Plant or fungal sequences? an alternative optimized PCR protocol to avoid ITS (nrDNA) Misamplification

Brazilian Archives of Biology and Technology

Volumn 53, Issue 1, 2010, Pages 141-152

  de Miranda, Vitor Fernandes Oliveira ^a   Martins, Vanderlei Geraldo ^b   Furlan, Antonio ^b   Bacci, Maurício ^b  

^a UNIVERSIDADE DE MOGI DAS CRUZES   (Brazil)

^b SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

Author keywords

DNA; Drosera; Fungi; Phylogeny; Polymerase

Indexed keywords

BASIDIOMYCOTA; BOVINAE; DROSERA; DROSERACEAE; FUNGI; HETEROBASIDIOMYCETES; USTILAGINOMYCETES;

EID: 77953338276     PISSN: 15168913     EISSN: 15168913     Source Type: Journal    
DOI: 10.1590/S1516-89132010000100018     Document Type: Article

References (45)

1. Alexopoulos C.J., Mims C.W. and Blackwell M. (1996), Introductory Mycology 4th.ed., John Wiley and Sons., New York.
2. Altschul S.F., Madden A.A.S., Zhang J., Zhang Z., Miller W. and Lipman D.J. (1997), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
3. Baldwin BG, Sanderson M.J., Porter M.J., Wojciechowski M.F., Campbell C.S. and Donoghue M.J. (1995), The ITS region of nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny. Ann. Missouri Bot. Gard., 82, 27-277.
4. Baum D.A., Small R.L. and Wendel J.F. (1998), Biogeography and floral evolution of baobabs (Adansonia, Bombacaceae) as inferred from multiple data sets. Systematic Biology, 47(2), 181-207.
5. Bobola M.S., Smith D.E. and Klein A.S. (1992), Five major ribosomal repeats represent a large and variable fraction of the total genomic DNA of Picea rubens and P. mariana. Mol. Biol. Evol., 9, 125-137.
6. Bremer K. (1988), The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42, 795-803.
7. Buckler IV E.S. and Holtsford T.P. (1996), Zea ribosomal repeat evolution and substitution patterns. Mol. Biol. Evol., 13, 612-622.
8. Buckler IV E.S., Ippolito A. and Holtsford T.P. (1997), The Evolution of Ribosomal DNA: Divergent Paralogues and Phylogenetic Implications. Genetics, 145, 821-832.
9. Chiang Y.C., Chou C.H., Lee P.R. and Chiang T.Y. (2001), Detection of leaf-associated fungi based on PCR and nucleotide sequence of the ribosomal internal transcribed spacer (ITS) in Miscanthus. Bot.Bull. Acad. Sin., 42, 39-44.
10. Chomczynski P., Mackey K., Drews R. and Wilfinger W. (1997), DNAzol: A reagent for the rapid isolation of genomic DNA. BioTechniques, 22, 550-553.
11. Chomczynski P., Wilfinger W. and Mackey K. (1998), Isolation of Genomic DNA from Human, Animal, and Plant Samples with DNAzol Reagents. Biotechnology International, 185-188.
12. Diels L. (1906), Drosera. In Engler A. (ed.) Das Pflanzenreich, Wilhelm Engelmann, Leipzig, pp. 61-128.
13. Dubcovsky J. and Dvorák J. (1995), Ribosomal RNA multigene loci: nomads of the Triticeae genomes. Genetics, 140, 1367-1377.
14. Dvorák J. (1990), Evolution of multigene families: the ribosomal RNA loci of wheat and related species. In Brown AHD and Clegg MT (eds.) Plant Population Genetics, Breeding and Genetics Resources, Sinauer Assoc., Sunderland, MA, pp.83-97.
15. Felsenstein J. (1985), Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783-791.
16. Ferrer C., Colom F., Frases S., Mulet E., Abad J.L. and Alio J.L. (2001), Detection and identification of fungal pathogens by PCR and by ITS2 and 5.8S ribosomal DNA typing in ocular infections. J. Clin. Microbiol., 39(8), 2873-2879.
17. Giribet G. and Wheeler W.C. (1999), On gaps. Molecular Phylogenetics and Evolution, 13 (1), 132-143.
18. Guo L.D., Hyde K.D. and Liew E.C.Y. (2001), Detection and Taxonomic Placement of Endophytic Fungi within Frond Tissues of Livistona chinensis Based on rDNA Sequences. Molecular Phylogenetics and Evolution,. 20 (1), 1-13.
19. Hall T.A. (1999), BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids. Symp. Ser., 41, 95-98.
20. Henegariu O.N., Heerema A., Dlouhy S.R., Vance G.H. and Vogt P.H. (1997), Multiplex PCR: Critical Parameters and Step-by-Step Protocol. BioTechniques, 23, 504-511.
