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Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae

机译：稻瘟病菌Magnaporthe oryzae的基因本体论注释

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BackgroundMagnaporthe oryzae, the causal agent of blast disease of rice, is the most destructive disease of rice worldwide. The genome of this fungal pathogen has been sequenced and an automated annotation has recently been updated to Version 6 http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/MultiDownloads.html. However, a comprehensive manual curation remains to be performed. Gene Ontology (GO) annotation is a valuable means of assigning functional information using standardized vocabulary. We report an overview of the GO annotation for Version 5 of M. oryzae genome assembly.MethodsA similarity-based (i.e., computational) GO annotation with manual review was conducted, which was then integrated with a literature-based GO annotation with computational assistance. For similarity-based GO annotation a stringent reciprocal best hits method was used to identify similarity between predicted proteins of M. oryzae and GO proteins from multiple organisms with published associations to GO terms. Significant alignment pairs were manually reviewed. Functional assignments were further cross-validated with manually reviewed data, conserved domains, or data determined by wet lab experiments. Additionally, biological appropriateness of the functional assignments was manually checked.ResultsIn total, 6,286 proteins received GO term assignment via the homology-based annotation, including 2,870 hypothetical proteins. Literature-based experimental evidence, such as microarray, MPSS, T-DNA insertion mutation, or gene knockout mutation, resulted in 2,810 proteins being annotated with GO terms. Of these, 1,673 proteins were annotated with new terms developed for Plant-Associated Microbe Gene Ontology (PAMGO). In addition, 67 experiment-determined secreted proteins were annotated with PAMGO terms. Integration of the two data sets resulted in 7,412 proteins (57%) being annotated with 1,957 distinct and specific GO terms. Unannotated proteins were assigned to the 3 root terms. The Version 5 GO annotation is publically queryable via the GO site http://amigo.geneontology.org/cgi-bin/amigo/go.cgi. Additionally, the genome of M. oryzae is constantly being refined and updated as new information is incorporated. For the latest GO annotation of Version 6 genome, please visit our website http://scotland.fgl.ncsu.edu/smeng/GoAnnotationMagnaporthegrisea.html. The preliminary GO annotation of Version 6 genome is placed at a local MySql database that is publically queryable via a user-friendly interface Adhoc Query System.ConclusionOur analysis provides comprehensive and robust GO annotations of the M. oryzae genome assemblies that will be solid foundations for further functional interrogation of M. oryzae.
机译：背景稻瘟病菌是稻瘟病的病原体，是全世界稻田最具破坏性的疾病。已对该真菌病原体的基因组进行了测序，并且最近将自动注释更新为第6版http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/MultiDownloads.html。但是，仍然需要执行全面的手动管理。基因本体（GO）注释是使用标准化词汇分配功能信息的一种有价值的方法。我们报告了米曲霉基因组装配第5版的GO注释的概述。方法进行了基于相似度（即计算）的GO注释并进行了人工审查，然后将其与基于文献的GO注释进行了计算辅助。对于基于相似度的GO注释，使用严格的互惠最佳匹配方法来识别米氏支原体的预测蛋白与来自多个生物体的GO蛋白（具有与GO术语的已公开关联）之间的相似性。手动检查重要的比对对。功能分配进一步与人工检查的数据，保守域或通过湿实验室实验确定的数据进行交叉验证。结果，共有6286个蛋白质通过基于同源性的注释获得了GO术语分配，其中包括2870个假设蛋白质。基于文献的实验证据，例如微阵列，MPSS，T-DNA插入突变或基因敲除突变，导致2,810个蛋白用GO术语标注。其中1,673种蛋白质用植物相关微生物基因本体论（PAMGO）开发的新术语标注。此外，用PAMGO术语注释了67种实验确定的分泌蛋白。这两个数据集的整合导致对7,412种蛋白质（57％）进行了注释，并带有1,957个不同和特定的GO术语。未注释的蛋白质分配给3个根词。可通过GO网站http://amigo.geneontology.org/cgi-bin/amigo/go.cgi公开查询第5版GO批注。此外，随着新信息的引入，米曲霉的基因组也在不断完善和更新。有关版本6基因组的最新GO注释，请访问我们的网站http://scotland.fgl.ncsu.edu/smeng/GoAnnotationMagnaporthegrisea.html。第6版基因组的初步GO注释放置在本地MySql数据库中，该数据库可通过用户友好的界面Adhoc Query System公开查询。结论我们的分析为米曲霉基因组装配体提供了全面而强大的GO注释，这些注释将为进一步分析米曲霉。

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