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Original Articles

megB1, a Novel Macroevolutionary Genomic Marker of the Fungal Phylum Basidiomycota

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Pages 1927-1939 | Received 13 Mar 2007, Accepted 08 May 2007, Published online: 22 May 2014

  • 1) Kimura, M., A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences. J. Mol. Evol., 16, 111–120 (1980).
  • 2) Peek, A. S., Vrijenhoek, R. C., and Gaut, B. S., Accelerated evolutionary rate in sulfur-oxidizing endosymbiotic bacteria associated with the mode of symbiont transmission. Mol. Biol. Evol., 15, 1514–1523 (1998).
  • 3) Bruns, T. D., Vilgalys, R., Barns, S. M., Gonzalez, D., Hibbett, D. S., Lane, D. J., Simon, L., Stickel, S., Szaro, T. M., Weisburg, W. G., and Sogin, M. L., Evolutionary relationships within the fungi: analyses of nuclear small subunit rRNA sequences. Mol. Phylog. Evol., 1, 231–241 (1992).
  • 4) Bruns, T. D., White, T. J., and Taylor, J. W., Fungal molecular systematics. Annu. Rev. Ecol. Syst., 22, 525–564 (1991).
  • 5) Hibbett, D. S., Ribosomal RNA and fungal systematics. Trans. Mycol. Soc. Japan, 33, 533–556 (1992).
  • 6) Moncalvo, J.-M., Lutzoni, F. M., Rehner, S. A., Johnson, J., and Vilgalys, R., Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences. Syst. Biol., 49, 278–305 (2000).
  • 7) Vilgalys, R., Murhsooms of North Carolina. http://biology.duke.edu/fungi/ (1996).
  • 8) Blackwell, M., Vilgalys, R., and Taylor, J. W., Fungi. Tree of Life. http://phylogeny.arizona.edu/tree/eukaryotes/fungi/fungi.html (1996).
  • 9) Spatafora, J., Assembling the fungal tree of life. http://aftol.org/ (2003).
  • 10) Walker, W. F., and Doolittle, W. F., Redividing the basidiomycetes on the basis of 5S rRNA sequences. Nature, 299, 723–724 (1982).
  • 11) Bruns, T., A kingdom revised. Nature, 443, 758–761 (2006).
  • 12) James, T. Y., Kauf, F., Schoch, C. L., Matheny, P. B., Hofstetter, V., Cox, C. J., Celio, G., Gueidan, C., Franker, E., Miadlikowska, J., Lumbsch, H. T., Rauhut, A., Reeb, V., Arnold, A. E., Amtoft, A., Stajich, J. E., Hosokawa, K., Sung, G.-H., Johnson, D., O’Rourke, B., Crockett, M., Binder, M., Curtis, J. M., Slot, J., Wang, Z., Wilson, A. W., Schüßler, A., Longcore, J. E., O’Donnell, K., Mozley-Standridge, S., Porter, D., Letcher, P., Powell, M. J., Taylor, J. W., White, M. M., Griffith, G. W., Davies, D. R., Humber, R. A., Morton, J. B., Sugiyama, J., Rossman, A. Y., Rogers, J. D., Pfister, D. H., Hewitt, D., Hansen, K., Hambleton, S., Shoemaker, R. A., Kohlmeyer, J., Volkmann-Kohlmeyer, B., Spotts, R., Serdani, M., Crous, P. W., Hughes, K. W., Matsuura, K., Langer, E., Langer, G., Untereiner, W. A., Lücking, R., Büdel, B., Geiser, D. M., Aptroot, A., Diederich, P., Schmitt, I., Schultz, M., Yahr, R., Hibbett, D. S., Lutzoni, F., MacLaughlin, D. J., Spatafora, J. W., and Vilgalys, R., Reconstructing the early evolution of fungi using a six-gene phylogeny. Nature, 443, 818–822 (2006).
  • 13) Venema, J., and Tollervey, D., Ribosome synthesis. Annu. Rev. Genet., 33, 261–311 (1999).
