Using Core Genome Alignments To Assign Bacterial Species

ABSTRACT With the exponential increase in the number of bacterial taxa with genome sequence data, a new standardized method to assign species designations is needed that is consistent with classically obtained taxonomic analyses. This is particularly acute for unculturable, obligate intracellular ba...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Matthew Chung, James B. Munro, Hervé Tettelin, Julie C. Dunning Hotopp
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	Anaplasma Rickettsia Rickettsiales Wolbachia bacterial taxonomy core genome alignment Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/31ca13ca02c94f3aad39daf373c55d3a
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:31ca13ca02c94f3aad39daf373c55d3a
record_format	dspace
spelling	oai:doaj.org-article:31ca13ca02c94f3aad39daf373c55d3a2021-12-02T18:39:46ZUsing Core Genome Alignments To Assign Bacterial Species10.1128/mSystems.00236-182379-5077https://doaj.org/article/31ca13ca02c94f3aad39daf373c55d3a2018-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00236-18https://doaj.org/toc/2379-5077ABSTRACT With the exponential increase in the number of bacterial taxa with genome sequence data, a new standardized method to assign species designations is needed that is consistent with classically obtained taxonomic analyses. This is particularly acute for unculturable, obligate intracellular bacteria with which classically defined methods, like DNA-DNA hybridization, cannot be used, such as those in the Rickettsiales. In this study, we generated nucleotide-based core genome alignments for a wide range of genera with classically defined species, as well as those within the Rickettsiales. We created a workflow that uses the length, sequence identity, and phylogenetic relationships inferred from core genome alignments to assign genus and species designations that recapitulate classically obtained results. Using this method, most classically defined bacterial genera have a core genome alignment that is ≥10% of the average input genome length. Both Anaplasma and Neorickettsia fail to meet this criterion, indicating that the taxonomy of these genera should be reexamined. Consistently, genomes from organisms with the same species epithet have ≥96.8% identity of their core genome alignments. Additionally, these core genome alignments can be used to generate phylogenomic trees to identify monophyletic clades that define species and neighbor-network trees to assess recombination across different taxa. By these criteria, Wolbachia organisms are delineated into species different from the currently used supergroup designations, while Rickettsia organisms are delineated into 9 distinct species, compared to the current 27 species. By using core genome alignments to assign taxonomic designations, we aim to provide a high-resolution, robust method to guide bacterial nomenclature that is aligned with classically obtained results. IMPORTANCE With the increasing availability of genome sequences, we sought to develop and apply a robust, portable, and high-resolution method for the assignment of genera and species designations that can recapitulate classically defined taxonomic designations. Using cutoffs derived from the lengths and sequence identities of core genome alignments along with phylogenetic analyses, we sought to evaluate or reevaluate genus- and species-level designations for diverse taxa, with an emphasis on the order Rickettsiales, where species designations have been applied inconsistently. Our results indicate that the Rickettsia genus has an overabundance of species designations, that the current Anaplasma and Neorickettsia genus designations are both too broad and need to be divided, and that there are clear demarcations of Wolbachia species that do not align precisely with the existing supergroup designations.Matthew ChungJames B. MunroHervé TettelinJulie C. Dunning HotoppAmerican Society for MicrobiologyarticleAnaplasmaRickettsiaRickettsialesWolbachiabacterial taxonomycore genome alignmentMicrobiologyQR1-502ENmSystems, Vol 3, Iss 6 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Anaplasma Rickettsia Rickettsiales Wolbachia bacterial taxonomy core genome alignment Microbiology QR1-502
spellingShingle	Anaplasma Rickettsia Rickettsiales Wolbachia bacterial taxonomy core genome alignment Microbiology QR1-502 Matthew Chung James B. Munro Hervé Tettelin Julie C. Dunning Hotopp Using Core Genome Alignments To Assign Bacterial Species
description	ABSTRACT With the exponential increase in the number of bacterial taxa with genome sequence data, a new standardized method to assign species designations is needed that is consistent with classically obtained taxonomic analyses. This is particularly acute for unculturable, obligate intracellular bacteria with which classically defined methods, like DNA-DNA hybridization, cannot be used, such as those in the Rickettsiales. In this study, we generated nucleotide-based core genome alignments for a wide range of genera with classically defined species, as well as those within the Rickettsiales. We created a workflow that uses the length, sequence identity, and phylogenetic relationships inferred from core genome alignments to assign genus and species designations that recapitulate classically obtained results. Using this method, most classically defined bacterial genera have a core genome alignment that is ≥10% of the average input genome length. Both Anaplasma and Neorickettsia fail to meet this criterion, indicating that the taxonomy of these genera should be reexamined. Consistently, genomes from organisms with the same species epithet have ≥96.8% identity of their core genome alignments. Additionally, these core genome alignments can be used to generate phylogenomic trees to identify monophyletic clades that define species and neighbor-network trees to assess recombination across different taxa. By these criteria, Wolbachia organisms are delineated into species different from the currently used supergroup designations, while Rickettsia organisms are delineated into 9 distinct species, compared to the current 27 species. By using core genome alignments to assign taxonomic designations, we aim to provide a high-resolution, robust method to guide bacterial nomenclature that is aligned with classically obtained results. IMPORTANCE With the increasing availability of genome sequences, we sought to develop and apply a robust, portable, and high-resolution method for the assignment of genera and species designations that can recapitulate classically defined taxonomic designations. Using cutoffs derived from the lengths and sequence identities of core genome alignments along with phylogenetic analyses, we sought to evaluate or reevaluate genus- and species-level designations for diverse taxa, with an emphasis on the order Rickettsiales, where species designations have been applied inconsistently. Our results indicate that the Rickettsia genus has an overabundance of species designations, that the current Anaplasma and Neorickettsia genus designations are both too broad and need to be divided, and that there are clear demarcations of Wolbachia species that do not align precisely with the existing supergroup designations.
format	article
author	Matthew Chung James B. Munro Hervé Tettelin Julie C. Dunning Hotopp
author_facet	Matthew Chung James B. Munro Hervé Tettelin Julie C. Dunning Hotopp
author_sort	Matthew Chung
title	Using Core Genome Alignments To Assign Bacterial Species
title_short	Using Core Genome Alignments To Assign Bacterial Species
title_full	Using Core Genome Alignments To Assign Bacterial Species
title_fullStr	Using Core Genome Alignments To Assign Bacterial Species
title_full_unstemmed	Using Core Genome Alignments To Assign Bacterial Species
title_sort	using core genome alignments to assign bacterial species
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/31ca13ca02c94f3aad39daf373c55d3a
work_keys_str_mv	AT matthewchung usingcoregenomealignmentstoassignbacterialspecies AT jamesbmunro usingcoregenomealignmentstoassignbacterialspecies AT hervetettelin usingcoregenomealignmentstoassignbacterialspecies AT juliecdunninghotopp usingcoregenomealignmentstoassignbacterialspecies
_version_	1718377730823684096

Using Core Genome Alignments To Assign Bacterial Species

Ejemplares similares