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 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.
- Authors:
-
- Univ. of California, San Diego, CA (United States). Scripps Inst. of Oceanography; Universidad Autónoma de Baja California., Ensenada, Baja California (Mexico)
- Univ. of California, San Diego, CA (United States). Scripps Inst. of Oceanography
- Univ. of California, San Diego, CA (United States). Scripps Inst. of Oceanography; Univ. Andrés Bella, Santiago, (Chile)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); National Science Foundation (NSF); National Institutes of Health (NIH); Amazon Web Services; Consejo Nacional de Ciencia y Tecnología; FCT/MEC
- OSTI Identifier:
- 1624295
- Grant/Contract Number:
- AC02-05CH11231; OCE-1235142; 2U19TW007401; 5R01GM085770; Fondecyt Iniciación 11140666; CONACyT-213497; PTDC/QUI-QUI/119116/2010; IF/00700/2014
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Scientific Reports
- Additional Journal Information:
- Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 2045-2322
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; science & technology; bacterial genomics; microbiology
Citation Formats
Millán-Aguiñaga, Natalie, Chavarria, Krystle L., Ugalde, Juan A., Letzel, Anne-Catrin, Rouse, Greg W., and Jensen, Paul R. Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations. United States: N. p., 2017.
Web. doi:10.1038/s41598-017-02845-3.
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. United States. https://doi.org/10.1038/s41598-017-02845-3
Millán-Aguiñaga, Natalie, Chavarria, Krystle L., Ugalde, Juan A., Letzel, Anne-Catrin, Rouse, Greg W., and Jensen, Paul R. Thu .
"Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations". United States. https://doi.org/10.1038/s41598-017-02845-3. https://www.osti.gov/servlets/purl/1624295.
@article{osti_1624295,
title = {Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations},
author = {Millán-Aguiñaga, Natalie and Chavarria, Krystle L. and Ugalde, Juan A. and Letzel, Anne-Catrin and Rouse, Greg W. and Jensen, Paul R.},
abstractNote = {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.},
doi = {10.1038/s41598-017-02845-3},
journal = {Scientific Reports},
number = 1,
volume = 7,
place = {United States},
year = {Thu Jun 15 00:00:00 EDT 2017},
month = {Thu Jun 15 00:00:00 EDT 2017}
}
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Works referencing / citing this record:
Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora
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