PLPA
638 Cumulative Readings
Spring 2004
Placing the fungi
*Animals
and fungi are each other's closest relatives: Congruent evidence from multiple
proteins
Sandra L. Baldauf and Jeffrey D. Palmer
Loculoascomycete
Origins and Evolution of Filamentous Ascomycete Morphology Based on 18s rRNA
Gene Sequence Data
Mary L. Berbee
*Dating
the Evolutionary Radiations of the True Fungi
Mary L. Berbee and John W. Taylor
New views on
fungal evolution based on DNA markers and the fossil record
Dirk Redecker
Phylogenetic
Relationships Among Ascomycetes: Evidence from an RNA Polymerse II Subunit
Yajuan J. Liu, Sally Whelen and Benjamin D. Hall
Classical genetics
Genetics Review.
Problem set is due Wednesday, April 7, 2004.
Slides used in lecture
Overheads used
in lecture
April
2 & 5, 2004
Moelcular genetic tools; transformation, mutagenesis/REMI
Lectures 3 & 4 (this
is a link to the notes)
Reference
List, PLPA638, April 2, 2004
B. G. Turgeon
Lectures 3, 4 Functional analysis: Tools: transformation, REMI and whole genome gene deletion/disruption
Transformation
*de
Groot MJ, Bundock P, Hooykaas PJ, Beijersbergen AG. 1998.
Agrobacterium
tumefaciens-mediated transformation of filamentous fungi.
Nat Biotechnol. 16(9):839-42.
Dunn-Coleman
N, Wang H.
Agrobacterium T-DNA: a silver bullet for filamentous fungi? 1998.
Nat Biotechnol. 16(9):817-8.
*Hinnen, A., J. B. Hicks, and G. R. Fink. 1978. Transformation of yeast. Proc. Natl. Acad. Sci. 75:1929-1933.
Ito, H., Y. Fukuda , K. Murata, and A. Kimura. 1983. Transformation of intact yeast cells treated with alkali. J. Bacteriol. 153:163-168.
Mandel, M. and A. Higa. 1970. Calcium-dependent bacteriophage DNA infection. J. Mol. Biol. 53:159-162.
*Turgeon, B. G., R. C. Garber, and O. C. Yoder. 1987. Development of a fungal transformation system based on selection of sequences with promoter activity. Mol Cell Biol 7:3297-3305.
Restriction Enzyme-Mediated Integration (REMI)
Kuspa, A. and W. F. Loomis. 1992. Tagging developmental genes in Dictyostelium by restriction enzyme-mediated integration of plasmid DNA. Proc. Natl. Acad. Sci. USA 89:8803-8807.
*Lu, S. W., L. Lyngholm, G. Yang, C. Bronson, O. C. Yoder, and B. G. Turgeon. 1994. Tagged mutations at the Tox1 locus of Cochliobolus heterostrophus using Restriction Enzyme Mediated Integration. Proc. Natl. Acad. Sci. USA 91:12649-12653
Schiestl, R. H. and T. D. Petes. 1991. Integration of DNA fragments by illegitimate recombination in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 88:7585-7589.
April
7, 2004
Molecular genetic tools; S. cerevisiae whole genome mutagenesis; random vs
directed
Yeast
Coelho PS, Kumar A, Snyder M. 2000. Genome-wide mutant collections: toolboxes for functional genomics. Curr Opin Microbiol. 3(3):309-15.
Kumar A, des Etages SA, Coelho PS, Roeder GS, Snyder M. 2000. High-throughput methods for the large scale analysis of gene function by transposon tagging. Methods Enzymol. 328:550-74.
*Kumar A, Snyder M. 2001. Emerging technologies in yeast genomics. Nat Rev Genet. Apr; 2 (4):302-12.
Ross-Macdonald
P. 2000. Functional analysis of the yeast genome.
Funct Integr Genomics, 1:99-113.
