Development of a Fusarium graminearum Affymetrix GeneChip for profiling fungal gene expression in vitro and in planta
Development of a Fusarium graminearum Affymetrix GeneChip for profiling fungal gene expression in vitro and in planta
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DOI：
10.1016/j.fgb.2006.01.005
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发表时间：
2006-05-01
影响因子：
3
通讯作者：
Kistler, H. Corby
中科院分区：
文献类型：
--
作者：
Gueldener, Ulrich;Seong, Kye-Yong;Kistler, H. Corby
最近，几种丝状真菌的基因组序列已经变得可用，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。我们报道了第一个Affymetrix基因芯片芯片的设计和验证，该芯片基于丝状真菌--子囊菌植物病原菌--禾谷镰刀菌的整个基因组。为了最大限度地表示阵列上所有推定基因(类似于14,000个)的可能性，使用了两组不同的自动预测基因调用，并将其整合到在线E graminearum基因组数据库中。从这些基因集中，人工注释了呼叫的子集，并将所有呼叫的非冗余提取与额外的EST序列和对照一起提交用于基因芯片设计。对禾谷镰刀菌基因芯片的性能进行了实验测试。利用基因组DNA进行的杂交实验证明了该阵列对禾谷镰刀菌和至少四种其他致病镰刀菌的实验是有用的。利用禾谷镰刀菌基因芯片检测了来自三种营养条件下培养的真菌的差异转录积累，并与感染大麦的真菌生长进行了比较。在植物中检测真菌基因的能力令人惊讶地敏感，即使没有努力丰富真菌转录本。植物表达数据库(PLEXdb，http：//www.plexdb.org)将被用作F graminearum基因芯片的原始和归一化表达数据的公共储存库。F graminearum基因芯片将有助于加速探索病原-宿主途径，这可能涉及真菌中致病基因与植物的病害反应之间的相互作用。(C)2006 Elsevier Inc.保留所有权利。
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 (similar to 14,000) on the array, two distinct sets of automatically predicted gene calls were used and integrated into the online E 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. (c) 2006 Elsevier Inc. All rights reserved.