Network-based data integration for selecting candidate virulence associated proteins in the cereal infecting fungus Fusarium graminearum.
Network-based data integration for selecting candidate virulence associated proteins in the cereal infecting fungus Fusarium graminearum.
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DOI：
10.1371/journal.pone.0067926
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Saqi M
中科院分区：
文献类型：
--
作者：
Lysenko A;Urban M;Bennett L;Tsoka S;Janowska-Sejda E;Rawlings CJ;Hammond-Kosack KE;Saqi M
鉴定植物病原真菌的毒力基因对于了解病原真菌的侵染过程、寄主范围和制定防治策略具有重要意义。在集成功能网络的背景下对已经验证的植物病原真菌毒力基因的分析可以为直接或间接与真菌病原性相关的潜在机制和途径提供线索，并可以为进一步的实验研究提供新的候选对象，使用“关联内疚”的方法。在这里，我们研究了全球重要的子囊菌真菌禾谷镰刀菌中的133个基因，这些基因已经过实验测试，表明它们参与了毒力。我们使用了一个整合的网络，该网络结合了来自基因共表达、预测的蛋白质-蛋白质相互作用和序列相似性的信息，使用100个已知毒力所需的基因，我们总共发现了215个可能与毒力相关的新蛋白质，其中29个被注释为假设蛋白质。这些潜在的毒力基因大多位于已知重组频率较低的染色体区域。我们还探索了这些候选者的分类多样性，发现了25个序列，它们可能是真菌特有的。我们详细讨论了一些潜在的新毒力相关基因的生物学相关性。在集成功能网络的背景下对已经验证的植物病原真菌毒力基因的分析可以为直接或间接与真菌病原性相关的潜在机制和途径提供线索，并可以为进一步的实验研究提供新的候选对象，使用“关联内疚”的方法。
The identification of virulence genes in plant pathogenic fungi is important for understanding the infection process, host range and for developing control strategies. The analysis of already verified virulence genes in phytopathogenic fungi in the context of integrated functional networks can give clues about the underlying mechanisms and pathways directly or indirectly linked to fungal pathogenicity and can suggest new candidates for further experimental investigation, using a ‘guilt by association’ approach. Here we study 133 genes in the globally important Ascomycete fungus Fusarium graminearum that have been experimentally tested for their involvement in virulence. An integrated network that combines information from gene co-expression, predicted protein-protein interactions and sequence similarity was employed and, using 100 genes known to be required for virulence, we found a total of 215 new proteins potentially associated with virulence of which 29 are annotated as hypothetical proteins. The majority of these potential virulence genes are located in chromosomal regions known to have a low recombination frequency. We have also explored the taxonomic diversity of these candidates and found 25 sequences, which are likely to be fungal specific. We discuss the biological relevance of a few of the potentially novel virulence associated genes in detail. The analysis of already verified virulence genes in phytopathogenic fungi in the context of integrated functional networks can give clues about the underlying mechanisms and pathways directly or indirectly linked to fungal pathogenicity and can suggest new candidates for further experimental investigation, using a ‘guilt by association’ approach.
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影响因子：
6.1
作者：
Dyer, RB;Plattner, RD;Brown, DW
通讯作者：
Brown, DW
影响因子：
4.5
作者：
Coleman JJ;Rounsley SD;Rodriguez-Carres M;Kuo A;Wasmann CC;Grimwood J;Schmutz J;Taga M;White GJ;Zhou S;Schwartz DC;Freitag M;Ma LJ;Danchin EG;Henrissat B;Coutinho PM;Nelson DR;Straney D;Napoli CA;Barker BM;Gribskov M;Rep M;Kroken S;Molnár I;Rensing C;Kennell JC;Zamora J;Farman ML;Selker EU;Salamov A;Shapiro H;Pangilinan J;Lindquist E;Lamers C;Grigoriev IV;Geiser DM;Covert SF;Temporini E;Vanetten HD
通讯作者：
Vanetten HD
影响因子：
3.7
作者：
Brown NA;Antoniw J;Hammond-Kosack KE
通讯作者：
Hammond-Kosack KE
影响因子：
9.5
作者：
Lysenko, Atem;Hindle, Matthew Morritt;Rawlings, Christopher John
通讯作者：
Rawlings, Christopher John
DOI：
10.1088/1742-5468/2008/10/p10008
发表时间：
2008-10-01
影响因子：
2.4
作者：
Blondel, Vincent D.;Guillaume, Jean-Loup;Lefebvre, Etienne
通讯作者：
Lefebvre, Etienne