Progress 10/01/08 to 09/30/14
Outputs
Target Audience: Researchers addressing questions of insect biology and pest management in Tribolium castaneum, Hessian fly and Manduca sexta. This includes scientists in several departments at KSU and the USDA ARS-GMPR, Manhattan, KS who access the databases on a daily basis. In addition, national and international research groups access Agripestbase for in depth knowledge about these genomes. More general audiences also access the database, including insect molecular geneticists, protein biochemists, genome biologists and genome scientists. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? We trained 4 graduate students and one undergraduate student. How have the results been disseminated to communities of interest? We have reported the results via international conference calls to specific research communities. We have presented our work at the Plant and Animal Genome Conference in San Diego, CA. ( 2010 and 2014) What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
A generic genome broswer was implemented at Agripestbaseto provide web-based access to genome information for research communities studying the red flour beetle, the tobacco hornworm and Hessian fly. This site provides bioinformatics tools for researchers to use in annotating genes of interests in these agriculturally important insects.We developed Offical Gene Sets for each species and submitted a new version of the Tribolium genome sequence (Tcas4.0) to NCBI.
Publications
- Type:
Websites
Status:
Published
Year Published:
2011
Citation:
www.agripestbase.org
- Type:
Journal Articles
Status:
Published
Year Published:
2010
Citation:
Kim, H., Murphy, T., Xia, J., Caragea, D., Park, Y., Beeman, R., Lorenzen, M., Butcher, S., Manak, J. and Brown, S (2010) Beetlebase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. Nucleic Acids Research epub doi:10.1093/nar/gkp807
- Type:
Journal Articles
Status:
Published
Year Published:
2008
Citation:
Wang, S, MD Lorenzen, R Beeman and SJ Brown (2008) Analysis of Repetitve DNA distribution patterns in the Tribolium castaneum Genome. Genome Biology epub 9:R61.
- Type:
Journal Articles
Status:
Published
Year Published:
2008
Citation:
Park, Y., J Aikins, LJ.Wang, RW Beeman, B. Oppert, J Lord, SJ Brown, MD Lorenzen, S. Richards, GM Weinstock and RA Gibbs. (2008) Analysis of transcriptome data in the red flour beetle, Tribolium castaneum. Insect Biochem. Mol Biol. 38:380-386.
- Type:
Journal Articles
Status:
Published
Year Published:
2008
Citation:
Wang, J., Y. Du, S.Wang, S. Brown and Y Park. (2008) Large diversity of the piggyBac-like elements in the genome of Tribolium castaneum. Insect Biochem. Mol Biol. 38:490-498.
- Type:
Journal Articles
Status:
Published
Year Published:
2008
Citation:
Stephen Richards et al. (The Tribolium Genome Sequencing Consortium). (2008) The genome of the model beetle and pest Tribolium castaneum. Nature 452:949-55.
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Progress 01/01/13 to 09/30/13
Outputs
Target Audience: Researchers addressing questions of insect biology and pest management in Tribolium castaneum, Hessian fly and Manduca sexta. This includes scientists in several departments at KSU and the USDA ARS-GMPR, Manhattan, KS who access the databases on a daily basis. In addition, national and international research groups access Agripestbase for in depth knowledge about these genomes. More general audiences also access the database, including insect molecular geneticists, protein biochemists, genome biologists and genome scientists Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? We current have 1 graduate student training on the databases. How have the results been disseminated to communities of interest? The databases are made available to research communites through genome sequencing projects that are coordinated by Baylor College of Medicine. There are link outs from NCBI to Agripestbase. They have been described at the Annual Arthropod Genomics Symposium. They are currently used to coordinate the efforts of the genome sequencing projects to annotate the genomes and develop Official Gene Sets. What do you plan to do during the next reporting period to accomplish the goals? We will complete the Official Gene Sets for Manduca and Hessian Fly and submit them to NCBI. We will also generate GBrowse intances for other Tribolium spieces.
Impacts
What was accomplished under these goals?
We expanded Beetlebase to include other insect genomes. These currently include the hessian fly and manduca sexta. Genome, transcript and protein sequences are searchable and downloadable. A BLAST website provides convenient access to relevant genes for interested researchers.
Publications
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Progress 01/01/12 to 12/31/12
Outputs
OUTPUTS: Activities: Agripestbase provides web-based access to genome information for research communities studying the red flour beetle, the tobacco hornworm and Hessian fly. This site provides bioinformatics tools for researchers to use in annotating genes of interests in these agriculturally important insects. Products: Databases for Manduca sexta, Tribolium castaneum and Hessian fly can be accessed at Agripestbase: www.agripestbase.org PARTICIPANTS: S J Brown, PI TARGET AUDIENCES: Researchers addressing questions of insect biology and pest management in Tribolium castaneum, Hessian fly and Manduca sexta. This includes scientists in several departments at KSU and the USDA ARS-GMPR, Manhattan, KS who access the databases on a daily basis. In addition, national and international research groups access Agripestbase for in depth knowledge about these genomes. More general audiences also access the database, including insect molecular geneticists, protein biochemists, genome biologists and genome scientists. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Individual researchers and research groups now access gene information at the database. This information is used to inform their experimental designs and methods and research techniques.
