplast Genomes in Five Uncaria Species Endemic to China
title_full_unstemmed Characterization and Comparative Analysis of Chloroplast Genomes in Five Uncaria Species Endemic to China
title_short Characterization and Comparative Analysis of Chloroplast Genomes in Five Uncaria Species Endemic to China
title_sort characterization and comparative analysis of chloroplast genomes in five uncaria species endemic to china
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9569570/
https://www.ncbi.nlm.nih.gov/pubmed/36232915
http://dx.doi.org/10.3390/ijms231911617
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