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Phylogenomics picks out the par excellence markers for species phylogeny in the genus Staphylococcus

Although genome sequencing has become a very promising approach to conduct microbial taxonomy, few labs have the resources to afford this especially when dealing with data sets of hundreds to thousands of isolates. The goal of this study was to identify the most adequate loci for inferring the phylo...

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Autores principales: Graña-Miraglia, Lucia, Arreguín-Pérez, César, López-Leal, Gamaliel, Muñoz, Alan, Pérez-Oseguera, Angeles, Miranda-Miranda, Estefan, Cossío-Bayúgar, Raquel, Castillo-Ramírez, Santiago
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6203942/
https://www.ncbi.nlm.nih.gov/pubmed/30386709
http://dx.doi.org/10.7717/peerj.5839
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author Graña-Miraglia, Lucia
Arreguín-Pérez, César
López-Leal, Gamaliel
Muñoz, Alan
Pérez-Oseguera, Angeles
Miranda-Miranda, Estefan
Cossío-Bayúgar, Raquel
Castillo-Ramírez, Santiago
author_facet Graña-Miraglia, Lucia
Arreguín-Pérez, César
López-Leal, Gamaliel
Muñoz, Alan
Pérez-Oseguera, Angeles
Miranda-Miranda, Estefan
Cossío-Bayúgar, Raquel
Castillo-Ramírez, Santiago
author_sort Graña-Miraglia, Lucia
collection PubMed
description Although genome sequencing has become a very promising approach to conduct microbial taxonomy, few labs have the resources to afford this especially when dealing with data sets of hundreds to thousands of isolates. The goal of this study was to identify the most adequate loci for inferring the phylogeny of the species within the genus Staphylococcus; with the idea that those who cannot afford whole genome sequencing can use these loci to carry out species assignation confidently. We retrieved 177 orthologous groups (OGs) by using a genome-based phylogeny and an average nucleotide identity analysis. The top 26 OGs showed topologies similar to the species tree and the concatenation of them yielded a topology almost identical to that of the species tree. Furthermore, a phylogeny of just the top seven OGs could be used for species assignment. We sequenced four staphylococcus isolates to test the 26 OGs and found that these OGs were far superior to commonly used markers for this genus. On the whole, our procedure allowed identification of the most adequate markers for inferring the phylogeny within the genus Staphylococcus. We anticipate that this approach will be employed for the identification of the most suitable markers for other bacterial genera and can be very helpful to sort out poorly classified genera.
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spelling pubmed-62039422018-10-31 Phylogenomics picks out the par excellence markers for species phylogeny in the genus Staphylococcus Graña-Miraglia, Lucia Arreguín-Pérez, César López-Leal, Gamaliel Muñoz, Alan Pérez-Oseguera, Angeles Miranda-Miranda, Estefan Cossío-Bayúgar, Raquel Castillo-Ramírez, Santiago PeerJ Ecology Although genome sequencing has become a very promising approach to conduct microbial taxonomy, few labs have the resources to afford this especially when dealing with data sets of hundreds to thousands of isolates. The goal of this study was to identify the most adequate loci for inferring the phylogeny of the species within the genus Staphylococcus; with the idea that those who cannot afford whole genome sequencing can use these loci to carry out species assignation confidently. We retrieved 177 orthologous groups (OGs) by using a genome-based phylogeny and an average nucleotide identity analysis. The top 26 OGs showed topologies similar to the species tree and the concatenation of them yielded a topology almost identical to that of the species tree. Furthermore, a phylogeny of just the top seven OGs could be used for species assignment. We sequenced four staphylococcus isolates to test the 26 OGs and found that these OGs were far superior to commonly used markers for this genus. On the whole, our procedure allowed identification of the most adequate markers for inferring the phylogeny within the genus Staphylococcus. We anticipate that this approach will be employed for the identification of the most suitable markers for other bacterial genera and can be very helpful to sort out poorly classified genera. PeerJ Inc. 2018-10-24 /pmc/articles/PMC6203942/ /pubmed/30386709 http://dx.doi.org/10.7717/peerj.5839 Text en ©2018 Graña-Miraglia et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Ecology
Graña-Miraglia, Lucia
Arreguín-Pérez, César
López-Leal, Gamaliel
Muñoz, Alan
Pérez-Oseguera, Angeles
Miranda-Miranda, Estefan
Cossío-Bayúgar, Raquel
Castillo-Ramírez, Santiago
Phylogenomics picks out the par excellence markers for species phylogeny in the genus Staphylococcus
title Phylogenomics picks out the par excellence markers for species phylogeny in the genus Staphylococcus
title_full Phylogenomics picks out the par excellence markers for species phylogeny in the genus Staphylococcus
title_fullStr Phylogenomics picks out the par excellence markers for species phylogeny in the genus Staphylococcus
title_full_unstemmed Phylogenomics picks out the par excellence markers for species phylogeny in the genus Staphylococcus
title_short Phylogenomics picks out the par excellence markers for species phylogeny in the genus Staphylococcus
title_sort phylogenomics picks out the par excellence markers for species phylogeny in the genus staphylococcus
topic Ecology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6203942/
https://www.ncbi.nlm.nih.gov/pubmed/30386709
http://dx.doi.org/10.7717/peerj.5839
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