Taxonomic Identity Resolution of Highly Phylogenetically Related Strains and Selection of Phylogenetic Markers by Using Genome-Scale Methods: The Bacillus pumilus Group Case

Espariz, Martín; Zuljan, Federico A.; Esteban, Luis; Magni, Christian

Taxonomic Identity Resolution of Highly Phylogenetically Related Strains and Selection of Phylogenetic Markers by Using Genome-Scale Methods: The Bacillus pumilus Group Case

dc.creator	Espariz, Martín
dc.creator	Zuljan, Federico A.
dc.creator	Esteban, Luis
dc.creator	Magni, Christian
dc.date.accessioned	2021-03-09T17:53:36Z
dc.date.available	2021-03-09T17:53:36Z
dc.date.issued	2016-09-22
dc.description	Bacillus pumilus group strains have been studied due their agronomic, biotechnological or pharmaceutical potential. Classifying strains of this taxonomic group at species level is a challenging procedure since it is composed of seven species that share among them over 99.5% of 16S rRNA gene identity. In this study, first, a whole-genome in silico approach was used to accurately demarcate B. pumilus group strains, as a case of highly phylogenetically related taxa, at the species level. In order to achieve that and consequently to validate or correct taxonomic identities of genomes in public databases, an average nucleotide identity correlation, a core-based phylogenomic and a gene function repertory analyses were performed. Eventually, more than 50% such genomes were found to be misclassified. Hierarchical clustering of gene functional repertoires was also used to infer ecotypes among B. pumilus group species. Furthermore, for the first time the machine-learning algorithm Random Forest was used to rank genes in order of their importance for species classification. We found that ybbP, a gene involved in the synthesis of cyclic di-AMP, was the most important gene for accurately predicting species identity among B. pumilus group strains. Finally, principal component analysis was used to classify strains based on the distances between their ybbP genes. The methodologies described could be utilized more broadly to identify other highly phylogenetically related species in metagenomic or epidemiological assessments.	es
dc.description.fil	Fil: Espariz, Martín. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular de Rosario (IBR-CONICET). Rosario; Argentina	es
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dc.identifier.other	https://doi.org/10.1371/journal.pone.0163098
dc.identifier.uri	http://hdl.handle.net/2133/20073
dc.language.iso	eng	es
dc.relation	info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0163098
dc.rights	openAccess	es
dc.rights.holder	Autores	es
dc.rights.text	http://creativecommons.org/licenses/by/4.0/	es
dc.rights.uri	https://creativecommons.org/licenses/by/4.0/	*
dc.subject	Microbiology	es
dc.subject	Genetics	es
dc.subject	Evolutionary Biology	es
dc.subject	Bacterial genomics	es
dc.subject	Principal component analysis	es
dc.subject	Phylogenetics	es
dc.subject	Bacillus pumilus	es
dc.subject	https://purl.org/becyt/ford/1.6
dc.subject	Ciencias biológicas
dc.title	Taxonomic Identity Resolution of Highly Phylogenetically Related Strains and Selection of Phylogenetic Markers by Using Genome-Scale Methods: The Bacillus pumilus Group Case	es
dc.type	other
dc.type	Producción en Tecnología
dc.type	publishedVersion
dc.type.collection	produccion_tecnologia
dc.type.version	publishedVersion	es