دورية أكاديمية
أعرض في EDS

Comparative genomics and phylogenomics of hemotrophic mycoplasmas.

التفاصيل البيبلوغرافية
العنوان: Comparative genomics and phylogenomics of hemotrophic mycoplasmas.
المؤلفون: Guimaraes AM; Department of Comparative Pathobiology, School of Veterinary Medicine, Purdue University, West Lafayette, Indiana, United States of America; Coordenação de Aperfeiçoamento de Pessoal de Ensino Superior (CAPES)-Fulbright Program, Ministério da Educação, Brasília, Distrito Federal, Brazil., Santos AP; Department of Comparative Pathobiology, School of Veterinary Medicine, Purdue University, West Lafayette, Indiana, United States of America., do Nascimento NC; Department of Comparative Pathobiology, School of Veterinary Medicine, Purdue University, West Lafayette, Indiana, United States of America., Timenetsky J; Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, São Paulo, Brazil., Messick JB; Department of Comparative Pathobiology, School of Veterinary Medicine, Purdue University, West Lafayette, Indiana, United States of America.
المصدر: PloS one [PLoS One] 2014 Mar 18; Vol. 9 (3), pp. e91445. Date of Electronic Publication: 2014 Mar 18 (Print Publication: 2014).
نوع المنشور: Comparative Study; Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE
أسماء مطبوعة: Original Publication: San Francisco, CA : Public Library of Science
مواضيع طبية MeSH: Genome, Bacterial* , Genomics* , Phylogeny*, Mycoplasma/*genetics , RNA, Ribosomal, 16S/*genetics, Codon ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome Size ; Metabolic Networks and Pathways/genetics ; Mycoplasma/classification ; Mycoplasma/metabolism ; Synteny
مستخلص: 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.
References: Bioinformatics. 2005 May 15;21(10):2531-3. (PMID: 15713735)
Annu Rev Genet. 2003;37:123-51. (PMID: 14616058)
J Bacteriol. 2012 Oct;194(19):5458-9. (PMID: 22965086)
Genome Res. 2007 Nov;17(11):1657-64. (PMID: 17916642)
Trends Genet. 2000 Jun;16(6):276-7. (PMID: 10827456)
Annu Rev Genet. 2012;46:515-36. (PMID: 22974303)
Vet Clin Pathol. 2004;33(1):2-13. (PMID: 15048620)
J Bacteriol. 2011 May;193(9):2369-70. (PMID: 21398558)
BMC Biol. 2009 May 05;7:20. (PMID: 19416510)
Int J Syst Evol Microbiol. 2009 Feb;59(Pt 2):285-94. (PMID: 19196767)
Nat Genet. 2004 Jul;36(7):760-6. (PMID: 15208628)
Am J Vet Res. 2002 Oct;63(10):1385-8. (PMID: 12371764)
Genome Res. 2003 Mar;13(3):407-12. (PMID: 12618371)
Malar J. 2005 Mar 18;4:17. (PMID: 15774020)
J Bacteriol. 2005 Aug;187(16):5568-77. (PMID: 16077101)
Bioinformatics. 2012 Jan 15;28(2):160-6. (PMID: 22121156)
Vet Res. 2012 Sep 28;43:66. (PMID: 23020168)
Vet Res. 2011 Jul 12;42:83. (PMID: 21749699)
J Bacteriol. 1995 May;177(10):2622-7. (PMID: 7751269)
J Clin Microbiol. 1997 Apr;35(4):823-9. (PMID: 9157135)
Mol Biol Evol. 2005 Oct;22(10):2073-83. (PMID: 15972845)
Mol Biol Evol. 2013 Jul;30(7):1653-64. (PMID: 23608703)
Trends Microbiol. 2004 Apr;12(4):148-54. (PMID: 15116722)
Mol Biol Evol. 1987 Jul;4(4):406-25. (PMID: 3447015)
Annu Rev Genet. 2004;38:771-92. (PMID: 15568993)
Mol Phylogenet Evol. 2012 Jan;62(1):515-28. (PMID: 22115576)
Bioinformatics. 2004 Aug 4;20 Suppl 1:i94-100. (PMID: 15262786)
Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13950-5. (PMID: 16172379)
PLoS Genet. 2007 May 18;3(5):e75. (PMID: 17511520)
Nat Genet. 2004 Jan;36(1):27-9. (PMID: 14661021)
Mol Biol Evol. 2011 Oct;28(10):2731-9. (PMID: 21546353)
Methods Mol Biol. 2007;408:93-108. (PMID: 18314579)
Int J Syst Evol Microbiol. 2001 May;51(Pt 3):891-899. (PMID: 11411711)
Clin Vaccine Immunol. 2011 Aug;18(8):1275-81. (PMID: 21653748)
Appl Microbiol Biotechnol. 2013 Feb;97(3):1259-67. (PMID: 22810301)
Exp Appl Acarol. 2004;32(4):301-12. (PMID: 15176735)
Plant Physiol. 2008 Dec;148(4):1772-81. (PMID: 18952863)
Genome Res. 2003 Sep;13(9):2178-89. (PMID: 12952885)
Vet Res. 2011 Sep 21;42:102. (PMID: 21936946)
Nucleic Acids Res. 2006 Jan 10;34(1):53-65. (PMID: 16407324)
Nucleic Acids Res. 1999 Jan 1;27(1):29-34. (PMID: 9847135)
BMC Evol Biol. 2012 Dec 12;12:243. (PMID: 23234643)
PLoS One. 2012;7(9):e45962. (PMID: 23049905)
BMC Bioinformatics. 2004 Aug 19;5:113. (PMID: 15318951)
PLoS One. 2012;7(4):e35698. (PMID: 22536428)
Nat Rev Microbiol. 2005 Sep;3(9):688-99. (PMID: 16138097)
J Am Vet Med Assoc. 2001 Jun 15;218(12):1943-5, 1936. (PMID: 11417738)
Science. 2006 Mar 3;311(5765):1283-7. (PMID: 16513982)
Int J Syst Evol Microbiol. 2006 Jan;56(Pt 1):13-4. (PMID: 16403858)
Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):19126-31. (PMID: 19855009)
PLoS Comput Biol. 2006 Jun 23;2(6):e62. (PMID: 16789820)
Biochem Biophys Res Commun. 2003 Jan 3;300(1):149-54. (PMID: 12480534)
Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10679-84. (PMID: 20495090)
Science. 2009 Nov 27;326(5957):1263-8. (PMID: 19965476)
J Mol Biol. 1990 Oct 5;215(3):403-10. (PMID: 2231712)
PLoS One. 2011 May 10;6(5):e19574. (PMID: 21573007)
J Bacteriol. 2012 Nov;194(22):6312-3. (PMID: 23105057)
J Bacteriol. 2012 Feb;194(4):905-6. (PMID: 22275103)
PLoS One. 2008 May 28;3(5):e2295. (PMID: 18509460)
المشرفين على المادة: 0 (Codon)
0 (RNA, Ribosomal, 16S)
تواريخ الأحداث: Date Created: 20140320 Date Completed: 20141229 Latest Revision: 20211021
رمز التحديث: 20240513
مُعرف محوري في PubMed: PMC3958358
DOI: 10.1371/journal.pone.0091445
PMID: 24642917
قاعدة البيانات: MEDLINE
الوصف
تدمد:1932-6203
DOI:10.1371/journal.pone.0091445