Advertisement

Genes to Genomics: Mapping the Fungal Genome

Abstract

Although we discussed molecular markers in the Chapter 7, and thereby leaned toward physical analysis, the theme of our story so far has been the use of the classic approach of genetics: making an organized series of crosses and using gene segregations to deduce chromosome maps. Entirely conventional procedures can result in those chromosomal maps showing the location of genes and centromeres. Then, by using molecular markers, the telomeres of the chromosome, and as many other loci as we are willing to characterize and include in our crosses, can be mapped along the chromosomes of an organism. Large-scale, high-density linkage maps can be assembled in this way. A high-density linkage map is conventionally considered to be one with one gene or marker for each 1% recombination in the genome.

Keywords

Neurospora Crassa Aspergillus Nidulans Optical Mapping Yeast Genome Schizosaccharomyces Pombe 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Publications and Websites Worth a Visit

  1. Aston, C. Mishra, B. & Schwartz, D.C. (1999). Optical mapping and its potential for large-scale sequencing projects. Trends in Biotechnology 17, 297–302.PubMedCrossRefGoogle Scholar
  2. Bennett, J.W. (1997). White paper: genomics for filamentous fungi. Fungal Genetics and Biology 21, 3–7.CrossRefGoogle Scholar
  3. Birren, B., Green, E.D., Klapholz, S., Myers, R.M. & Roskams, J. (1997). Genome Analysis: A Laboratory Manual. Vol. 1, Analyzing DNA. Vol. 2, Detecting Genes. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY.Google Scholar
  4. Cho, R.J. & Campbell, M.J. (2000). Transcription, genomes, function. Trends in Genetics 16, 409–415.PubMedCrossRefGoogle Scholar
  5. Delneri, D., Brancia, F.L. & Oliver, S.G. (2001). Towards a truly integrative biology through the functional genomics of yeast. Current Opinion in Biotechnology 12, 87–91.PubMedCrossRefGoogle Scholar
  6. Farman, M.L. (2001). Genome analysis in filamentous fungi. In Molecular and Cellular Biology of Filamentous Fungi (N.J. Talbot, ed.), pp. 91–117. Oxford University Press: Oxford, U.K.Google Scholar
  7. Horiike, T., Hamada, K., Kanaya, S. & Shinozawa, T. (2001). Origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria is revealed by homology-hit analysis. Nature Cell Biology 3, 210–214.PubMedCrossRefGoogle Scholar
  8. Jansen, R.C. & Nap, J.-P. (2001). Genetical genomics: the added value from segregation. Trends in Genetics 17, 388–391.PubMedCrossRefGoogle Scholar
  9. Kupfer, D.M., Reece, CA., Clifton, S.W., Roe, B.A. & Prade, R.A. (1997). Multicellular ascomycetous fungal genomes contain more than 8000 genes. Fungal Genetics and Biology 21, 364–372.PubMedCrossRefGoogle Scholar
  10. Murray, A.W. (2000). Whither genomics? Genome Biology 1, comment003.1-003.6. The journal Nature operates a Genome Gateway, which is intended to be a comprehensive web resource devoted to genomics that includes original research papers, a news service, and a set of links to the most useful and informative genomics sites on the web. Access is free at http://www.nature.com/genomics/intro.html.Google Scholar
  11. Nitta, N, Farman, M.L. & Leong, S.A. (1997). Genome organization of Magnaporthe grisea: integration of genetics maps, clustering of transposable elements and identification of genome duplications and rearrangements. Theoretical and Applied Genetics 5, 20–32.Google Scholar
  12. Pandolfo, M. (1999). Molecular pathogenesis of Friedreich Ataxia. Archives of Neurology 56, 1201–1208.PubMedCrossRefGoogle Scholar
  13. Peterson, S.N. & Fraser, CM. (2001). The complexity of simplicity. Genome Biology 2, comment2002.1-2002.8. The electronic version of this article can be found online at http://genomebiology.com/2001/2/2/comment/2002.Google Scholar
  14. Prade, R.A. (2000). The reliability of the Aspergillus nidulans physical map. Fungal Genetics and Biology 29, 175–185.PubMedCrossRefGoogle Scholar
  15. Raamsdonk, L.M., Teusink, B., Broadhurst, D., Zhang, N, Hayes, A., Walsh, M.C & Berden, J.A. (2001). A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nature Biotechnology 19, 45–50.PubMedCrossRefGoogle Scholar
  16. Sharman, A. (2001). The many uses of a genome sequence. Genome Biology 2, reports 4013.1-4013.4. The electronic version of this article can be found online at http://genomebiology.com/2001/2/6/reports/4013.Google Scholar
  17. Spurr, N.K., Young, B.D. & Bryant, S.P. (1998). ICRF Handbook of Genome Analysis (in two volumes). Blackwell Science Ltd: Oxford, U.K.Google Scholar
  18. Tait, E., Simon, M.C., King, S., Brown, A.J., Gow, N.A.R. & Shaw, DJ. (1997). A Candida albicans genome project: cosmid contigs, physical mapping, and gene isolation. Fungal Genetics and Biology 21, 308–314.PubMedCrossRefGoogle Scholar
  19. Thompson, A., Lucchini, S. & Hinton, J.C.D. (2001). It’s easy to build your own microarrayer! Trends in Microbiology 9, 154–156.PubMedCrossRefGoogle Scholar
  20. Washburn, M.P. & Yates, J.R. III (2000). Analysis of the microbial proteome. Current Opinion in Microbiology 3, 292–297.PubMedCrossRefGoogle Scholar
  21. Zhu, H., Choi, S., Johnson, A.K., Wing, R.A. & Dean, R.A. (1997). A large-insert (130 kbp) bacterial artificial chromosome library of the rice blast fungus Magnaporthe grisea: genome analysis, contig assembly, and gene cloning. Fungal Genetics and Biology 21, 337–347.PubMedCrossRefGoogle Scholar

Historical Publications Worth Knowing About

  1. Bell, G.I., DeGennaro, L.J., Gelfand, D.H., Bishop, R.J., Valenzuela, P. & Rutter, WJ. (1977). Ribosomal RNA genes of Saccharomyces cerevisiae. I. Physical map of the repeating unit and location of the regions coding for 5S, 5.8S, 18S and 25S ribosomal RNAs. Journal of Biological Chemistry 252, 8118–8125.PubMedGoogle Scholar
  2. Broda, P., Oliver, S.G. & Sims, REG. (1993). The Eukaryotic Genome. Cambridge University Press: Cambridge, U.K.Google Scholar
  3. Metzenberg, R.L., Stevens, J.N., Selker, E.U. & Morzycka-Wroblewska, E. (1985). Identification and chromosomal distribution of 5 S rRNA genes in Neurospora crassa. Proceedings of the National Academy of Sciences of the United States of America 82, 2067–2071.PubMedCrossRefGoogle Scholar
  4. Schwartz, D.C., Li, X., Hernandez, L.I., Ramnarain, S.P., Huff, E.J. & Wang, Y.-K. (1993). Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science 262, 110–114.PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag New York, Inc. 2002

Personalised recommendations