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Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales)
Astelia pumila (G.Forst.) Gaudich. (Asteliaceae, Asparagales) is a major element of West Patagonian cushion peat bog vegetation. With the aim to identify appropriate chloroplast markers for the use in a phylogeographic study, the complete chloroplast genomes of five A. pumila accessions from almost...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6339776/ https://www.ncbi.nlm.nih.gov/pubmed/30671303 http://dx.doi.org/10.7717/peerj.6244 |
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author | Pfanzelt, Simon Albach, Dirk C. von Hagen, K. Bernhard |
author_facet | Pfanzelt, Simon Albach, Dirk C. von Hagen, K. Bernhard |
author_sort | Pfanzelt, Simon |
collection | PubMed |
description | Astelia pumila (G.Forst.) Gaudich. (Asteliaceae, Asparagales) is a major element of West Patagonian cushion peat bog vegetation. With the aim to identify appropriate chloroplast markers for the use in a phylogeographic study, the complete chloroplast genomes of five A. pumila accessions from almost the entire geographical range of the species were assembled and screened for variable positions. The chloroplast genome sequence was obtained via a mapping approach, using Eustrephus latifolius (Asparagaceae) as a reference. The chloroplast genome of A. pumila varies in length from 158,215 bp to 158,221 bp, containing a large single copy region of 85,981–85,983 bp, a small single copy region of 18,182–18,186 bp and two inverted repeats of 27,026 bp. Genome annotation predicted a total of 113 genes, including 30 tRNA and four rRNA genes. Sequence comparisons revealed a very low degree of intraspecific genetic variability, as only 37 variable sites (18 indels, 18 single nucleotide polymorphisms, one 3-bp mutation)—most of them autapomorphies—were found among the five assembled chloroplast genomes. A Maximum Likelihood analysis, based on whole chloroplast genome sequences of several Asparagales accessions representing six of the currently recognized 14 families (sensu APG IV), confirmed the phylogenetic position of A. pumila. The chloroplast genome of A. pumila is the first to be reported for a member of the astelioid clade (14 genera with c. 215 species), a basally branching group within Asparagales. |
format | Online Article Text |
id | pubmed-6339776 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-63397762019-01-22 Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales) Pfanzelt, Simon Albach, Dirk C. von Hagen, K. Bernhard PeerJ Biogeography Astelia pumila (G.Forst.) Gaudich. (Asteliaceae, Asparagales) is a major element of West Patagonian cushion peat bog vegetation. With the aim to identify appropriate chloroplast markers for the use in a phylogeographic study, the complete chloroplast genomes of five A. pumila accessions from almost the entire geographical range of the species were assembled and screened for variable positions. The chloroplast genome sequence was obtained via a mapping approach, using Eustrephus latifolius (Asparagaceae) as a reference. The chloroplast genome of A. pumila varies in length from 158,215 bp to 158,221 bp, containing a large single copy region of 85,981–85,983 bp, a small single copy region of 18,182–18,186 bp and two inverted repeats of 27,026 bp. Genome annotation predicted a total of 113 genes, including 30 tRNA and four rRNA genes. Sequence comparisons revealed a very low degree of intraspecific genetic variability, as only 37 variable sites (18 indels, 18 single nucleotide polymorphisms, one 3-bp mutation)—most of them autapomorphies—were found among the five assembled chloroplast genomes. A Maximum Likelihood analysis, based on whole chloroplast genome sequences of several Asparagales accessions representing six of the currently recognized 14 families (sensu APG IV), confirmed the phylogenetic position of A. pumila. The chloroplast genome of A. pumila is the first to be reported for a member of the astelioid clade (14 genera with c. 215 species), a basally branching group within Asparagales. PeerJ Inc. 2019-01-17 /pmc/articles/PMC6339776/ /pubmed/30671303 http://dx.doi.org/10.7717/peerj.6244 Text en ©2019 Pfanzelt 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 | Biogeography Pfanzelt, Simon Albach, Dirk C. von Hagen, K. Bernhard Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales) |
title | Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales) |
title_full | Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales) |
title_fullStr | Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales) |
title_full_unstemmed | Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales) |
title_short | Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales) |
title_sort | extremely low levels of chloroplast genome sequence variability in astelia pumila (asteliaceae, asparagales) |
topic | Biogeography |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6339776/ https://www.ncbi.nlm.nih.gov/pubmed/30671303 http://dx.doi.org/10.7717/peerj.6244 |
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