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Volume 11   Issue 2   Year 2016
Shpynov S.N., Gumenuk A.S., Pozdnichenko N.N.

Application of the Numerical Characteristic of Formal Order Analysis of the Prokaryotic Genomes for Reclassification within the Genus Rickettsia

Mathematical Biology & Bioinformatics. 2016;11(2):336-350.

doi: 10.17537/2016.11.336.

References

 

  1. Merhej V., Raoult D. Rickettsial evolution in the light of comparative genomics. Biol. Rev. Camb. Philos. Soc. 2011;86(2):379-405. doi: 10.1111/j.1469-185X.2010.00151.x
  2. Weiss E., Moulder J.W. Order I. Rickettsiales Gieszczkiewicz 1939. In: Bergey’s manual of systematic bacteriology;1. Eds N.R. Krieg and J.G. Holt. Baltimore, Md.: The Williams & Wilkins Co.; 1984. P. 687-703.
  3. Stothard D.R., Clark J.B., Fuerst P.A. Ancestral divergence of Rickettsia bellii from the spotted fever and typhus groups of Rickettsia and antiquity of the genus Rickettsia. Int. J. Syst. Bacteriol. 1994;44:798-804. doi: 10.1099/00207713-44-4-798
  4. Tamura A., Ohashi N., Urakami H., Miyamura S. Classification of Rickettsia tsutsugamushi in a new genus, Orientia gen. nov., as Orientia tsutsugamushi comb. nov. Int. J. Syst. Bacteriol. 1995;45:589-591. doi: 10.1099/00207713-45-3-589
  5. Gillespie J.J., Beier M.S., Rahman M.S., Ammerman N.C., Shallom J.M., Purkayastha A., Sobral B.S., Azad A.F. Plasmids and rickettsial evolution: insight from Rickettsia felis. PLoS One. 2007;2. Article No e266. doi: 10.1371/journal.pone.0000266
  6. Roux V., Raoult D. Phylogenetic analysis and taxonomic relationships among the genus Rickettsia. In: Rickettsiae and Rickettsial diseases at the turn of the third millennium. Marseille: Elsevier production; 1999. P. 52-66.
  7. Fournier P.E., Dumler J.S., Greub G., Zhang J., Wu Y., Raoult D. Gene sequence-based criteria for identification of new rickettsia isolates and description of Rickettsia heilongjiangensis sp. nov. J. Clin. Microbiol. 2003;41:5456-5465. doi: 10.1128/JCM.41.12.5456-5465.2003
  8. Markov A.V., Zakharov I.A. Application of quantitative measures of gene order similarity to phylogenetic reconstructions (exemplified by bacteria of the genus Rickettsia. Russian Journal of Genetics. 2008;44(4):389-398. doi: 10.1134/S1022795408040029
  9. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990;215(3):403-410. doi: 10.1016/S0022-2836(05)80360-2
  10. Kumar S., Stecher G., Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution. 2016;33:1870-1874. doi: 10.1093/molbev/msw054
  11. Darling A.E., Mau B., Perna N.T. ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One. 2010;25(5. Article No e11147).
  12. Du W., Cao Z., Wang Y., Sun Y., Blanzieri E., Liang Y. Prokaryotic phylogenies inferred from whole-genome sequence and annotation data. Biomed. Res. Int. 2013. Article No. 409062. doi: 10.1155/2013/409062
  13. McLeod M.P., Qin X., Karpathy S.E., Gioia J., Highlander S.K., Fox G.E., McNeill T.Z., Jiang H., Muzny D., Jacob L.S., Hawes A.C., Sodergren E., Gill R., Hume J., Morgan M., Fan G., Amin A.G., Gibbs R.A., Hong C., Yu X.J., Walker D.H., Weinstock G.M. Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae. J. Bacteriol. 2004;186:5842-5855. doi: 10.1128/JB.186.17.5842-5855.2004
  14. Ogata H., Audic S., Renesto-Audiffren P., Fournier P. E., Barbe V., Samson D., Roux V., Cossart P., Weissenbach J., Claverie J.M., Raoult D. Mechanisms of evolution in Rickettsia conorii and R. prowazekii. Science. 2001;293:2093-2098. doi: 10.1126/science.1061471
  15. Nair A.S.S., Mahalakshmi T. Visualization of genomic data using inter-nucleotide distance signals. In: Proceedings of IEEE Genomic Signal Processing. Bucharest, 2005.
  16. Afreixo V., Bastos C.A.C., Pinho A.J., Garcia S.P., Ferreira P.J.S.G. Genome analysis with inter-nucleotide distances. Bioinformatics. 2009;25(23):3064-3070. doi: 10.1093/bioinformatics/btp546
  17. Mazur M. Kachestvennaia teoriia informatsii (Qualitative information theory). Moscow; 1974. 240 p. (Translation from Polish of: Mazur M. Jakościowa teoria informacji. Warszawa, 1970).
  18. Gumenuk A.S., Pozdnichenko N.N., Rodionov I.N., Shpynov S.N. Formal analysis of structures of nucleotide chains. Mathematical Biology and Bioinformatics. 2013;8(1):373-397. doi: 10.17537/2013.8.373
