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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...

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Autores principales: Pfanzelt, Simon, Albach, Dirk C., von Hagen, K. Bernhard
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2019
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.
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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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