Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations

Abstract 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 majo...

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Autores principales:	Natalie Millán-Aguiñaga, Krystle L. Chavarria, Juan A. Ugalde, Anne-Catrin Letzel, Greg W. Rouse, Paul R. Jensen
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/72d2d509d99847f2a9d72e282bad86a6
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spelling	oai:doaj.org-article:72d2d509d99847f2a9d72e282bad86a62021-12-02T12:32:16ZPhylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations10.1038/s41598-017-02845-32045-2322https://doaj.org/article/72d2d509d99847f2a9d72e282bad86a62017-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-02845-3https://doaj.org/toc/2045-2322Abstract 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.Natalie Millán-AguiñagaKrystle L. ChavarriaJuan A. UgaldeAnne-Catrin LetzelGreg W. RousePaul R. JensenNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-11 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Natalie Millán-Aguiñaga Krystle L. Chavarria Juan A. Ugalde Anne-Catrin Letzel Greg W. Rouse Paul R. Jensen Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations
description	Abstract 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	article
author	Natalie Millán-Aguiñaga Krystle L. Chavarria Juan A. Ugalde Anne-Catrin Letzel Greg W. Rouse Paul R. Jensen
author_facet	Natalie Millán-Aguiñaga Krystle L. Chavarria Juan A. Ugalde Anne-Catrin Letzel Greg W. Rouse Paul R. Jensen
author_sort	Natalie Millán-Aguiñaga
title	Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations
title_short	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_sort	phylogenomic insight into salinispora (bacteria, actinobacteria) species designations
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/72d2d509d99847f2a9d72e282bad86a6
work_keys_str_mv	AT nataliemillanaguinaga phylogenomicinsightintosalinisporabacteriaactinobacteriaspeciesdesignations AT krystlelchavarria phylogenomicinsightintosalinisporabacteriaactinobacteriaspeciesdesignations AT juanaugalde phylogenomicinsightintosalinisporabacteriaactinobacteriaspeciesdesignations AT annecatrinletzel phylogenomicinsightintosalinisporabacteriaactinobacteriaspeciesdesignations AT gregwrouse phylogenomicinsightintosalinisporabacteriaactinobacteriaspeciesdesignations AT paulrjensen phylogenomicinsightintosalinisporabacteriaactinobacteriaspeciesdesignations
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Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations

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