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Complete chloroplast genome comparisons for Pityopsis (Asteraceae)

Pityopsis includes several regionally and one federally endangered species of herbaceous perennials. Four species are highly localized, including the federally endangered P. ruthii. The genus includes several ploidy levels and interesting ecological traits such as drought tolerance and fire-dependen...

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Autores principales: Hatmaker, E. Anne, Wadl, Phillip A., Rinehart, Timothy A., Carroll, Jennifer, Lane, Thomas S., Trigiano, Robert N., Staton, Margaret E., Schilling, Edward E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7769439/
https://www.ncbi.nlm.nih.gov/pubmed/33370297
http://dx.doi.org/10.1371/journal.pone.0241391
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author Hatmaker, E. Anne
Wadl, Phillip A.
Rinehart, Timothy A.
Carroll, Jennifer
Lane, Thomas S.
Trigiano, Robert N.
Staton, Margaret E.
Schilling, Edward E.
author_facet Hatmaker, E. Anne
Wadl, Phillip A.
Rinehart, Timothy A.
Carroll, Jennifer
Lane, Thomas S.
Trigiano, Robert N.
Staton, Margaret E.
Schilling, Edward E.
author_sort Hatmaker, E. Anne
collection PubMed
description Pityopsis includes several regionally and one federally endangered species of herbaceous perennials. Four species are highly localized, including the federally endangered P. ruthii. The genus includes several ploidy levels and interesting ecological traits such as drought tolerance and fire-dependent flowering. Results from previous cladistic analyses of morphology and from initial DNA sequence studies did not agree with one another or with the infrageneric taxonomic classification, with the result that infrageneric relationships remain unresolved. We sequenced, assembled, and compared the chloroplast (cp) genomes of 12 species or varieties of Pityopsis to better understand generic evolution. A reference cp genome 152,569 bp in length was assembled de novo from P. falcata. Reads from other sampled species were then aligned to the P. falcata reference and individual chloroplast genomes were assembled for each, with manual gapfilling and polishing. After removing the duplicated second inverted region, a multiple sequence alignment of the cp genomes was used to construct a maximum likelihood (ML) phylogeny for the twelve cp genomes. Additionally, we constructed a ML phylogeny from the nuclear ribosomal repeat region after mapping reads to the Helianthus annuus region. The chloroplast phylogeny supported two clades. Previously proposed clades and taxonomic sections within the genus were largely unsupported by both nuclear and chloroplast phylogenies. Our results provide tools for exploring hybridity and examining the physiological and genetic basis for drought tolerance and fire-dependent flowering. This study will inform breeding and conservation practices, and general knowledge of evolutionary history, hybridization, and speciation within Pityopsis.
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spelling pubmed-77694392021-01-08 Complete chloroplast genome comparisons for Pityopsis (Asteraceae) Hatmaker, E. Anne Wadl, Phillip A. Rinehart, Timothy A. Carroll, Jennifer Lane, Thomas S. Trigiano, Robert N. Staton, Margaret E. Schilling, Edward E. PLoS One Research Article Pityopsis includes several regionally and one federally endangered species of herbaceous perennials. Four species are highly localized, including the federally endangered P. ruthii. The genus includes several ploidy levels and interesting ecological traits such as drought tolerance and fire-dependent flowering. Results from previous cladistic analyses of morphology and from initial DNA sequence studies did not agree with one another or with the infrageneric taxonomic classification, with the result that infrageneric relationships remain unresolved. We sequenced, assembled, and compared the chloroplast (cp) genomes of 12 species or varieties of Pityopsis to better understand generic evolution. A reference cp genome 152,569 bp in length was assembled de novo from P. falcata. Reads from other sampled species were then aligned to the P. falcata reference and individual chloroplast genomes were assembled for each, with manual gapfilling and polishing. After removing the duplicated second inverted region, a multiple sequence alignment of the cp genomes was used to construct a maximum likelihood (ML) phylogeny for the twelve cp genomes. Additionally, we constructed a ML phylogeny from the nuclear ribosomal repeat region after mapping reads to the Helianthus annuus region. The chloroplast phylogeny supported two clades. Previously proposed clades and taxonomic sections within the genus were largely unsupported by both nuclear and chloroplast phylogenies. Our results provide tools for exploring hybridity and examining the physiological and genetic basis for drought tolerance and fire-dependent flowering. This study will inform breeding and conservation practices, and general knowledge of evolutionary history, hybridization, and speciation within Pityopsis. Public Library of Science 2020-12-28 /pmc/articles/PMC7769439/ /pubmed/33370297 http://dx.doi.org/10.1371/journal.pone.0241391 Text en https://creativecommons.org/publicdomain/zero/1.0/ This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 (https://creativecommons.org/publicdomain/zero/1.0/) public domain dedication.
spellingShingle Research Article
Hatmaker, E. Anne
Wadl, Phillip A.
Rinehart, Timothy A.
Carroll, Jennifer
Lane, Thomas S.
Trigiano, Robert N.
Staton, Margaret E.
Schilling, Edward E.
Complete chloroplast genome comparisons for Pityopsis (Asteraceae)
title Complete chloroplast genome comparisons for Pityopsis (Asteraceae)
title_full Complete chloroplast genome comparisons for Pityopsis (Asteraceae)
title_fullStr Complete chloroplast genome comparisons for Pityopsis (Asteraceae)
title_full_unstemmed Complete chloroplast genome comparisons for Pityopsis (Asteraceae)
title_short Complete chloroplast genome comparisons for Pityopsis (Asteraceae)
title_sort complete chloroplast genome comparisons for pityopsis (asteraceae)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7769439/
https://www.ncbi.nlm.nih.gov/pubmed/33370297
http://dx.doi.org/10.1371/journal.pone.0241391
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