Dataset Information

Genomic resources of Magnaporthe oryzae (GROMO): a comprehensive and integrated database on rice blast fungus.

ABSTRACT: BACKGROUND: Magnaporthe oryzae, rice blast fungus, is the most devastating pathogen of rice. It has emerged as a model phytopathogen for the study of host-pathogen interactions. A large body of data has been generated on different aspects of biology of this fungus and on host-pathogen interactions. However, most of the data is scattered and is not available as a single resource for researchers in this field. DESCRIPTION: Genomic Resources of Magnaporthe oyzae (GROMO), is a specialized, and comprehensive database for rice blast fungus, integrating information from several resources. GROMO contains information on genomic sequence, mutants available, gene expression, localization of proteins obtained from a variety of repositories, as primary data. In addition, prediction of domains, pathways, protein-protein interactions, sumolyation sites and biochemical properties that were obtained after computational analysis of protein sequences have also been included as derived data. This database has an intuitive user interface that shall prompt the user to explore various possible information resources available on a given gene or a protein, from a single source. CONCLUSION: Currently, information on M. oryzae is available from different resources like BROAD MIT Magnaporthe database, Agrobacterium tumefaciens-mediated transformation (ATMT) M. oryzae database, Magnaporthe grisea--Oryza sativa (MGOS) and Massive Parallel Signature Sequencing (MPSS) databases. In the GROMO project, an effort has been made to integrate information from all these databases, derive some new data based on the available information analyzed by relevant programs and make more insightful predictions to better understand the biology of M. oryzae. The database is currently available at: http://gromo.msubiotech.ac.in/

SUBMITTER: Thakur S

PROVIDER: S-EPMC2721851 | biostudies-literature | 2009

REPOSITORIES: biostudies-literature

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Genomic resources of Magnaporthe oryzae (GROMO): a comprehensive and integrated database on rice blast fungus.

Thakur Shalabh S Jha Sanjay S Roy-Barman Subhankar S Chattoo Bharat B

BMC genomics 20090715

<h4>Background</h4>Magnaporthe oryzae, rice blast fungus, is the most devastating pathogen of rice. It has emerged as a model phytopathogen for the study of host-pathogen interactions. A large body of data has been generated on different aspects of biology of this fungus and on host-pathogen interactions. However, most of the data is scattered and is not available as a single resource for researchers in this field.<h4>Description</h4>Genomic Resources of Magnaporthe oyzae (GROMO), is a specializ ...[more]

PMID: 19604367

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Project description:BACKGROUND: Magnaporthe 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. METHODS: 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 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. RESULTS: 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 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. CONCLUSION: Our 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.

Dataset Information

Genomic resources of Magnaporthe oryzae (GROMO): a comprehensive and integrated database on rice blast fungus.

Publications

Genomic resources of Magnaporthe oryzae (GROMO): a comprehensive and integrated database on rice blast fungus.

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