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Comparative Genomics and Phylogenomics of Hemotrophic Mycoplasmas
Hemotrophic mycoplasmas (hemoplasmas) are a group of animal pathogens of the Mollicutes class. Recently, the genomes of 8 hemoplasmas have been completely sequenced. The aim of this study was to gain a better understanding of their genomic features and relationship to other Mycoplasma species. The g...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3958358/ https://www.ncbi.nlm.nih.gov/pubmed/24642917 http://dx.doi.org/10.1371/journal.pone.0091445 |
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author | Guimaraes, Ana M. S. Santos, Andrea P. do Nascimento, Naíla C. Timenetsky, Jorge Messick, Joanne B. |
author_facet | Guimaraes, Ana M. S. Santos, Andrea P. do Nascimento, Naíla C. Timenetsky, Jorge Messick, Joanne B. |
author_sort | Guimaraes, Ana M. S. |
collection | PubMed |
description | Hemotrophic mycoplasmas (hemoplasmas) are a group of animal pathogens of the Mollicutes class. Recently, the genomes of 8 hemoplasmas have been completely sequenced. The aim of this study was to gain a better understanding of their genomic features and relationship to other Mycoplasma species. The genome structure and dynamics of hemoplasmas were analyzed by evaluating gene synteny, adaptive evolution of paralogous gene families (PGF) and horizontal gene transfer (HGT). The Mollicutes class was then phylogenetically analyzed by constructing a distance matrix of the 16S rRNA genes and a phylogenetic tree with 32 conserved, concatenated proteins. Our results suggest that the hemoplasmas have dynamic genomes. The genome size variation (from 547 to 1,545 genes) indicates substantial gene gain/loss throughout evolution. Poorly conserved gene syntenies among hemoplasmas, positional shuffling of paralogous genes between strains, HGT, and codons under positive selection in PGFs were also observed. When compared to other Mollicutes species, the hemoplasmas experienced further metabolic reduction, and the 16S rRNA gene distance matrix of the available mollicutes suggests that these organisms presently constitute the most divergent clade within its class. Our phylogenetic tree of concatenated proteins showed some differences when compared to the 16S rRNA gene tree, but non-mycoplasma organisms, such as Ureaplasma spp. and Mesoplasma spp., continue to branch within Mycoplasma clades. In conclusion, while the hemoplasmas experienced further metabolic shrinkage through gene loss, PGFs with positively selected codons are likely beneficial to these species. Phylogeny of the mollicutes based on 16S rRNA genes or concatenated proteins do not obey the current taxonomy. The metabolism and genetic diversity of the mollicutes, the presence of HGT, and lack of standard for genus circumscription are likely to hinder attempts to classify these organisms based on phylogenetic analyses. |
format | Online Article Text |
id | pubmed-3958358 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-39583582014-03-27 Comparative Genomics and Phylogenomics of Hemotrophic Mycoplasmas Guimaraes, Ana M. S. Santos, Andrea P. do Nascimento, Naíla C. Timenetsky, Jorge Messick, Joanne B. PLoS One Research Article Hemotrophic mycoplasmas (hemoplasmas) are a group of animal pathogens of the Mollicutes class. Recently, the genomes of 8 hemoplasmas have been completely sequenced. The aim of this study was to gain a better understanding of their genomic features and relationship to other Mycoplasma species. The genome structure and dynamics of hemoplasmas were analyzed by evaluating gene synteny, adaptive evolution of paralogous gene families (PGF) and horizontal gene transfer (HGT). The Mollicutes class was then phylogenetically analyzed by constructing a distance matrix of the 16S rRNA genes and a phylogenetic tree with 32 conserved, concatenated proteins. Our results suggest that the hemoplasmas have dynamic genomes. The genome size variation (from 547 to 1,545 genes) indicates substantial gene gain/loss throughout evolution. Poorly conserved gene syntenies among hemoplasmas, positional shuffling of paralogous genes between strains, HGT, and codons under positive selection in PGFs were also observed. When compared to other Mollicutes species, the hemoplasmas experienced further metabolic reduction, and the 16S rRNA gene distance matrix of the available mollicutes suggests that these organisms presently constitute the most divergent clade within its class. Our phylogenetic tree of concatenated proteins showed some differences when compared to the 16S rRNA gene tree, but non-mycoplasma organisms, such as Ureaplasma spp. and Mesoplasma spp., continue to branch within Mycoplasma clades. In conclusion, while the hemoplasmas experienced further metabolic shrinkage through gene loss, PGFs with positively selected codons are likely beneficial to these species. Phylogeny of the mollicutes based on 16S rRNA genes or concatenated proteins do not obey the current taxonomy. The metabolism and genetic diversity of the mollicutes, the presence of HGT, and lack of standard for genus circumscription are likely to hinder attempts to classify these organisms based on phylogenetic analyses. Public Library of Science 2014-03-18 /pmc/articles/PMC3958358/ /pubmed/24642917 http://dx.doi.org/10.1371/journal.pone.0091445 Text en © 2014 Guimaraes 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, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Guimaraes, Ana M. S. Santos, Andrea P. do Nascimento, Naíla C. Timenetsky, Jorge Messick, Joanne B. Comparative Genomics and Phylogenomics of Hemotrophic Mycoplasmas |
title | Comparative Genomics and Phylogenomics of Hemotrophic Mycoplasmas |
title_full | Comparative Genomics and Phylogenomics of Hemotrophic Mycoplasmas |
title_fullStr | Comparative Genomics and Phylogenomics of Hemotrophic Mycoplasmas |
title_full_unstemmed | Comparative Genomics and Phylogenomics of Hemotrophic Mycoplasmas |
title_short | Comparative Genomics and Phylogenomics of Hemotrophic Mycoplasmas |
title_sort | comparative genomics and phylogenomics of hemotrophic mycoplasmas |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3958358/ https://www.ncbi.nlm.nih.gov/pubmed/24642917 http://dx.doi.org/10.1371/journal.pone.0091445 |
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