Long PCR amplification of the entire mitochondrial genome from individual helminths for direct sequencing (original) (raw)

References

  1. Hu, M. & Gasser, R.B. Mitochondrial genomics of parasitic nematodes—advances and perspectives. Trends Parasitol. 22, 78–84 (2006).
    Article CAS PubMed Google Scholar
  2. Boore, J.L. Animal mitochondrial genomes. Nucleic Acids Res. 27, 1767–1780 (1999).
    Article CAS PubMed Central PubMed Google Scholar
  3. Lang, B.F., Gray, M.W. & Burger, G. Mitochondrial genome evolution and the origin of eukaryotes. Ann. Rev. Genet. 33, 351–397 (1999).
    Article CAS PubMed Google Scholar
  4. Saccone, C., De Giorgi, C., Gissi, C., Pesole, G. & Reyes, A. Evolutionary genomics in metazoa: the mitochondrial DNA as a model system. Gene 238, 195–209 (1999).
    Article CAS PubMed Google Scholar
  5. Saccone, C. et al. Evolution of the mitochondrial genetic system: an overview. Gene 261, 153–159 (2000).
    Article CAS PubMed Google Scholar
  6. Saccone, C. et al. Mitochondrial DNA in metazoan: degree of freedom in a frozen event. Gene 286, 3–12 (2002).
    Article CAS PubMed Google Scholar
  7. Macey, J.R., Larson, A., Ananjeva, N.B., Fang, Z. & Papenfuss, T.J. Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Mol. Biol. Evol. 14, 91–104 (1997).
    Article CAS PubMed Google Scholar
  8. Dowton, M.P., Castro, L.R. & Austin, A.D. Mitochondrial gene rearrangements as phylogenetic characters in the invertebrates: the examination of genome 'morphology'. Invertebr. Syst. 16, 345–356 (2002).
    Article Google Scholar
  9. Yokobori, S.I. & Pääbo, S. tRNA editing in metazoans. Nature 377, 490 (1995).
    Article CAS PubMed Google Scholar
  10. Börner, G.V., Yokobori, S., Mörl, M., Dörner, M. & Pääbo, S. RNA editing metazoan mitochondria: staying fit without sex. FEBS Lett. 409, 320–324 (1997).
    Article PubMed Google Scholar
  11. Lavrov, D.V., Brown, W.M. & Boore, J.L. A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus. Proc. Natl. Acad. Sci. USA 97, 13738–13742 (2000).
    Article CAS PubMed Central PubMed Google Scholar
  12. Ingman, M., Kaessmann, H., PÍÍbo, S. & Gyllensten, U. Mitochondrial genome variation and the origin of modern humans. Nature 408, 708–713 (2000).
    Article CAS PubMed Google Scholar
  13. Platt, H.M. The Phylogenetic Systematics of Free-living Nematodes (ed. Lorenzen, S.) i–ii (The Ray Society, London, 1994).
    Google Scholar
  14. Le, T.H., Blair, D. & McManus, D.P. Mitochondrial genomes of human helminths and their use as markers in population genetics and phylogeny. Acta Trop. 77, 243–256 (2000).
    Article CAS PubMed Google Scholar
  15. Lavrov, D.V. & Brown, W.M. Trichinella spiralis mtDNA: a nematode mitochondrial genome that encodes a putative ATP8 and normally structured tRNAs and has a gene arrangement relatable to those of coelmate metazoans. Genetics 157, 621–637 (2001).
    CAS PubMed PubMed Central Google Scholar
  16. Hu, M., Chilton, N.B. & Gasser, R.B. The mitochondrial genomics of parasitic nematodes of socio-economic importance: recent progress, and implications for population genetics and systematics. Adv. Parasitol. 56, 133–212 (2004).
    Article PubMed Google Scholar