  • 14) Vilgalys, R., and Gonzalez, D., Organization of ribosomal DNA in the basidiomycete Thanatephorus praticola. Curr. Genet., 18, 277–280 (1990).
  • 15) Mougey, E. B., Pape, L. K., and Sollner-Webb, B., Virtually the entire Xenopus laevis rDNA multikilobase intergenic spacer serves to stimulate polymerase I transcription. J. Biol. Chem., 271, 27138–27145 (1996).
  • 16) Guerin-Laguett, A., Matsushita, N., Kikuchi, K., Iwase, K., Lapeyrie, F., and Suzuki, K., Identification of a prevalent Tricholoma matsutake ribotype in Japan by rDNA IGS1 spacer characterization. Mycol. Res., 106, 435–443 (2002).
  • 17) Saito, T., Tanaka, N., and Shinozawa, T., Characterization of subrepeat regions within rDNA intergenic spacers of the edible basidiomycete Lentinula edodes. Biosci. Biotechnol. Biochem., 66, 2125–2133 (2002).
  • 18) Coetzee, M. P. A., Wingfield, B. D., Bloomer, P., and Wingfield, M. J., Phylogenetic analyses of DNA sequence reveal species partitions amongst isolates of Armillaria from Africa. Mycol. Res., 109, 1223–1234 (2005).
  • 19) Harrington, T. C., and Wingfield, B. D., A PCR based identification method for species of Armillaria. Mycologia, 87, 280–288 (1995).
  • 20) Schnabel, G., Ash, J. S., and Bryson, P. K., Identification and characterization of Armillaria tabescens from the southern United States. Mycol. Res., 109, 1208–1222 (2005).
  • 21) Zhang, J. X., Huang, C. Y., Ng, T. B., and Wang, H. X., Genetic polymorphism of ferula mushroom growing on Ferula sinkiangensis. Appl. Microbiol. Biotechnol., 71, 304–309 (2005).
  • 22) Shedlock, A. M., Takahashi, K., and Okada, N., SINEs of speciation: tracking lineages with retroposons. Trends Ecol. Evol., 19, 545–553 (2004).
  • 23) Bennetzen, J. L., Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol., 42, 251–269 (2000).
  • 24) Bushman, F., “Lateral DNA Transfer: Mechanisms and Consequences,” Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp. 1–448 (2002).
  • 25) Brosius, J., Retroposons-seeds of evolution. Science, 251, 753 (1991).
  • 26) Lee, S. B., and Taylor, J. W., Isolation of DNA from fungal mycelia and single spores. In “PCR Protocoles: A Guide to Methods and Applications,” eds. Innis, M. A., Gelfand, D. H., Sninsky, J. J., and White, T. J., Acadmic Press, San Diego, pp. 282–299 (1990).
  • 27) Pérez-Sierra, A., Guillaumin, J.-J., Spooner, B. M., and Bridge, P. D., Characterization of Armillaria heimii from Africa. Plant Pathol., 53, 220–230 (2004).
  • 28) Murata, H., Yamada, A., and Babasaki, K., Identification of repetitive sequences containing motifs of retrotransposons in the ectomycorrhizal basidiomycete Tricholoma matsutake. Mycologia, 91, 766–775 (1999).
  • 29) Sambrook, J., and Russell, D. W., “Molecular Cloning, a Laboratory Manual” 3rd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor (2001).
  • 30) Corpet, F., Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res., 16, 10881–10890 (1988).
  • 31) Thompson, J. D., Higgins, D. G., and 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, 4673–4680 (1994).
  • 32) Taprab, Y., Johjima, T., Maeda, Y., Moriya, S., Trakulnaleamsai, S., Noparatnaraporn, N., Ohkuma, M., and Kudo, T., Symbiotic fungi produce laccase potentially involved in phenol degradation in fungus combs of fungus-growing termites in Thailand. Appl. Environ. Microbiol., 71, 7696–7704 (2005).
