PLPA
638 Cumulative Readings
Spring 2005
Spring 2004
March
28, 2005
Assembling
The Fungal Tree of Life: Progress, Classification, and Evolution of Subcellular
Traits
Franc¸Ois
Lutzoni, Frank Kauff, Cymon J. Cox, David McLaughlin, Gail Celio, Bryn Dentinger,
Mahajabeen Padamsee, David Hibbett, Timothy Y. James, Elisabeth Baloch, Martin
Grube, Vale´ Rie Reeb, Vale´ Rie Hofstetter, Conrad Schoch, A. Elizabeth
Arnold, Jolanta Miadlikowska, Joseph Spatafora, Desiree Johnson, Sarah Hambleton,
Michael Crockett, Robert Shoemaker, Gi-Ho Sung, Robert Lu¨ Cking, Thorsten
Lumbsch, Kerry O’Donnell, Manfred Binder, Paul Diederich, Damien Ertz, Ce´
Cile Gueidan, Karen Hansen, Richard C. Harris, Kentaro Hosaka, Young-Woon Lim,
Brandon Matheny, Hiromi Nishida, Don Pfister, Jack Rogers, Amy Rossman, Imke
Schmitt, Harrie Sipman, Jeffrey Stone, Junta Sugiyama, Rebecca Yahr, And Rytas
Vilgalys
*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
March 30, 2005
Classical genetics
Genetics Review. Problem set
Problem set is due Monday, April 4, 2005.
Slides
used in lecture
April 1 & 4, 2005
Molecular genetic tools; transformation, mutagenesis/REMI
Lectures 3 & 4 (this is a link
to the notes)
Lectures 3, 4 Functional analysis: Tools: transformation, REMI and whole genome gene deletion/disruption
Transformation
Reference List, PLPA638
*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 6, 2005
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.
Large-Scale
Mutagenesis of the Yeast Genome Using a Tn7-Derived Multipurpose Transposon
Anuj Kumar, Michael Seringhaus, Matthew C. Biery, Robert J. Sarnovsky, Lara
Umansky, Stacy Piccirillo, Matthew Heidtman, Kei-Hoi Cheung, Craig J. Dobry,
Mark B. Gerstein, Nancy L. Craig and Michael Snyder
April 8 & 11, 2005
Sequenced fungal genomes; S. cerevisiae
*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
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
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
April 18, 2005
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 20, 2005
Gene
annotation tools
Overheads used in class
April 22 & 25, 2005
Slides used in lecture
Slides used in lecture
Nicholas J. Talbot
*The
genome sequence of the rice blast fungus Magnaporthe grisea
Ralph
A. Dean, Nicholas J. Talbot, Daniel J. Ebbole, Mark L. Farman, Thomas K. Mitchell,
Marc J. Orbach, Michael Thon, Resham Kulkarni, Jin-Rong Xu, Huaqin Pan, Nick
D. Read, Yong-Hwan Lee, Ignazio Carbone, Doug Brown, Yeon Yee Oh, Nicole Donofrio,
Jun Seop Jeong, Darren M. Soanes, Slavica Djonovic, Elena Kolomiets, Cathryn
Rehmeyer, Weixi Li, Michael Harding, Soonok Kim, Marc-Henri Lebrun, Heidi Bohnert,
Sean Coughlan, Jonathan Butler, Sarah Calvo, Li-Jun Ma, Robert Nicol, Seth Purcell,
Chad Nusbaum, James E. Galagan & Bruce W. Birren
Howard, R. J. M. A. Ferrari, D. H Roach, and N. P. Money. 1991. Penetration of hard substrates by a fungus employing enormous turgor pressures. PNAS. 88:11281-84.
Park, G., K. S. Bruno, C. J. Staiger, N. J. Talbot, and J.-R Xu. 2004. Independent genetic mechanisms mediate turgor generation and penetration peg formation during plant infection in the rice blast fungus. Molec. Microbiol. 53:1695-1707.
Talbot, N. J., M. J. Kershaw, G. E. Wakley, O. M. H. de Vries, J. G. H. Wessels, and J. E. Hamer. 1996. MPGI encodes a funga1 hydrophobin involved in surface interactions during infection-related development of Magnaporthe grisea. The Plant Cell, Vol. 8, 985-999.