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Variable-Number-of-Tandem-Repeats Analysis of Genetic Diversity in Pasteuria ramosa

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Abstract

Variable-number-of-tandem-repeats (VNTR) markers are increasingly being used in population genetic studies of bacteria. They were recently developed for Pasteuria ramosa, an endobacterium that infects Daphnia species. In the present study, we genotyped P. ramosa in 18 infected hosts from the United Kingdom, Belgium, and two lakes in the United States using seven VNTR markers. Two Daphnia species were collected: D. magna and D. dentifera. Six loci showed length polymorphism, with as many as five alleles identified for a single locus. Similarity coefficient calculations showed that the extent of genetic variation between pairs of isolates within populations differed according to the population, but it was always less than the genetic distances among populations. Analysis of the genetic distances performed using principal component analysis revealed strong clustering by location of origin, but not by host Daphnia species. Our study demonstrated that the VNTR markers available for P. ramosa are informative in revealing genetic differences within and among populations and may therefore become an important tool for providing detailed analysis of population genetics and epidemiology.

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References

  1. Bois PR (2003) Hypermutable minisatellites, a human affair? Genomics 81:349–355

    Article  PubMed  CAS  Google Scholar 

  2. Bzymek M, Lovett ST (2001) Instability of repetitive DNA sequences: The role of replication in multiple mechanisms. Proc Natl Acad Sci U S A 98:8319–8325

    Article  PubMed  CAS  Google Scholar 

  3. Carius HJ, Little T, Ebert D (2001) Genetic variation in a host-parasite association: Potential for coevolution and frequency-dependent selection. Evolution 55:1146–1152

    Google Scholar 

  4. Colbourne JK, Robison B, Bogart K, Lynch M (2004) Five hundred and twenty-eight microsatellite markers for ecological genomic investigations using Daphnia. Mol Ecol Notes 3:485–490

    Article  CAS  Google Scholar 

  5. Davies KG, Redden M (1997) Diversity and partial characterization of putative virulence determinants in Pasteuria penetrans, the hyperparasitic bacterium of root-knot nematodes (Meloidogyne spp.). J Appl Microbiol 83:227–235

    Article  PubMed  CAS  Google Scholar 

  6. Decaestecker E, Declerck S, De Meester L, Ebert D (2005) Ecological implications of parasites in natural Daphnia populations. Oecologia 144:382–390

    Article  PubMed  Google Scholar 

  7. Decaestecker E, Lefever C, De Meester L, Ebert D (2004) Haunted by the past: Evidence for dormant stage banks of microparasites and epibionts of Daphnia. Limnol Oceanogr 49:1355–1364

    Article  Google Scholar 

  8. Decaestecker E, Vergote A, Ebert D, De Meester L (2003) Evidence for strong host-clone-parasite interactions in the Daphnia microparasite system. Evolution 57:784–792

    PubMed  Google Scholar 

  9. Duncan AB, Mitchell SE, Little TJ (2006) Parasite-mediated selection and the role of sex and diapause in Daphnia. J Evol Biol 19:1183–1189

    Article  PubMed  CAS  Google Scholar 

  10. Ebert D (2005) Ecology, epidemiology, and evolution of parasitism in Daphnia. Bethesda, MD: National Library of Medicine, National Center for Biotechnology Information. Available from: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=books. Accessed:

  11. Ebert D, Carius H-J, Little TJ, Decaestecker E (2004) The evolution of virulence when parasites cause host castration and gigantism. Am Nat 164(Suppl.):S19–S32

    Article  PubMed  Google Scholar 

  12. Ebert D, Rainey P, Embley TM, Scholz D (1996) Development, life cycle, ultrastructure and phylogenetic position of Pasteuria ramosa Metchnikoff 1888: Rediscovery of an obligate endoparasite of Daphnia magna Straus. Phil Trans Royal Soc London B 351:1689–1701

    Article  Google Scholar 

  13. Ebert D, Zshokke-Rohringer CD, Carius HJ (1998) Within- and between-population variation for resistance of Daphnia magna to the bacterial endoparasites Pasteuria ramosa. Proc R Soc Lond B Biol Sci 265:2127–2134