  • 33) Shimomura, M., Yasue, H., Ohshima, K., Abe, H., Kato, H., Kishiro, T., Goto, M., Munechika, I., and Okada, N., Molecular evidence from retroposons that whales form a clade within even-toed ungulates. Nature, 388, 666–670 (1997).
  • 34) Murata, H., Miyazaki, Y., and Yamada, A., marY2N, a LINE-like non-long terminal repeat (non-LTR) retroelement from the ectomycorrhizal homobasidiomycete Tricholoma matsutake. Biosci. Biotechnol. Biochem., 65, 2301–2305 (2001).
  • 35) Murata, H., and Yamada, A., marY1, a member of the gypsy group of long terminal repeat retroelements from the ectomycorrhizal basidiomycete Tricholoma matsutake. Appl. Environ. Microbiol., 66, 3642–3645 (2000).
  • 36) Murata, H., and Babasaki, K., Intra- and Inter-specific variations in the copy number of two types of retrotransposons from the ectomycorrhizal basidiomycete Tricholoma matsutake. Mycorrhiza, 15, 381–386 (2005).
  • 37) Murata, H., Babasaki, K., and Yamada, A., Highly polymorphic DNA markers to specify strains of the ectomycorrhizal basidiomycete Tricholoma matsutake based on σmarY1, the long terminal repeat of gypsy-type retroelement marY1. Mycorrhiza, 15, 179–186 (2004).
  • 38) Murata, H., Babasaki, K., Miyazaki, Y., and Yamada, A., Genetic evidence that two types of retroelements evolved through different pathways in ectomycorrhizal homobasidiomycetes Tricholoma spp. Biosci. Biotechnol. Biochem., 66, 1880–1886 (2002).
  • 39) Murata, H., Ohta, A., Yamada, A., Narimatsu, M., and Futamura, N., Genetic mosaics in the massive persistent rhizosphere colony “shiro” of the ectomycorrhizal basidiomycete Tricholoma matsutake. Mycorrhiza, 15, 505–512 (2005).
  • 40) Anaya, N., and Roncero, M. I. G., Skippy, a retrotransposon from the fungal plant pathogen Fusarium oxysporum. Mol. Gen. Genet., 249, 637–647 (1995).
  • 41) Dobinson, K. F., Harris, R. E., and Hamer, J. E., Grasshopper, a long terminal repeat (LTR) retroelement in the phytopathogenic fungus, Magnaporthe grisea. Mol. Plant-Microbe Interact., 6, 114–126 (1993).
  • 42) Farman, M. L., Tosa, Y., Nitta, N., and Leong, S. A., MAGGY, a retrotransposon in the genome of the rice blast fungus Magnaporthe grisea. Mol. Gen. Genet., 251, 665–674 (1996).
  • 43) Hamer, J. E., Farrall, L., Orbach, M. J., Valent, B., and Chumley, F. G., Host species-specific conservation of a family of repeated DNA sequences in the genome of a fungal pathogen. Proc. Natl. Acad. Sci. USA, 86, 9981–9985 (1989).
  • 44) McHale, M. T., Roberts, I. N., Noble, S. M., Beaumont, C., Whitehead, M. P., Seth, D., and Oliver, R. P., CfT-I: an LTR-retrotransposon in Cladoporium fulvum, a fungal pathogen of tomato. Mol. Gen. Genet., 233, 337–347 (1992).
  • 45) Sone, T., Suto, M., and Tomita, F., Host species-specific repetitive DNA sequence in the genome of Magnaporthe grisea, the rice blast fungus. Biosci. Biotechnol. Biochem., 57, 1228–1230 (1993).
  • 46) Ota, Y., Matsushita, N., Nagasawa, E., Terashita, T., Fukuda, K., and Suzuki, K., Biological species of Armillaria in Japan. Plant Disease, 82, 537–543 (1998).
  • 47) Babasaki, K., Masuno, K., and Murata, H., Interactions of heterologous mycelia colonized in the substrate govern fruit body production in the cultivated homobasidiomycete Pholiota nameko. Biosci. Biotechnol. Biochem., 67, 100–106 (2003).

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