Publications
- No publications reported this period
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Progress 01/01/11 to 12/31/11
Outputs
OUTPUTS: Activities: We have expanded beetlebase to include two additional species of agricultural pests. The new database is called Agripestbase. In addition to Tribolium castaneum, we now curate genome data and provide web-accessible databases of genomic information to the research communities for Manduca sexta and Hessian fly. We provided the automated annotation of these genomes using the MAKER pipeline. These CHADO databases are accessible through GBROWSE and BLAST servers. Products: Agripestbase can be viewed at: www.agripestbase.org PARTICIPANTS: S J Brown TARGET AUDIENCES: Researchers addressing questions of insect biology and pest management in Tribolium castaneum, Hessian fly and Manduca sexta. This includes scientists in several departments at KSU and the USDA ARS-GMPR, Manhattan, KS who access the databases on a daily basis. In addition, national and international research groups access Agripestbase for in depth knowledge about these genomes. More general audiences also access the database, including insect molecular geneticists, protein biochemists, genome biologists and genome scientists. PROJECT MODIFICATIONS: We will continue add new species as the data become available.
Impacts
The addition of Hessian fly and Manduca genome data expand the utility of these databases to two additional research communities. We are currently providing a web-start version of Apollo to assist in manual annotation of the Hessian fly and Manduca genomes.
Publications
- No publications reported this period
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Progress 01/01/10 to 12/31/10
Outputs
OUTPUTS: We curate Tribolium genome data provide a database of genomic information to the research community. We have implemented a new version of Beetlebase including a new homepage powered by Drupal to allow faster more efficient news updates and announcements. We have implemented the latest versions of GBrowse, a module from GMOD, and CHADO, the data schema for the database. We have implemented a second genome browser JBrowse, which increases the speed and usability of the database. Finally, we are implementing Textpresso, a text mining tool that annotates gene models with data from the literature. To preserve nonelectronic publications of Triboloium research data, the "Research notes" and "Mutant analysis" sections of the entire Tribolium Information Bulletin collection, 1956-2002 had been scanned and retyped into text searchable format. Products: A new version of the database, including new modules can be found at: www.Beetlebase.org. PARTICIPANTS: S J Brown TARGET AUDIENCES: Scientists using Tribolium castaneum as a model in which to address questions of insect biology and pest management, found in several departments at KSU and the USDA ARS-GMPR, Manhattan, KS access the database on a daily basis. In addition, national and international research groups access Beetlebase for in depth knowledge about the Tribolium genome. More general audiences also access the database, including insect molecular geneticists, protein biochemists, genome biologists and genome scientists. PROJECT MODIFICATIONS: We will be expanding our genome databases to include the Hessian Fly and Manduca; both of these pest insect species are the focus of multiple research groups at KSU.
Impacts
The implementation of the JBrowse genome browser modules allows the user community to quickly move between neighboring regions on a chromosome. This improves the ablity to explore a chromosomal region ad identify all regions that inform gene structure, including new, previously unannotated exons, promoters and UTRs. The inclusion of information extracted from 45 years of TIBs in the Textpresso database is a priceless archive of original research information not available elsewhere.
Publications
- Shin, H., Murphy, T., Xia, J., Caragea, D., Park, Y., Beeman, R., Lorenzen, M., Butcher, S., Manak, J. and Brown, S., (2010) Beetlebase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum Nucleic Acids Research doi:10.1093/nar/gkp807.
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Progress 01/01/09 to 12/31/09
Outputs
OUTPUTS: Activities: The genome sequence of the red flour beetle Tribolium castaneum is an important resource for scientists studying pest management and insect biology. We develop and curate a genome database for the Tribolium research community. We have updated beetlebase to include tracks in the genome browser for ESTs, computational gene models, NCBI reference sequences and the official gene set. In addition we have added the raw data from DNA tiling arrays for more than 16 different life-stages. We are developing new tracks to include all relevant genomic data. A completely new, updated version of Beetlebase can be found at: www.Beetlebase.org. PARTICIPANTS: S J Brown TARGET AUDIENCES: Scientists using Tribolium castaneum as a model in which to address questions of insect biology and pest management, found in several departments at KSU and the USDA ARS-GMPR, Manhattan, KS access the database on a daily basis. In addition, national and international research groups access beetlebase for in depth knowledge about the Tribolium genome. More general audiences also access the database, including insect molecular geneticists, genome biologists and genome scientists. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
The DNA tiling arrays are important resources for researchers trying to understand and work with Tribolium genes. The array data provide insight into complete gene sequences that can be verified in the laboratory.
Publications
- No publications reported this period
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Progress 01/01/08 to 12/31/08
Outputs
OUTPUTS: Activities: The red flour beetle, Tribolium castaneum, is an important pest of stored grain and a model for studies in developmental biology. We are using the CHADO data schema to construct a relational database for the Tribolium research community. We have adapted several modules from the Generic Model Organism database. The user can access genome data from the Gbrowse moduleor through an accessory BLAST server with links that can be followed to the Gbrowse module. The user can view each chromosome, the scaffolds that contribute to the assemble for that chromosome, the contigs that contribute to the scaffolds and the estimated size of the sequencing gaps (captured gaps). Separate tracks contain, GLEAN gene models, manually currated genes, Refseq gene models from NCBI and the official gene set, which is a non-redundant union of these gene sets. We are currently adding tracks for DNA tiling array results, transposon insertion sites, and molecular markers from the genetic map. PARTICIPANTS: S J Brown TARGET AUDIENCES: The target audiences for this project include local Tribolium researchers at KSU and the USDA ARS-GMPR, Manhattan, KS as well as national and international Tribolium research labs, insect molecular geneticists and genome biologists, and genome scientists in general. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
Beetlebase version 3.0 is accessible at the following URL: www.Beetlebase.org. The nonredundant official gene set is an essential data set for comparative genomic studies.
Publications
- No publications reported this period
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