Ross-Macdonald
P, Coelho PS, Roemer T, Agarwal S, Kumar A, Jansen R, Cheung KH, Sheehan A,
Symoniatis D, Umansky L, Heidtman M, Nelson FK, Iwasaki H, Hager K, Gerstein
M, Miller P, Roeder GS, Snyder M. 1999. Large-scale analysis of the yeast
genome by transposon tagging and gene disruption. Nature. 25;402(6760):413-8.
Ross-Macdonald
P, Sheehan A, Roeder GS, Snyder M. 1997
A multipurpose transposon system for analyzing protein production, localization,
and function
in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 7;94(1):190-5.
Vidan
S, Snyder M. 2001. Large-scale mutagenesis: yeast genetics in the genome era.
Curr Opin Biotechnol. 12(1):28-34.
*Life
with 6000 Genes
A. Goffeau, B. G. Barrell, H. Bussey, R. W. Davis, B. Dujon, H. Feldmann,
F. Galibert, J. D. Hoheisel, C. Jacq, M. Johnston, E. J. Louis, H. W. Mewes,
Y. Murakami, P. Philippsen, H. Tettelin, S. G. Oliver
April
12, 2004
Sequenced
fungal genomes; comparative genomics S. pombe compared to S. cerevisiae
*The
genome sequence of Schizosaccharomyces pombe
V. Wood, R. Gwilliam, M.-A. Rajandream, M. Lyne, R. Lyne, A. Stewart, J. Sgouros,
N. Peat, J. Hayles, S. Baker, D.Basham, S. Bowman, K. Brooks, D. Brown, S.
Brown, T. Chillingworth, C. Churcher, M. Collins, R. Connor, A. Cronin, P.
Davis, T. Feltwell, A. Fraser, S. Gentles, A. Goble, N. Hamlin, D. Harris,
J. Hidalgo, G. Hodgson, S. Holroyd, T. Hornsby, S. Howarth, E. J. Huckle,
S. Hunt, K. Jagels, K. James, L. Jones, M. Jones, S. Leather, S. McDonald,
J. McLean, P. Mooney, S. Moule, K. Mungall, L. Murphy, D. Niblett, C. Odell,
K. Oliver, S. O'Neil, D. Pearson, M. A. Quail, E. Rabbinowitsch, K. Rutherford,
S. Rutter, D. Saunders, K. Seeger, S. Sharp, J. Skelton, M. Simmonds, R. Squares,
S. Squares, K. Stevens, K. Taylor, R. G. Taylor, A. Tivey, S. Walsh, T. Warren,
S. Whitehead, J. Woodward, G. Volckaert, R. Aert, J. Robben, B. Grymonprez,
I. Weltjens, E. Vanstreels, M. Rieger, M. SchaÈ fer, S.MuÈ ller-Auer,
C. Gabel, M. Fuchs, C. Fritzc, E. Holzer D. Moestl 6 , H. Hilbert, K. Borzym,
I. Langer, A. Beck, H. Lehrach, R. Reinhardt, T. M. Pohl, P. Eger, W. Zimmermann,
H. Wedler, R. Wambutt, B. Purnelle,A. Goffeau, E. Cadieu, S. Dre ano,
S. Gloux, V. Lelaure, S. Mottier, F. Galibert, S. J. Aves, Z. Xiang, C. Hunt,
K. Moore, S. M. Hurst, M. Lucas, M. Rochet, C. Gaillardin, V. A. Tallada,
A. Garzon , G. Thode , R. R. Daga, L. Cruzado, J. Jimenez, M. Sa nchez,
F. del Rey, J. Benito, A. DomõÂnguez, J. L. Revuelta, S. Moreno,
J. Armstrong, S. L. Forsburg, L. Cerrutti, T. Lowe, W. R. McCombie, I. Paulsen,
J. Potashkin, G. V. Shpakovski, D. Ussery , B. G. Barrell& P. Nurse
April
23, 2004
Sequenced
fungal genomes; comparative genomics N. crassa compared to S. cerevisiae
and S.
