Comparative genomics and phylogenomics of hemotrophic mycoplasmas
| العنوان: | Comparative genomics and phylogenomics of hemotrophic mycoplasmas |
|---|---|
| المؤلفون: | Naíla C. do Nascimento, Jorge Timenetsky, Joanne B. Messick, Ana Marcia Sá Guimarães, Andrea Pires dos Santos |
| المصدر: | Repositório Institucional da USP (Biblioteca Digital da Produção Intelectual) Universidade de São Paulo (USP) instacron:USP PLoS ONE, Vol 9, Iss 3, p e91445 (2014) PLoS ONE |
| سنة النشر: | 2014 |
| مصطلحات موضوعية: | Veterinary Microbiology, lcsh:Medicine, Mesoplasma, Mycoplasma, Genome Size, RNA, Ribosomal, 16S, Phylogenomics, lcsh:Science, Genome Evolution, Phylogeny, Genetics, Multidisciplinary, biology, Phylogenetic tree, Genomics, Bacterial Pathogens, Phylogenetics, Medical Microbiology, Horizontal gene transfer, Metabolic Networks and Pathways, Veterinary Pathology, Research Article, Evolutionary Processes, Gene Transfer, Horizontal, Paralogous Gene, Synteny, Microbiology, Evolution, Molecular, Evolutionary Adaptation, Evolutionary Systematics, Codon, Microbial Pathogens, Comparative genomics, Evolutionary Biology, Bacterial Evolution, Bacterial Taxonomy, lcsh:R, Biology and Life Sciences, Computational Biology, Bacteriology, MICROBIOLOGIA, Comparative Genomics, biology.organism_classification, Organismal Evolution, Microbial Evolution, Mollicutes, Veterinary Science, lcsh:Q, Genome, Bacterial |
| الوصف: | 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. |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::14ebc2e57b60943b33d73665e93800a6 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....14ebc2e57b60943b33d73665e93800a6 |
| قاعدة البيانات: | OpenAIRE |
| الوصف غير متاح. |