Development of a Fusarium graminearum Affymetrix GeneChip for profiling fungal gene expression in vitro and in planta

Ulrich Güldener, Kye Yong Seong, Jayanand Boddu, Seungho Cho, Frances Trail, Jin Rong Xu, Gerhard Adam, Hans Werner Mewes, Gary J. Muehlbauer, H. Corby Kistler

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163 Scopus citations


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 (∼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, 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.

Original languageEnglish (US)
Pages (from-to)316-325
Number of pages10
JournalFungal Genetics and Biology
Issue number5
StatePublished - May 2006

Bibliographical note

Funding Information:
The authors thank Sam Gale and Karen Hilburn for excellent technical support and Ruth Dill-Macky for providing strain Butte 86. The project was supported by the National Research Initiative of the USDA Cooperative State Research, Education and Extension Service (Grant No. 2004-35604-14327 to HCK, JRX, and FT) the Austrian genome program GEN-AU (bm:bwk - Federal Ministry for Education, Science and Culture, GZ 200.051/6-VI/1/2001 to GA) and a grant from the German Federal Ministry of Education and Research (BMBF) within the BFAM framework (031U112C/212C—to UG and HWM). The US Wheat and Barley Scab Initiative is also acknowledged by G.J.M., F.T., J.R.X., and H.C.K. for the continuing support of research. The mention of firm names or trade products does not imply that they are endorsed or recommended by the U.S. Department of Agriculture over other firms or similar products not mentioned.


  • Fusarium asiaticum
  • Fusarium boothii
  • Fusarium culmorum
  • Fusarium head blight
  • Fusarium oxysporum
  • Fusarium pseudograminearum
  • Fusarium verticillioides
  • RNA profiling


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