Bamboozled Again! Inadvertent Isolation of Fungal rDNA Sequences from Bamboos (Poaceae: Bambusoideae)

Molecular Phylogenetics and Evolution

Volumn 8, Issue 2, 1997, Pages 205-217

  Zhang, Weiping ^a   Wendel, Jonathan F ^a   Clark, Lynn G ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL DNA; PLANT DNA; PRIMER DNA; RIBOSOME DNA; RNA 5.8S;

ARTICLE; CLASSIFICATION; FUNGUS; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT; POLYMERASE CHAIN REACTION; SCANNING ELECTRON MICROSCOPY; SEQUENCE HOMOLOGY;

BASE SEQUENCE; DNA PRIMERS; DNA, FUNGAL; DNA, PLANT; DNA, RIBOSOMAL; FUNGI; MICROSCOPY, ELECTRON, SCANNING; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANTS; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 5.8S; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 0031253701     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1006/mpev.1997.0422     Document Type: Article

References (63)

1. Alexopoulos C. J., Mims C. W., Blackwell M. Introductory Mycology. 1996;Wiley, New York.
2. Altschul S. F., Gish W., Miller W., Mayers E. W., Lipman D. J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410.
3. Bacon C. W., Hill N. S. Symptomless grass endophytes: Products of coevolutionary symbioses and their role in the ecological adaptations of grasses. Endophytic Fungi in Grasses and Woody Plants. 1996;APS Press, St. Paul. p. 155-178.
4. Baldwin B. G., Campbell C. S., Porter J. M., Sanderson M. J., Wojciechowski M. F., Donoghue M. J. The ITS region of nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny. Ann. Mo. Bot. Gard. 82:1995;247-277.
5. Bentham G., Hooker J. D. Genera Plantarum 3(2). 1883;L. Reeve, London.
6. Blaney C. Fungi in the family tree. BioScience. 45:1995;746.
7. Bobola M. S., Smith D. E., Klein A. S. Five major ribosomal repeats represent a large and variable fraction of the total genomic DNA ofPicea rubensP. mariana. Mol. Biol. Evol. 9:1992;125-137.
8. Bremer K. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution. 42:1988;795-803.
9. Cayouette M., Gackstetter T., Moores J. The effects of various additives on experimentally determined PCR annealing temperatures. Strategies. 9:1996;33-35.
10. Clark L. G., Zhang W., Wendel J. F. The phylogeny of the grass family (Poaceae) based onndhF. Syst. Bot. 20:1995;436-460.
11. Clay K. Fungal endophytes of grasses: A defensive mutualism between plants and fungi. Ecology. 69:1988;10-16.
12. Clay K. Fungal endophytes of grass. Annu. Rev. Ecol. Syst. 21:1990;275-295.
13. Clay K., Leuchtmann A. Infection of woodland grasses by fungal endophytes. Mycologia. 81:1989;805-811.
14. Clayton W. D., Renvoize S. A. Genera Graminum. 1986;Her Majesty's Stationery Office, London.
15. Downie S. R., Katz-Downie D. S. A molecular phylogeny of Apiaceae subfamily Apioideae: Evidence from nuclear ribosomal DNA internal transcribed spacer sequence. Am. J. Bot. 83:1996;234-251.
16. Frothingham R., Blitchington R. B., Lee D. H., Greene R. C., Wilson K. H. UV absorption complicates PCR decontamination. BioTechniques. 13:1992;208-210.
17. Hershkovitz M. A., Lewis L. A. Deep-level diagnostic value of the rDNA-ITS region. Mol. Biol. Evol. 13:1996;1276-1295.
18. Hino I. Icones Fungorum Bambusicolorum Japonicorum. 1961;The Fuji Bamboo Garden.
19. Holttum R. E. The classification of bamboos. Phytomorph. 6:1956;73-90.
20. Hsiao C., Chatterton N. J., Asay K. H., Jensen K. B. Phylogenetic relationships of 10 grass species: An assessment of phylogenetic utility of the internal transcribed spacer region in nuclear ribosomal DNA in monocots. Genome. 37:1993;112-120.
21. Hsiao C., Chatterton N. J., Asay K. H., Jensen K. B. Phylogenetic relationships of the monogenomic species of the wheat tribe, Triticeae (Poaceae), inferred from nuclear rDNA (internal transcribed spacer) sequences. Genome. 38:1994;211-223.
22. Hsiao C., Chatterton N. J., Asay K. H., Jensen K. B. Molecular phylogeny of the Pooideae (Poaceae) based on nuclear rDNA (ITS) sequences. Theor. Appl. Genet. 90:1995;389-398.
23. P. T.-W. Hsiau, 1996, The Taxonomy and Phylogeny of the Mycangial Fungi fromDendroctonus brevicomisD. frontalis, Iowa State University, Ames.
24. Hunziker J. H., Stebbins G. L. Chromosomal evolution in the Gramineae. Soderstrom T. R., Hilu K. W., Campbell C. S., Barkworth M. E. Grass Systematics and Evolution. 1987;179-187 Smithsonian Institution Press, Washington.
25. Kelchner S. A., Clark L. G. Molecular evolution and phylogenetic utility of the chloroplastrpl16Chusquea. Mol. Phyl. Evol. 1997.
26. Kellogg E. A., Watson L. Phylogenetic studies of a large data set. I. Bambusoideae, Andropogonodae, and Pooideae (Gramineae). Bot. Rev. 59:1993;273-343.
27. Keng P. C. A systematic key to the tribes and genera of subfam. Bambusoideae (Gramineae) occurring in China and its neighborhoods. J. Bamboo Res. 6:1987;13-28.
28. Keng Y. L. Flora Illustralis Plantarum Sinicarum - Gramineae. 1959.
