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A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae): a traditional herbal medicinal genus
The herbal medicinal genus Aconitum L., belonging to the Ranunculaceae family, represents the earliest diverging lineage within the eudicots. It currently comprises of two subgenera, A. subgenus Lycoctonum and A. subg. Aconitum. The complete chloroplast (cp) genome sequences were characterized in th...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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PeerJ Inc.
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5680694/ https://www.ncbi.nlm.nih.gov/pubmed/29134154 http://dx.doi.org/10.7717/peerj.4018 |
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author | Kong, Hanghui Liu, Wanzhen Yao, Gang Gong, Wei |
author_facet | Kong, Hanghui Liu, Wanzhen Yao, Gang Gong, Wei |
author_sort | Kong, Hanghui |
collection | PubMed |
description | The herbal medicinal genus Aconitum L., belonging to the Ranunculaceae family, represents the earliest diverging lineage within the eudicots. It currently comprises of two subgenera, A. subgenus Lycoctonum and A. subg. Aconitum. The complete chloroplast (cp) genome sequences were characterized in three species: A. angustius, A. finetianum, and A. sinomontanum in subg. Lycoctonum and compared to other Aconitum species to clarify their phylogenetic relationship and provide molecular information for utilization of Aconitum species particularly in Eastern Asia. The length of the chloroplast genome sequences were 156,109 bp in A. angustius, 155,625 bp in A. finetianum and 157,215 bp in A. sinomontanum, with each species possessing 126 genes with 84 protein coding genes (PCGs). While genomic rearrangements were absent, structural variation was detected in the LSC/IR/SSC boundaries. Five pseudogenes were identified, among which Ψrps19 and Ψycf1 were in the LSC/IR/SSC boundaries, Ψrps16 and ΨinfA in the LSC region, and Ψycf15 in the IRb region. The nucleotide variability (Pi) of Aconitum was estimated to be 0.00549, with comparably higher variations in the LSC and SSC than the IR regions. Eight intergenic regions were revealed to be highly variable and a total of 58–62 simple sequence repeats (SSRs) were detected in all three species. More than 80% of SSRs were present in the LSC region. Altogether, 64.41% and 46.81% of SSRs are mononucleotides in subg. Lycoctonum and subg. Aconitum, respectively, while a higher percentage of di-, tri-, tetra-, and penta- SSRs were present in subg. Aconitum. Most species of subg. Aconitum in Eastern Asia were first used for phylogenetic analyses. The availability of the complete cp genome sequences of these species in subg. Lycoctonum will benefit future phylogenetic analyses and aid in germplasm utilization in Aconitum species. |
format | Online Article Text |
id | pubmed-5680694 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-56806942017-11-13 A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae): a traditional herbal medicinal genus Kong, Hanghui Liu, Wanzhen Yao, Gang Gong, Wei PeerJ Biodiversity The herbal medicinal genus Aconitum L., belonging to the Ranunculaceae family, represents the earliest diverging lineage within the eudicots. It currently comprises of two subgenera, A. subgenus Lycoctonum and A. subg. Aconitum. The complete chloroplast (cp) genome sequences were characterized in three species: A. angustius, A. finetianum, and A. sinomontanum in subg. Lycoctonum and compared to other Aconitum species to clarify their phylogenetic relationship and provide molecular information for utilization of Aconitum species particularly in Eastern Asia. The length of the chloroplast genome sequences were 156,109 bp in A. angustius, 155,625 bp in A. finetianum and 157,215 bp in A. sinomontanum, with each species possessing 126 genes with 84 protein coding genes (PCGs). While genomic rearrangements were absent, structural variation was detected in the LSC/IR/SSC boundaries. Five pseudogenes were identified, among which Ψrps19 and Ψycf1 were in the LSC/IR/SSC boundaries, Ψrps16 and ΨinfA in the LSC region, and Ψycf15 in the IRb region. The nucleotide variability (Pi) of Aconitum was estimated to be 0.00549, with comparably higher variations in the LSC and SSC than the IR regions. Eight intergenic regions were revealed to be highly variable and a total of 58–62 simple sequence repeats (SSRs) were detected in all three species. More than 80% of SSRs were present in the LSC region. Altogether, 64.41% and 46.81% of SSRs are mononucleotides in subg. Lycoctonum and subg. Aconitum, respectively, while a higher percentage of di-, tri-, tetra-, and penta- SSRs were present in subg. Aconitum. Most species of subg. Aconitum in Eastern Asia were first used for phylogenetic analyses. The availability of the complete cp genome sequences of these species in subg. Lycoctonum will benefit future phylogenetic analyses and aid in germplasm utilization in Aconitum species. PeerJ Inc. 2017-11-07 /pmc/articles/PMC5680694/ /pubmed/29134154 http://dx.doi.org/10.7717/peerj.4018 Text en ©2017 Kong et al. http://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/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Biodiversity Kong, Hanghui Liu, Wanzhen Yao, Gang Gong, Wei A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae): a traditional herbal medicinal genus |
title | A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae): a traditional herbal medicinal genus |
title_full | A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae): a traditional herbal medicinal genus |
title_fullStr | A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae): a traditional herbal medicinal genus |
title_full_unstemmed | A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae): a traditional herbal medicinal genus |
title_short | A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae): a traditional herbal medicinal genus |
title_sort | comparison of chloroplast genome sequences in aconitum (ranunculaceae): a traditional herbal medicinal genus |
topic | Biodiversity |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5680694/ https://www.ncbi.nlm.nih.gov/pubmed/29134154 http://dx.doi.org/10.7717/peerj.4018 |
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