21. Hillis D.M. and Dixon M.T. (1991), Ribosomal DNA: molecular evolution and phylogenetic inference. The Quarterly Review of Biology, 66 (4), 411-453.
22. Innis M.A. and Gelfand D.H. (1990), Optimization of PCRs. In Innis MA, Gelfand DH; Sninsky JJ, White TJ (eds.) PCR Protocols: a guide to methods and applications, Academic Press, San Diego, pp. 3-12.
23. Juniper B.E., Robins R.J. and Joel D.M. (1989), The Carnivorous Plants, Academic Press, San Diego.
24. Lee S. and Taylor J. (1990), Isolation of DNA from fungal mycelia and single spores. In: Innis M.A., Gelfand D.H.; Sninsky J.J., White T.J. (eds.) PCR Protocols: a guide to methods and applications, Academic Press, San Diego, pp. 282-287.
25. Liston A. and Alvarez-Buylla E. (1995), Internal transcribed spacer sequences of conifers: There is a fungus among us. Inoculum, 46, 26. (Abstract).
26. Liston A., Robinson W.A., Oliphant J.M. and Alvarez-Buylla E.R. (1996), Length variation in the nuclear ribosomal DNA internal transcribed spacer region of non-flowering seeds plants. Syst. Bot., 21, 109-120.
27. Long E.O. and Dawid I.B. (1980), Repeated genes in eukariotes. Annu. Rev. Biochem., 49, 727-764.
28. Maheshwari R. (2004), What is an endophytic fungus? Current Science, 90 (10), 1309.
29. Page R.D.M. (1998), TreeView: Tree drawing software for Apple Macintosh and Microsoft Windows, version 1.5.2. Institute of Biomedical and Life Sciences, University of Glasgow, Scotl, UK.
30. nd ed., Sinauer Associates, Inc., Sunderland, pp.205-247.
31. Pant D.D. and Bhatnagar S. (1977), Morphological studies in Nepenthes (Nepenthaceae). Phytomorphology, 27, 13-34.
32. Peixoto Neto P.A.S., Azevedo J. L. and Caetano L. C. (2004), Microrganismos endofíticos em plantas: status atual e perspectivas. BLACPMA, 3 (4), 69-72.
33. Rivadavia F., Kondo K., Kato M. and Hasebe M. (2003), Phylogeny of the sundews, Drosera (Droseraceae), based on chloroplast rbcL and nuclear 18S ribosomal DNA sequences. American Journal of Botany, 90(1), 123-130.
34. Sarkar G. and Sommer S.S. (1990), Shedding light on PCR contamination. Nature, 343, 27.
35. Sekiguchi H. (2001), A single band does not always represent single bacterial strains in denaturing gradient gel electrophoresis analysis. Biotechnology Letters, 23 (15), 1205-1208.
36. Smith D.E. and Klein A.S. (1994), Phylogenetic inferences on the relationship of North American and European Picea species based on nuclear ribosomal 18S sequences and the internal transcribed spacer 1 region. Mol. Phylogenet. Evol., 3, 17-26.
37. Smith D.E. and Klein A.S. (1996), Erratum. Mol. Phylogenet. Evol, 5, 286-287.
38. Sorenson M.D. (1996), TreeRot. University of Michigan, Ann Arbor, Michigan, USA.
39. Suh Y., Thien L.B., Reeve H.E. and Zimmer E.A. (1993), Molecular evolution and phylogenetic implications of internal transcribed spacers sequences of ribosomal DNA in Wintereceae. Am. J. Bot., 80, 1042-1055.
40. nd ed., Sinauer Associates, Inc., Sunderland, pp.407-425.
41. Swofford D.L. (1999), PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods), version 4.0. Sinauer Associates, Sunderland, Massachusetts.
42. Thompson J.D., Higgins D.G. and Gibson T.J. (1994), CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Research, 22, 4673-4680.
43. White T.J., Bruns T., Lee S. and Taylor J. (1990), Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In Innis MA, Gelfand DH; Sninsky JJ, White TJ (eds.) PCR Protocols: a guide to methods and applications, Academic Press, San Diego, pp. 315-322.
44. Wolfe K.H., Li W. and Sharp P.M. (1987), Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc. Natl. Acad. Sci. USA, 84, 9054-9058.
45. Zhang W., Wendel J.F. and Clark L.G. (1997), Bamboozled Again! Inadvertment Isolation of Fungal rDNA Sequences from Bamboos (Poaceae: Bambusoideae). Mol. Phylogenet. Evol., 8 (2), 205-217.