  19. Shpynov S., Pozdnichenko N., Gumenuk A. Approach for classification and taxonomy within family Rickettsiaceae based on the Formal Order Analysis. Microbes and Infection. 2015;17(11):839-844. doi: 10.1016/j.micinf.2015.09.012
  20. Ignatovich V.F. Zhurnal gigieny, epidemiologii, mikrobiologii i immunologii (Journal of Hygiene, Epidemiology, Microbiology and Immunology). 1977;21(1):48-52.(in Russ.).
  21. Raoult D., Roux V. Rickettsioses as paradigms of new or emerging infectious diseases. Clin. Microbiol. Rev. 1997;10(4):694-719.
  22. Socolovschi C., Pages F., Ndiath M.O., Ratmanov P., Raoult D. Rickettsia species in African Anopheles mosquitoes. PLoS One. 2012;7(10). Article No. e48254.
  23. Ishikura M., Ando S., Shinagawa Y., Matsuura K., Hasegawa S., Nakayama T., Fujita H., Watanabe M. Phylogenetic analysis of spotted fever group rickettsiae based on gltA, 17-kDa, and rOmpA genes amplified by nested PCR from ticks in Japan. Microbiol. Immunol. 2003;47:823-832. doi: 10.1111/j.1348-0421.2003.tb03448.x
  24. Choi Y.J., Lee E.M., Park J.M., Lee K.M., Han S.H., Kim J.K., Lee S.H., Song H.J., Choi M.S., Kim I.S., Park K.H., Jang W.J. Molecular detection of various rickettsiae in mites (acari: trombiculidae) in southern Jeolla Province, Korea. Microbiol. Immunol. 2007;51:307-312. doi: 10.1111/j.1348-0421.2007.tb03912.x
  25. Oliveira K.A., Oliveira L.S., Dias C.C., Silva A.Jr., Almeida M.R., Almada G., Bouyer D.H., Galvao M.A., Mafra C. Molecular identification of Rickettsia felis in ticks and fleas from an endemic area for Brazilian Spotted Fever. Mem. Inst. Oswaldo. Cruz. 2008;103(2):191-194. doi: 10.1590/S0074-02762008000200011
  26. Abarca K., López J., Acosta-Jamett G., Martínez-Valdebenito C. Rickettsia felis in Rhipicephalus sanguineus from two distant Chilean cities. Vector Borne Zoonotic Dis. 2013;13(8):607-609. doi: 10.1089/vbz.2012.1201
  27. Soares H.S., Barbieri A.R., Martins T.F., Minervino A.H., de Lima J.T., Marcili A., Gennari S.M., Labruna M.B. Ticks and rickettsial infection in the wildlife of two regions of the Brazilian Amazon. Exp. Appl. Acarol. 2015;65(1):125-140. doi: 10.1007/s10493-014-9851-6
  28. Mediannikov O., Aubadie-Ladrix M., Raoult D. Candidatus ‘Rickettsia senegalensis’ in cat fleas in Senegal. New Microbe and New Infect. 2015;3:24-28. doi: 10.1016/j.nmni.2014.10.005
  29. Jiang J., Maina A.N., Knobel D.L., Cleaveland S., Laudisoit A., Wamburu K. Molecular detection of Rickettsia felis and Candidatus Rickettsia asemboensis in fleas from human habitats, Asembo, Kenya. Vector Borne Zoonotic Dis. 2013;13(8). Article No. 550e8.
  30. Simser J.A., Rahman M.S., Dreher-Lesnick S.M., Azad A.F. A novel and naturally occurring transposon, ISRpe1 in the Rickettsia peacockii genome disrupting the rickA gene involved in actin-based motility. Mol. Microbiol. 2005;58(1):71-79. doi: 10.1111/j.1365-2958.2005.04806.x
  31. Felsheim R.F., Kurtti T.J., Munderloh U.G. Genome sequence of the endosymbiont Rickettsia peacockii and comparison with virulent Rickettsia rickettsii: identification of virulence factors. PLoS One. 2009;21(4). Article No. e8361.
  32. Jado I., Oteo J.A., Aldámiz M., Gil H., Escudero R., Ibarra V., Portu J., Portillo A., Lezaun M.J., García-Amil C., Rodríguez-Moreno I., Anda P. Rickettsia monacensis and human disease, Spain. Emerg. Infect. Dis. 2007;13:1405-1407. Article No. 9.
  33. Winkler H.L. Verbreitung und Ursache der Parthenogenesis im Pflanzen- und Tierreiche. Jena: Verlag Fischer; 1920. doi: 10.5962/bhl.title.1460
  34. Lederberg J., McCraw A.T. 'Ome sweet 'omics- a genealogical treasury of words. Scientist. 2001;15(7):8.
  35. Merhej V., Raoult D. Rhizome of life, catastrophes, sequence exchanges, gene creations, and giant viruses: how microbial genomics challenges Darwin. Front. Cell. Infect. Microbiol. 2012;28(2):113. doi: 10.3389/fcimb.2012.00113
Table of Contents
Original Article
Math. Biol. Bioinf.
2016;11(2):336-350
doi: 10.17537/2016.11.336
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References

 
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