pombe
*The
Genome Sequence of the Filamentous Fungus Neurospora crassa
James E. Galagan, Sarah E. Calvo, Katherine A. Borkovich, Eric U. Selker,
Nick D. Read, David Jaffe1, William FitzHugh, Li-Jun Ma, Serge Smirnov, Seth
Purcell, Bushra Rehman, Timothy Elkins, Reinhard Engels, Shunguang Wang, Cydney
B. Nielsen, Jonathan Butler, Matthew Endrizzi, Dayong Qui, Peter Ianakiev,
Deborah Bell-Pedersen, Mary Anne Nelson, Margaret Werner-Washburne, Claude
P. Selitrennikoff, John A. Kinsey, Edward L. Braun, Alex Zelter, Ulrich Schulte,
Gregory O. Kothe, Gregory Jedd, Werner Mewes, Chuck Staben, Edward Marcotte,
David Greenberg, Alice Roy, Karen Foley, Jerome Naylor, Nicole Stange-Thomann,
Robert Barrett, Sante Gnerre, Michael Kamal, Manolis Kamvysselis, Evan Mauceli,
Cord Bielke, Stephen Rudd, Dmitrij Frishman, Svetlana Krystofova, Carolyn
Rasmussen, Robert L. Metzenberg, David D. Perkins, Scott Kroken, Carlo Cogoni,
Giuseppe Macino, David Catcheside22, Weixi Li16, Robert J. Pratt6, Stephen
A. Osmani23, Colin P. C. DeSouza, Louise Glass, Marc J. Orbach, J. Andrew
Berglund, Rodger Voelker, Oded Yarden, Michael Plamann, Stephan Seiler, Jay
Dunlap, Alan Radford, Rodolfo Aramay, Donald O. Natvig, Lisa A. Alex, Gertrud
Mannhaupt, Daniel J. Ebbole, Michael Freitag, Ian Paulsen, Matthew S. Sachs,
Eric S. Lander, Chad Nusbaum & Bruce Birren
Lessons
from the Genome Sequence of Neurospora crassa: Tracing the Path from Genomic
Blueprint to Multicellular Organism
Katherine A. Borkovich, Lisa A. Alex, Oded Yarden, Michael Freitag, Gloria
E. Turner, Nick D. Read, Stephan Seiler, Deborah Bell-Pedersen, John Paietta,
Nora Plesofsky, Michael Plamann, Marta Goodrich-Tanrikulu, Ulrich Schulte,
Gertrud Mannhaupt, Frank E. Nargang, Alan Radford, Claude Selitrennikoff,
James E. Galagan, Jay C. Dunlap, Jennifer J. Loros, David Catcheside, Hirokazu
Inoue, Rodolfo Aramayo, Michael Polymenis, Eric U. Selker, Matthew S. Sachs,
George A. Marzluf, Ian Paulsen, Rowland Davis, Daniel J. Ebbole, Alex Zelter,
Eric R. Kalkman, Rebecca O’Rourke, Frederick Bowring, Jane Yeadon, Chizu Ishii,
Keiichiro Suzuki, Wataru Sakai, and Robert Pratt
April
28, 2004
Expression profiling
*Gasch.
A.P. et al 2000.
11:4241-57 Molecular Biology of the Cell.
April 30, 2004
Filamentous fungal gene annotation tools; features of the fungal genome
See handout and K-drive/everyone/plpa 638
May
3, 2004
Plant/Microbe interactions
*ON
THE TRAIL OF A CEREAL KILLER: Exploring the Biology ofMagnaporthe grisea
Nicholas J. Talbot
May
5, 2004
Phylogenomics, cross genome comparisons
See handout and k-drive/everyone/plpa638
Whole-Genome
Analysis of Two-Component Signal Transduction Genes in Fungal Pathogens
Natalie L. Catlett, Olen C. Yoder, and B. Gillian Turgeon
Phylogenomic
analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes
Scott Kroken, N. Louise Glass, John W. Taylor, O. C. Yoder, and B. Gillian
Turgeon
A complete inventory of fungal kinesins in representative filamentous ascomycetes
Conrad L. Schoch, James R. Aist, Olen C. Yoder, and B. Gillian Turgeon