Development of a Fusarium graminearum Affymetrix GeneChip for profiling fungal gene expression in vitro and in planta.
Recently the genome sequences of several filamentous fungi have become available, providing the opportunity for large-scale functional analysis including genome-wide expression analysis. We report the design and validation of the first Affymetrix GeneChip microarray based on the entire genome of a filamentous fungus, the ascomycetous plant pathogen Fusarium graminearum. To maximize the likelihood of representing all putative genes (approximately 14,000) on the array, two distinct sets of automatically predicted gene calls were used and integrated into the online F. graminearum Genome DataBase. From these gene sets, a subset of calls was manually annotated and a non-redundant extract of all calls together with additional EST sequences and controls were submitted for GeneChip design. Experiments were conducted to test the performance of the F. graminearum GeneChip. Hybridization experiments using genomic DNA demonstrated the usefulness of the array for experimentation with F. graminearum and at least four additional pathogenic Fusarium species. Differential transcript accumulation was detected using the F. graminearum GeneChip with treatments derived from the fungus grown in culture under three nutritional regimes and in comparison with fungal growth in infected barley. The ability to detect fungal genes in planta is surprisingly sensitive even without efforts to enrich for fungal transcripts. The Plant Expression Database (PLEXdb, http://www.plexdb.org) will be used as a public repository for raw and normalized expression data from the F. graminearum GeneChip. The F. graminearum GeneChip will help to accelerate exploration of the pathogen-host pathways that may involve interactions between pathogenicity genes in the fungus and disease response in the plant.
Technische Universität München, Center of Life and Food Science, D-85350 Freising-Weihenstephan, Germany.
Ulrich
U
Güldener
Kye-Yong
KY
Seong
Jayanand
J
Boddu
Seungho
S
Cho
Frances
F
Trail
Jin-Rong
JR
Xu
Gerhard
G
Adam
Hans-Werner
HW
Mewes
Gary J
GJ
Muehlbauer
H Corby
HC
Kistler
D019295:Computational Biology; D003470:Culture Media / Q000737:chemistry; D005670:Fusarium / Q000235:genetics* / Q000254:growth & development; D020869:Gene Expression Profiling / Q000379:methods*; D016681:Genome, Fungal; D001467:Hordeum / Q000382:microbiology; D020411:Oligonucleotide Array Sequence Analysis; D010935:Plant Diseases / Q000382:microbiology
D003470:Culture Media