    Article  Google Scholar 

  14. Haldane JBS (1949) Disease and evolution. Ric Sci 19:2–11

    Google Scholar 

  15. Hamilton WD (1980) Sex versus non-sex versus parasite. Oikos 35:282–290

    Article  Google Scholar 

  16. Keim P, Price LB, Klevytska AM, Smith KL, Schupp JM, Okinaka R et al (2000) Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis. J Bacteriol 182:2928–2936

    Article  PubMed  CAS  Google Scholar 

  17. Klevytska AM, Brice LB, Schupp JM, Worsham PL, Wong J, Keim P (2001) Identification and characterization of variable-number of tandem repeats in the Yersinia pestis genome. J Clin Microbiol 39:3179–3185

    Article  PubMed  CAS  Google Scholar 

  18. Kosman E, Leonard KJ (2005) Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haploid, diploid, and polyploid species. Mol Ecol 14:415–424

    Article  PubMed  CAS  Google Scholar 

  19. Liao J-C, Li C-C, Chiou C-S (2006) Use of multilocus variable-number tandem repeat analysis method for molecular subtyping and phylogenetic analysis Neisseria meningitides isolates. BMC Microbiol 6:44

    Article  PubMed  CAS  Google Scholar 

  20. Lindstedt B-A (2005) Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria. Electrophoresis 26:2567–2582

    Article  PubMed  CAS  Google Scholar 

  21. Maiden MC, Bygraves JA, Feil E, Morelli G, Russel JE, Urwin R et al (1998) Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 95:3140–3145

    Article  PubMed  CAS  Google Scholar 

  22. Mouton L, Nong G, Preston J, Ebert D (2007) Identification and characterization of variable number tandem repeats in an obligate endoparasite of Daphnia species. Appl Environ Microbiol 73:3715–3718

    Article  PubMed  CAS  Google Scholar 

  23. Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleasis. Proc Natl Acad Sci U S A 76:5269–5273

    Article  PubMed  CAS  Google Scholar 

  24. Preston JF, Maruniak JE, Nong G, Brito JA, Schmidt LM, Giblin-Davis RM (2003) Pasteuria spp.: Systematics and phylogeny of these bacterial parasites of phytopathogenic nematodes. J Nematol 35:198–207

    CAS  PubMed  Google Scholar 

  25. Sneath PA, Sokal RR (1973) Numerical taxonomy. Freeman, San Francisco, CA

    Google Scholar 

  26. Top J, Schouh LM, Bonten MJ, Willems RJ (2004) Multilocus variable number of tandem repeats analysis, a novel typing scheme to study the genetic relatedness and epidemiology of Enterococcus faecium isolates. J Clin Microbiol 42:4503–4511

    Article  PubMed  CAS  Google Scholar 

  27. van Belkum A, Scherer S, van Alphen L, Verbrugh H (1998) Short-sequence DNA repeats in prokaryotic genomes. Microbiol Mol Biol Rev 62:275–293

    PubMed  Google Scholar 

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Acknowledgments

We thank I. Colson and L. Du Pasquier for useful discussion and comments, B. Aeschbach for technical help, and T. Little, E. Decaestecker, and S. Hall for providing samples. S. Zweizig and I. Colson improved the English language of the manuscript. This work was supported by grants from the Swiss Nationalfonds and the Freiwillige Akademische Geselschaft, Basel, Switzerland.

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Authors and Affiliations

  1. Evolutionsbiologie, Zoologisches Institut der Universitat Basel, Basel, Switzerland

    L. Mouton & D. Ebert

  2. Laboratoire de Biometrie et Biologie Evolutive, Universite de Lyon, Villeurbanne, France

    L. Mouton

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  1. L. Mouton
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  2. D. Ebert
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Correspondence to L. Mouton.

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Mouton, L., Ebert, D. Variable-Number-of-Tandem-Repeats Analysis of Genetic Diversity in Pasteuria ramosa . Curr Microbiol 56, 447–452 (2008). https://doi.org/10.1007/s00284-008-9104-1

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  • DOI: https://doi.org/10.1007/s00284-008-9104-1

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