29. Kim K.-J., Jansen R. K. Comparisons of phylogenetic hypotheses among different data sets in dwarf dandelion (Krigia, Plant Syst. Evol. 190:1994;157-185.
30. Liston A., Alvarez-Buylla E. Internal transcribed spacer sequences of conifers: "There is a fungus among us" Inoculum. 46:1995;26.
31. Liston A., Robinson W. A., Oliphant J. M., Alvarez-Buylla E. R. Length variation in the nuclear ribosomal DNA internal transcribed spacer region of non-flowering seed plants. Syst. Bot. 21:1996;109-120.
32. Lu Y. H., Negre S. Use of glycerol for enhanced efficiency and specificity of PCR amplification. Trends Genet. 9:1993;297.
33. Lyal C. H. C. Coevolutionary relationships of lice and their hosts: A test of Farenholtz's Rule. Stone A. R., Hawksworth D. L. Coevolution and Systematics. 1986;77-91 Clarendon Press, Oxford.
34. McClure F. A. Genera of bamboos native to the New World. Smithsonian Contr. Bot. 9:1973;1-148.
35. Munro W. A monograph of the Bambusaceae, including descriptions of all the species. Trans. Linn. Soc. London. 26:1868;1-157.
36. Nishida H., Sugiyama J. A common group I intron between a plant parasitic fungus and its host. Mol. Biol. Evol. 12:1995;883-886.
37. Olmstead R. G., Palmer J. D. Chloroplast DNA systematics: A review of methods and data analysis. Am. J. Bot. 81:1994;1205-1224.
38. Paterson A. H., Brubaker C. L., Wendel J. F. A rapid method for extraction of cotton (Gossypium. Plant Mol. Bio. Rep. 11:1993;122-127.
39. Pearson W. P., Lipman D. J. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA. 85:1988;2444-2448.
40. Rao V. B. Strategies for direct sequencing of PCR-amplified DNA. PCR Methods Appl. 4:1994;15-23.
41. Ritland C. E., Straus N. A. High evolutionary divergence of the 5.8S ribosomal DNA inMimulus glaucescens. Plant Mol. Biol. 22:1993;691-699.
42. Ritland C. E., Ritland K., Straus N. A. Variation in the ribosomal internal transcribed spacers (ITS1 and ITS2) among eight taxa of theMimulus guttatus. Mol. Biol. Evol. 10:1993;1273-1288.
43. Roberts L. Finding DNA sequencing errors. Science. 252:1991;1255-1256.
44. Rollo F., Sassaroli S., Ubaldi M. Molecular phylogeny of the fungi of the iceman's grass clothing. Curr. Genet. 28:1995;289-297.
45. Roux K. H. Optimization and troubleshooting in PCR. PCR Methods Applic. 4:1995;185-194.
46. Sambrook J. E., Fritsch F., Mariatis T. Molecular Cloning. 1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
47. Sarkar G., Sommer S. S. Shedding light on PCR contamination. Nature. 343:1990;27.
48. Schultz B., Wanke U., Draeger S., Aust H.-J. Endophytes from herbaceous plants and shrubs: Effectiveness of surface-sterilization methods. Mycol. Res. 97:1993;1447-1450.
49. Smith D. E., Klein A. S. Phylogenetic inferences on the relationship of North American and EuropeanPicea. Mol. Phylogenet. Evol. 3:1994;17-26.
50. Smith D. E., Klein A. S. Erratum. Mol. Phylogenet. Evol. 5:1996;286-287.
51. Soderstrom T. R. Some evolutionary trends in the Bambusoideae (Poaceae). Ann. Mo. Bot. Gard. 68:1981;15-47.
52. Soderstrom T. R., Ellis R. The position of bamboo genera and allies in a system of grass classification. Soderstrom T. R., Hilu K. W., Campbell C. S., Barkworth M. E. Grass systematics and evolution. 1987;225-238 Smithsonian Institution Press, Washington.
53. Suh Y., Thien L. B., Reeve H. E., Zimmer E. A. Molecular evolution and phylogenetic implications of internal transcribed spacer sequences of ribosomal DNA in Winteraceae. Am. J. Bot. 80:1993;1042-1055.
54. D. L. Swofford, 1993, PAUP: Phylogenetic Analysis Using Parsimony, Illinois Natural History Survey, Champaign, IL.
55. Thompson J. The Coevolutionary Process. 1994;Chicago Univ. Press, Chicago.
56. Thompson J. D., Higgins D. G., Gibson T. J. Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:1994;4673-4680.
57. White J. F. The widespread distribution of endophytes in the Poaceae. Plant Dis. 71:1987;340-342.
58. White J. F. Structure and mating system of the graminicolous fungal epibiontEchinodothis tuberiformis. Am. J. Bot. 80:1993;1465-1471.
59. White J. F., Glenn A. E. A study of two fungal epibionts of grasses: Structural features, host relationships, and classification in the genusMyriogenospora. Am. J. Bot. 81:1994;216-223.
60. White J. F., Morgan-Jones G. Morphological and physiological adaptations of Balansieae and trends in the evolution of grass endophytes. Redlin S. C., Carris L. M. Endophytic Fungi in Grasses and Woody Plants. 1996;133-154 APS Press, St. Paul.
61. White J. F., Breen J. P., Morgan-Jones G. Substrate utilization in selectedAcremonium, Atkinsonella,Balansia. Mycologia. 83:1991;601-610.
62. White T. J., Burns T., Lee S., Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Innis M. A., Gelfand D. H., Sninsky J. J., White T. J. PCR Protocols: A Guide to Methods and Application. 1990;315-322 Academic Press, San Diego.
63. Zhang W. The classification of Bambuseae (Poaceae) in China. J. Am. Bamboo Soc. 9:1992;25-42.