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Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations
Bacteria represent the most genetically diverse kingdom of life. While great progress has been made in describing this diversity, it remains difficult to identify the phylogenetic and ecological characteristics that delineate groups of bacteria that possess species-like properties. One major challen...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5472633/ https://www.ncbi.nlm.nih.gov/pubmed/28620214 http://dx.doi.org/10.1038/s41598-017-02845-3 |
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author | Millán-Aguiñaga, Natalie Chavarria, Krystle L. Ugalde, Juan A. Letzel, Anne-Catrin Rouse, Greg W. Jensen, Paul R. |
author_facet | Millán-Aguiñaga, Natalie Chavarria, Krystle L. Ugalde, Juan A. Letzel, Anne-Catrin Rouse, Greg W. Jensen, Paul R. |
author_sort | Millán-Aguiñaga, Natalie |
collection | PubMed |
description | Bacteria represent the most genetically diverse kingdom of life. While great progress has been made in describing this diversity, it remains difficult to identify the phylogenetic and ecological characteristics that delineate groups of bacteria that possess species-like properties. One major challenge associated with species delineations is that not all shared genes have the same evolutionary history, and thus the choice of loci can have a major impact on phylogenetic reconstruction. Sequencing the genomes of large numbers of closely related strains provides new opportunities to distinguish ancestral from acquired alleles and assess the effects of recombination on phylogenetic inference. Here we analyzed the genomes of 119 strains of the marine actinomycete genus Salinispora, which is currently comprised of three named species that share 99% 16S rRNA gene sequence identity. While 63% of the core genome showed evidence of recombination, this had no effect on species-level phylogenomic resolution. Recombination did however blur intra-species relationships and biogeographic resolution. The genome-wide average nucleotide identity provided a new perspective on Salinispora diversity, revealing as many as seven new species. Patterns of orthologous group distributions reveal a genetic basis to delineation the candidate taxa and insight into the levels of genetic cohesion associated with bacterial species. |
format | Online Article Text |
id | pubmed-5472633 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-54726332017-06-21 Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations Millán-Aguiñaga, Natalie Chavarria, Krystle L. Ugalde, Juan A. Letzel, Anne-Catrin Rouse, Greg W. Jensen, Paul R. Sci Rep Article Bacteria represent the most genetically diverse kingdom of life. While great progress has been made in describing this diversity, it remains difficult to identify the phylogenetic and ecological characteristics that delineate groups of bacteria that possess species-like properties. One major challenge associated with species delineations is that not all shared genes have the same evolutionary history, and thus the choice of loci can have a major impact on phylogenetic reconstruction. Sequencing the genomes of large numbers of closely related strains provides new opportunities to distinguish ancestral from acquired alleles and assess the effects of recombination on phylogenetic inference. Here we analyzed the genomes of 119 strains of the marine actinomycete genus Salinispora, which is currently comprised of three named species that share 99% 16S rRNA gene sequence identity. While 63% of the core genome showed evidence of recombination, this had no effect on species-level phylogenomic resolution. Recombination did however blur intra-species relationships and biogeographic resolution. The genome-wide average nucleotide identity provided a new perspective on Salinispora diversity, revealing as many as seven new species. Patterns of orthologous group distributions reveal a genetic basis to delineation the candidate taxa and insight into the levels of genetic cohesion associated with bacterial species. Nature Publishing Group UK 2017-06-15 /pmc/articles/PMC5472633/ /pubmed/28620214 http://dx.doi.org/10.1038/s41598-017-02845-3 Text en © The Author(s) 2017 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Millán-Aguiñaga, Natalie Chavarria, Krystle L. Ugalde, Juan A. Letzel, Anne-Catrin Rouse, Greg W. Jensen, Paul R. Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations |
title | Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations |
title_full | Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations |
title_fullStr | Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations |
title_full_unstemmed | Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations |
title_short | Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations |
title_sort | phylogenomic insight into salinispora (bacteria, actinobacteria) species designations |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5472633/ https://www.ncbi.nlm.nih.gov/pubmed/28620214 http://dx.doi.org/10.1038/s41598-017-02845-3 |
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