Gene Ontology annotation of the rice blast fungus, <it>Magnaporthe oryzae</it>
<p>Abstract</p> <p>Background</p> <p><it>Magnaporthe oryzae</it>, 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 bee...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2009-02-01
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| Series: | BMC Microbiology |
| Online Access: | http://pamgo.vbi.vt.edu |
| _version_ | 1818351751591362560 |
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| author | Deng Jixin Oh Yeon Torto-Alalibo Trudy Ebbole Daniel J Brown Douglas E Meng Shaowu Mitchell Thomas K Dean Ralph A |
| author_facet | Deng Jixin Oh Yeon Torto-Alalibo Trudy Ebbole Daniel J Brown Douglas E Meng Shaowu Mitchell Thomas K Dean Ralph A |
| author_sort | Deng Jixin |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p><it>Magnaporthe oryzae</it>, 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 <url>http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/MultiDownloads.html</url>. 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 <it>M. oryzae </it>genome assembly.</p> <p>Methods</p> <p>A 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 <it>M. oryzae </it>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.</p> <p>Results</p> <p>In 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 <url>http://amigo.geneontology.org/cgi-bin/amigo/go.cgi</url>. Additionally, the genome of <it>M. oryzae </it>is constantly being refined and updated as new information is incorporated. For the latest GO annotation of Version 6 genome, please visit our website <url>http://scotland.fgl.ncsu.edu/smeng/GoAnnotationMagnaporthegrisea.html</url>. 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.</p> <p>Conclusion</p> <p>Our analysis provides comprehensive and robust GO annotations of the <it>M. oryzae </it>genome assemblies that will be solid foundations for further functional interrogation of <it>M. oryzae</it>.</p> |
| first_indexed | 2024-12-13T18:42:43Z |
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| institution | Directory Open Access Journal |
| issn | 1471-2180 |
| language | English |
| last_indexed | 2024-12-13T18:42:43Z |
| publishDate | 2009-02-01 |
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| series | BMC Microbiology |
| spelling | doaj.art-321dbcd85084400b892a0ca6b2bd1b002022-12-21T23:35:09ZengBMCBMC Microbiology1471-21802009-02-019Suppl 1S810.1186/1471-2180-9-S1-S8Gene Ontology annotation of the rice blast fungus, <it>Magnaporthe oryzae</it>Deng JixinOh YeonTorto-Alalibo TrudyEbbole Daniel JBrown Douglas EMeng ShaowuMitchell Thomas KDean Ralph A<p>Abstract</p> <p>Background</p> <p><it>Magnaporthe oryzae</it>, 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 <url>http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/MultiDownloads.html</url>. 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 <it>M. oryzae </it>genome assembly.</p> <p>Methods</p> <p>A 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 <it>M. oryzae </it>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.</p> <p>Results</p> <p>In 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 <url>http://amigo.geneontology.org/cgi-bin/amigo/go.cgi</url>. Additionally, the genome of <it>M. oryzae </it>is constantly being refined and updated as new information is incorporated. For the latest GO annotation of Version 6 genome, please visit our website <url>http://scotland.fgl.ncsu.edu/smeng/GoAnnotationMagnaporthegrisea.html</url>. 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.</p> <p>Conclusion</p> <p>Our analysis provides comprehensive and robust GO annotations of the <it>M. oryzae </it>genome assemblies that will be solid foundations for further functional interrogation of <it>M. oryzae</it>.</p>http://pamgo.vbi.vt.edu |
| spellingShingle | Deng Jixin Oh Yeon Torto-Alalibo Trudy Ebbole Daniel J Brown Douglas E Meng Shaowu Mitchell Thomas K Dean Ralph A Gene Ontology annotation of the rice blast fungus, <it>Magnaporthe oryzae</it> BMC Microbiology |
| title | Gene Ontology annotation of the rice blast fungus, <it>Magnaporthe oryzae</it> |
| title_full | Gene Ontology annotation of the rice blast fungus, <it>Magnaporthe oryzae</it> |
| title_fullStr | Gene Ontology annotation of the rice blast fungus, <it>Magnaporthe oryzae</it> |
| title_full_unstemmed | Gene Ontology annotation of the rice blast fungus, <it>Magnaporthe oryzae</it> |
| title_short | Gene Ontology annotation of the rice blast fungus, <it>Magnaporthe oryzae</it> |
| title_sort | gene ontology annotation of the rice blast fungus it magnaporthe oryzae it |
| url | http://pamgo.vbi.vt.edu |
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