Güldener Ulrich, Seong Kye-Yong, Boddu Jayanand, Cho Seungho, Trail Frances, Xu Jin-Rong, Adam Gerhard, Mewes Hans-Werner, Muehlbauer Gary J, Kistler H Corby
Technische Universität München, Center of Life and Food Science, D-85350 Freising-Weihenstephan, Germany.
Fungal Genet Biol. 2006 May;43(5):316-25. doi: 10.1016/j.fgb.2006.01.005. Epub 2006 Mar 13.
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.
最近，几种丝状真菌的基因组序列已可获取，这为包括全基因组表达分析在内的大规模功能分析提供了机会。我们报告了首个基于丝状真菌——子囊菌植物病原菌禾谷镰刀菌全基因组的Affymetrix基因芯片微阵列的设计与验证。为了最大程度地在阵列上呈现所有推定基因（约14,000个），使用了两组不同的自动预测基因调用，并将其整合到在线禾谷镰刀菌基因组数据库中。从这些基因集中，手动注释了一部分调用，并将所有调用的非冗余提取物以及额外的EST序列和对照提交用于基因芯片设计。进行了实验以测试禾谷镰刀菌基因芯片的性能。使用基因组DNA的杂交实验证明了该阵列对于禾谷镰刀菌以及至少另外四种致病镰刀菌物种实验的有用性。使用禾谷镰刀菌基因芯片检测了在三种营养条件下培养的真菌以及与感染大麦中真菌生长相比的处理下的差异转录本积累。即使不努力富集真菌转录本，在植物中检测真菌基因的能力也出奇地灵敏。植物表达数据库（PLEXdb，http://www.plexdb.org）将用作禾谷镰刀菌基因芯片原始和标准化表达数据的公共储存库。禾谷镰刀菌基因芯片将有助于加速对病原体-宿主途径的探索，这些途径可能涉及真菌中的致病基因与植物中的疾病反应之间的相互作用。
