Cargando…
Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae
BACKGROUND: The green algae represent one of the most successful groups of photosynthetic eukaryotes, but compared to their land plant relatives, surprisingly little is known about their evolutionary history. This is in great part due to the difficulty of recognizing species diversity behind morphol...
Autores principales: | , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4189289/ https://www.ncbi.nlm.nih.gov/pubmed/25270575 http://dx.doi.org/10.1186/s12862-014-0211-2 |
_version_ | 1782338343365771264 |
---|---|
author | Lemieux, Claude Otis, Christian Turmel, Monique |
author_facet | Lemieux, Claude Otis, Christian Turmel, Monique |
author_sort | Lemieux, Claude |
collection | PubMed |
description | BACKGROUND: The green algae represent one of the most successful groups of photosynthetic eukaryotes, but compared to their land plant relatives, surprisingly little is known about their evolutionary history. This is in great part due to the difficulty of recognizing species diversity behind morphologically similar organisms. The Trebouxiophyceae is a species-rich class of the Chlorophyta that includes symbionts (e.g. lichenized algae) as well as free-living green algae. Members of this group display remarkable ecological variation, occurring in aquatic, terrestrial and aeroterrestrial environments. Because a reliable backbone phylogeny is essential to understand the evolutionary history of the Trebouxiophyceae, we sought to identify the relationships among the major trebouxiophycean lineages that have been previously recognized in nuclear-encoded 18S rRNA phylogenies. To this end, we used a chloroplast phylogenomic approach. RESULTS: We determined the sequences of 29 chlorophyte chloroplast genomes and assembled amino acid and nucleotide data sets derived from 79 chloroplast genes of 61 chlorophytes, including 35 trebouxiophyceans. The amino acid- and nucleotide-based phylogenies inferred using maximum likelihood and Bayesian methods and various models of sequence evolution revealed essentially the same relationships for the trebouxiophyceans. Two major groups were identified: a strongly supported clade of 29 taxa (core trebouxiophyceans) that is sister to the Chlorophyceae + Ulvophyceae and a clade comprising the Chlorellales and Pedinophyceae that represents a basal divergence relative to the former group. The core trebouxiophyceans form a grade of strongly supported clades that include a novel lineage represented by the desert crust alga Pleurastrosarcina brevispinosa. The assemblage composed of the Oocystis and Geminella clades is the deepest divergence of the core trebouxiophyceans. Like most of the chlorellaleans, early-diverging core trebouxiophyceans are predominantly planktonic species, whereas core trebouxiophyceans occupying more derived lineages are mostly terrestrial or aeroterrestrial algae. CONCLUSIONS: Our phylogenomic study provides a solid foundation for addressing fundamental questions related to the biology and ecology of the Trebouxiophyceae. The inferred trees reveal that this class is not monophyletic; they offer new insights not only into the internal structure of the class but also into the lifestyle of its founding members and subsequent adaptations to changing environments. |
format | Online Article Text |
id | pubmed-4189289 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-41892892014-10-09 Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae Lemieux, Claude Otis, Christian Turmel, Monique BMC Evol Biol Research Article BACKGROUND: The green algae represent one of the most successful groups of photosynthetic eukaryotes, but compared to their land plant relatives, surprisingly little is known about their evolutionary history. This is in great part due to the difficulty of recognizing species diversity behind morphologically similar organisms. The Trebouxiophyceae is a species-rich class of the Chlorophyta that includes symbionts (e.g. lichenized algae) as well as free-living green algae. Members of this group display remarkable ecological variation, occurring in aquatic, terrestrial and aeroterrestrial environments. Because a reliable backbone phylogeny is essential to understand the evolutionary history of the Trebouxiophyceae, we sought to identify the relationships among the major trebouxiophycean lineages that have been previously recognized in nuclear-encoded 18S rRNA phylogenies. To this end, we used a chloroplast phylogenomic approach. RESULTS: We determined the sequences of 29 chlorophyte chloroplast genomes and assembled amino acid and nucleotide data sets derived from 79 chloroplast genes of 61 chlorophytes, including 35 trebouxiophyceans. The amino acid- and nucleotide-based phylogenies inferred using maximum likelihood and Bayesian methods and various models of sequence evolution revealed essentially the same relationships for the trebouxiophyceans. Two major groups were identified: a strongly supported clade of 29 taxa (core trebouxiophyceans) that is sister to the Chlorophyceae + Ulvophyceae and a clade comprising the Chlorellales and Pedinophyceae that represents a basal divergence relative to the former group. The core trebouxiophyceans form a grade of strongly supported clades that include a novel lineage represented by the desert crust alga Pleurastrosarcina brevispinosa. The assemblage composed of the Oocystis and Geminella clades is the deepest divergence of the core trebouxiophyceans. Like most of the chlorellaleans, early-diverging core trebouxiophyceans are predominantly planktonic species, whereas core trebouxiophyceans occupying more derived lineages are mostly terrestrial or aeroterrestrial algae. CONCLUSIONS: Our phylogenomic study provides a solid foundation for addressing fundamental questions related to the biology and ecology of the Trebouxiophyceae. The inferred trees reveal that this class is not monophyletic; they offer new insights not only into the internal structure of the class but also into the lifestyle of its founding members and subsequent adaptations to changing environments. BioMed Central 2014-10-01 /pmc/articles/PMC4189289/ /pubmed/25270575 http://dx.doi.org/10.1186/s12862-014-0211-2 Text en © Lemieux et al.; licensee BioMed Central Ltd. 2014 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, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Lemieux, Claude Otis, Christian Turmel, Monique Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae |
title | Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae |
title_full | Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae |
title_fullStr | Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae |
title_full_unstemmed | Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae |
title_short | Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae |
title_sort | chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class trebouxiophyceae |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4189289/ https://www.ncbi.nlm.nih.gov/pubmed/25270575 http://dx.doi.org/10.1186/s12862-014-0211-2 |
work_keys_str_mv | AT lemieuxclaude chloroplastphylogenomicanalysisresolvesdeeplevelrelationshipswithinthegreenalgalclasstrebouxiophyceae AT otischristian chloroplastphylogenomicanalysisresolvesdeeplevelrelationshipswithinthegreenalgalclasstrebouxiophyceae AT turmelmonique chloroplastphylogenomicanalysisresolvesdeeplevelrelationshipswithinthegreenalgalclasstrebouxiophyceae |