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...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
PeerJ Inc.
2018-10-01
|
| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/5839.pdf |
| _version_ | 1827611029616459776 |
|---|---|
| author | Lucia Graña-Miraglia César Arreguín-Pérez Gamaliel López-Leal Alan Muñoz Angeles Pérez-Oseguera Estefan Miranda-Miranda Raquel Cossío-Bayúgar Santiago Castillo-Ramírez |
| author_facet | Lucia Graña-Miraglia César Arreguín-Pérez Gamaliel López-Leal Alan Muñoz Angeles Pérez-Oseguera Estefan Miranda-Miranda Raquel Cossío-Bayúgar Santiago Castillo-Ramírez |
| author_sort | Lucia Graña-Miraglia |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-09T07:59:18Z |
| format | Article |
| id | doaj.art-1490c9ee00de4cb7bb183804fdd7030e |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:59:18Z |
| publishDate | 2018-10-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-1490c9ee00de4cb7bb183804fdd7030e2023-12-03T00:48:23ZengPeerJ Inc.PeerJ2167-83592018-10-016e583910.7717/peerj.5839Phylogenomics picks out the par excellence markers for species phylogeny in the genus StaphylococcusLucia Graña-Miraglia0César Arreguín-Pérez1Gamaliel López-Leal2Alan Muñoz3Angeles Pérez-Oseguera4Estefan Miranda-Miranda5Raquel Cossío-Bayúgar6Santiago Castillo-Ramírez7Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, MexicoCentro Nacional de Investigación Disciplinaria en Parasitología Veterinaria del Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Jiutepec, Morelos, MexicoDepartamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, MexicoPrograma de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, MexicoPrograma de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, MexicoCentro Nacional de Investigación Disciplinaria en Parasitología Veterinaria del Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Jiutepec, Morelos, MexicoCentro Nacional de Investigación Disciplinaria en Parasitología Veterinaria del Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Jiutepec, Morelos, MexicoPrograma de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, MexicoAlthough 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.https://peerj.com/articles/5839.pdfStaphylococcusPhylogenomicsBacterial speciesInfectious diseasesEvolutionary biology |
| spellingShingle | Lucia Graña-Miraglia César Arreguín-Pérez Gamaliel López-Leal Alan Muñoz Angeles Pérez-Oseguera Estefan Miranda-Miranda Raquel Cossío-Bayúgar Santiago Castillo-Ramírez Phylogenomics picks out the par excellence markers for species phylogeny in the genus Staphylococcus PeerJ Staphylococcus Phylogenomics Bacterial species Infectious diseases Evolutionary biology |
| 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 | Staphylococcus Phylogenomics Bacterial species Infectious diseases Evolutionary biology |
| url | https://peerj.com/articles/5839.pdf |
| work_keys_str_mv | AT luciagranamiraglia phylogenomicspicksouttheparexcellencemarkersforspeciesphylogenyinthegenusstaphylococcus AT cesararreguinperez phylogenomicspicksouttheparexcellencemarkersforspeciesphylogenyinthegenusstaphylococcus AT gamaliellopezleal phylogenomicspicksouttheparexcellencemarkersforspeciesphylogenyinthegenusstaphylococcus AT alanmunoz phylogenomicspicksouttheparexcellencemarkersforspeciesphylogenyinthegenusstaphylococcus AT angelesperezoseguera phylogenomicspicksouttheparexcellencemarkersforspeciesphylogenyinthegenusstaphylococcus AT estefanmirandamiranda phylogenomicspicksouttheparexcellencemarkersforspeciesphylogenyinthegenusstaphylococcus AT raquelcossiobayugar phylogenomicspicksouttheparexcellencemarkersforspeciesphylogenyinthegenusstaphylococcus AT santiagocastilloramirez phylogenomicspicksouttheparexcellencemarkersforspeciesphylogenyinthegenusstaphylococcus |