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Comparative analysis of chloroplast genomes of three medicinal Carpesium species: Genome structures and phylogenetic relationships

Carpesium (Asteraceae) is a genus that contains many plant species with important medicinal values. However, the lack of chloroplast genome research of this genus has greatly hindered the study of its molecular evolution and phylogenetic relationship. This study used the Illumina sequencing platform...

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Autores principales: Shi, Xingyu, Xu, Wenfen, Wan, Mingxiang, Sun, Qingwen, Chen, Qiyu, Zhao, Chao, Sun, Kaifen, Shu, Yanxia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9355210/
https://www.ncbi.nlm.nih.gov/pubmed/35930571
http://dx.doi.org/10.1371/journal.pone.0272563
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author Shi, Xingyu
Xu, Wenfen
Wan, Mingxiang
Sun, Qingwen
Chen, Qiyu
Zhao, Chao
Sun, Kaifen
Shu, Yanxia
author_facet Shi, Xingyu
Xu, Wenfen
Wan, Mingxiang
Sun, Qingwen
Chen, Qiyu
Zhao, Chao
Sun, Kaifen
Shu, Yanxia
author_sort Shi, Xingyu
collection PubMed
description Carpesium (Asteraceae) is a genus that contains many plant species with important medicinal values. However, the lack of chloroplast genome research of this genus has greatly hindered the study of its molecular evolution and phylogenetic relationship. This study used the Illumina sequencing platform to sequence three medicinal plants of the Carpesium genus: Carpesium abrotanoides, Carpesium cernuum, and Carpesium faberi, obtaining three complete chloroplast genome sequences after assembly and annotation. It was revealed that the three chloroplast genomes were typical quadripartite structures with lengths of 151,389 bp (C. abrotanoides), 151,278 bp (C. cernuum), and 151,250 bp (C. faberi), respectively. A total of 114 different genes were annotated, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Abundant SSR loci were detected in all three chloroplast genomes, with most composed of A/T. The expansion and contraction of the IR region indicate that the boundary regions of IR/SC are relatively conserved for the three species. Using C. abrotanoides as a reference, most of the non-coding regions of the chloroplast genomes were significantly different among the three species. Five different mutation hot spots (trnC-GCA-petN, psaI, petA-psbJ, ndhF, ycf1) with high nucleotide variability (Pi) can serve as potential DNA barcodes of Carpesium species. Additionally, phylogenetic evolution analysis of the three species suggests that C. cernuum has a closer genetic relationship to C. faberi than C. abrotanoides. Simultaneously, Carpesium is a monophyletic group closely related to the genus Inula. Complete chloroplast genomes of Carpesium species can help study the evolutionary and phylogenetic relationships and are expected to provide genetic marker assistance to identify Carpesium species.
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spelling pubmed-93552102022-08-06 Comparative analysis of chloroplast genomes of three medicinal Carpesium species: Genome structures and phylogenetic relationships Shi, Xingyu Xu, Wenfen Wan, Mingxiang Sun, Qingwen Chen, Qiyu Zhao, Chao Sun, Kaifen Shu, Yanxia PLoS One Research Article Carpesium (Asteraceae) is a genus that contains many plant species with important medicinal values. However, the lack of chloroplast genome research of this genus has greatly hindered the study of its molecular evolution and phylogenetic relationship. This study used the Illumina sequencing platform to sequence three medicinal plants of the Carpesium genus: Carpesium abrotanoides, Carpesium cernuum, and Carpesium faberi, obtaining three complete chloroplast genome sequences after assembly and annotation. It was revealed that the three chloroplast genomes were typical quadripartite structures with lengths of 151,389 bp (C. abrotanoides), 151,278 bp (C. cernuum), and 151,250 bp (C. faberi), respectively. A total of 114 different genes were annotated, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Abundant SSR loci were detected in all three chloroplast genomes, with most composed of A/T. The expansion and contraction of the IR region indicate that the boundary regions of IR/SC are relatively conserved for the three species. Using C. abrotanoides as a reference, most of the non-coding regions of the chloroplast genomes were significantly different among the three species. Five different mutation hot spots (trnC-GCA-petN, psaI, petA-psbJ, ndhF, ycf1) with high nucleotide variability (Pi) can serve as potential DNA barcodes of Carpesium species. Additionally, phylogenetic evolution analysis of the three species suggests that C. cernuum has a closer genetic relationship to C. faberi than C. abrotanoides. Simultaneously, Carpesium is a monophyletic group closely related to the genus Inula. Complete chloroplast genomes of Carpesium species can help study the evolutionary and phylogenetic relationships and are expected to provide genetic marker assistance to identify Carpesium species. Public Library of Science 2022-08-05 /pmc/articles/PMC9355210/ /pubmed/35930571 http://dx.doi.org/10.1371/journal.pone.0272563 Text en © 2022 Shi et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Shi, Xingyu
Xu, Wenfen
Wan, Mingxiang
Sun, Qingwen
Chen, Qiyu
Zhao, Chao
Sun, Kaifen
Shu, Yanxia
Comparative analysis of chloroplast genomes of three medicinal Carpesium species: Genome structures and phylogenetic relationships
title Comparative analysis of chloroplast genomes of three medicinal Carpesium species: Genome structures and phylogenetic relationships
title_full Comparative analysis of chloroplast genomes of three medicinal Carpesium species: Genome structures and phylogenetic relationships
title_fullStr Comparative analysis of chloroplast genomes of three medicinal Carpesium species: Genome structures and phylogenetic relationships
title_full_unstemmed Comparative analysis of chloroplast genomes of three medicinal Carpesium species: Genome structures and phylogenetic relationships
title_short Comparative analysis of chloroplast genomes of three medicinal Carpesium species: Genome structures and phylogenetic relationships
title_sort comparative analysis of chloroplast genomes of three medicinal carpesium species: genome structures and phylogenetic relationships
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9355210/
https://www.ncbi.nlm.nih.gov/pubmed/35930571
http://dx.doi.org/10.1371/journal.pone.0272563
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