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Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations

Journal Article · · Scientific Reports
 [1];  [2];  [3];  [2];  [2];  [2]
  1. Univ. of California, San Diego, CA (United States). Scripps Inst. of Oceanography; Universidad Autónoma de Baja California., Ensenada, Baja California (Mexico); DOE/OSTI
  2. Univ. of California, San Diego, CA (United States). Scripps Inst. of Oceanography
  3. Univ. of California, San Diego, CA (United States). Scripps Inst. of Oceanography; Univ. Andrés Bella, Santiago, (Chile)
+ Show Author Affiliations

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.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
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
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1624295
Journal Information:
Scientific Reports, Journal Name: Scientific Reports Journal Issue: 1 Vol. 7; ISSN 2045-2322
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English

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Cited By (4)

Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential journal January 2018
Metabolomic Fingerprinting of Salinispora From Atlantic Oceanic Islands journal December 2018
Awakening ancient polar Actinobacteria: diversity, evolution and specialized metabolite potential journal November 2019
Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora journal January 2019

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
bacterial genomics
microbiology
science & technology