  17. Boore, J.L., Macey, J.R. & Medina, M. Sequencing and comparing whole mitochondrial genomes of animals. In Molecular Evolution: Producing the Biochemical Data, Part B Vol. 395 (eds. Zimmer, E.A. & Roalson, E.H.) 311–348 Methods in Enzymology Series (Elsevier, Burlington, Massachusetts, 2005).
    Chapter Google Scholar
  18. Simison, W.B., Lindberg, D.R. & Boore, J.L. Rolling circle amplification of metazoan mitochondrial genomes. Mol. Phylogenet. Evol. 39, 562–567 (2006).
    Article CAS PubMed Google Scholar
  19. Burger, G., Lavrov, D.V., Forget, L. & Lang, B.F. Sequencing complete mitochondrial and plastid genomes. Nat. Protoc. 2, 603–614 (2007).
    Article CAS PubMed Google Scholar
  20. Lang, B.F. & Burger, G. Purification of mitochondrial and plastid DNA. Nat. Protoc. 2, 652–660 (2007).
    Article CAS PubMed Google Scholar
  21. Anderson, T.J., Blouin, M.S. & Beech, R.N. Population biology of parasitic nematodes: applications of genetic markers. Adv. Parasitol. 41, 219–283 (1998).
    Article CAS PubMed Google Scholar
  22. Blouin, M.S. Mitochondrial DNA diversity in nematodes. J. Helminthol. 72, 285–289 (1998).
    Article CAS PubMed Google Scholar
  23. Hu, M., Chilton, N.B. & Gasser, R.B. Long PCR-based amplification of the entire mitochondrial genome from single parasitic nematodes. Mol. Cell. Probes 16, 261–267 (2002).
    Article CAS PubMed Google Scholar
  24. Hu, M., Chilton, N.B. & Gasser, R.B. The mitochondrial genomes of the human hookworms, Ancylostoma duodenale and Necator americanus (Nematoda: Secernentea). Int. J. Parasitol. 32, 145–158 (2002).
    Article CAS PubMed Google Scholar
  25. Hu, M., Gasser, R.B., Abs El-Osta, Y.G. & Chilton, N.B. Structure and organization of the mitochondrial genome of the canine heartworm, Dirofilaria immitis. Parasitology 127, 37–51 (2003).
    Article CAS PubMed Google Scholar
  26. Hu, M., Chilton, N.B., Abs El-Osta, Y.G. & Gasser, R.B. Comparative analysis of mitochondrial genome data for Necator americanus from two endemic regions reveals substantial genetic variation. Int. J. Parasitol. 33, 955–963 (2003).
    Article CAS PubMed Google Scholar
  27. Hu, M., Chilton, N.B. & Gasser, R.B. The mitochondrial genome of Strongyloides stercoralis (Nematoda)—idiosyncratic gene order and evolutionary implications. Int. J. Parasitol. 33, 1393–1408 (2003).
    Article CAS PubMed Google Scholar
  28. Zhang, D.X. & Hewitt, G.M. Insect mitochondrial control region: a review of its structure, evolution and usefulness in evolutionary studies. Biochem. Syst. Ecol. 25, 99–120 (1997).
    Article Google Scholar
  29. Okimoto, R., Macfarlane, J.L., Clary, D.O. & Wolstenholme, D.R. The mitochondrial genome of two nematodes, Caenorhabditis elegans and Ascaris suum. Genetics 130, 471–498 (1992).
    CAS PubMed PubMed Central Google Scholar
  30. Keddie, E.M., Higazi, T. & Unnasch, T.R. The mitochondrial genome of Onchocerca volvulus: sequence, structure and phylogenetic analysis. Mol. Biochem. Parasitol. 95, 111–127 (1998).
    Article CAS PubMed Google Scholar
  31. Zhang, D.X. & Hewitt, G.M. Nuclear integrations: challenges for mitochondrial DNA markers. Tree 11, 247–251 (1996).
    CAS PubMed Google Scholar
  32. Nelson, W.S., Prodöhl, P.A. & Avise, J.C. Development and application of long-PCR for the assay of full-length animal mitochondrial DNA. Mol. Ecol. 5, 807–810 (1996).
    Article CAS PubMed Google Scholar

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