Honey Bee Brain EST Project

Gene E. Robinson, PI

The W. M. Keck Center for Comparative and Functional Genomics
University of Illinois at Urbana-Champaign

To accelerate the molecular analysis of behavior in the honey bee (Apis mellifera), we created an expressed sequence tag (EST) resource for the bee brain. Bees of different ages performing a wide variety of natural behaviors were collected from a field colony at the University of Illinois. Brains were then dissected and mRNA extracted. A normalized unidirectional cDNA library was made in the laboratory of Prof. Bento Soares, University of Iowa. The library was subsequently subtracted. Over 20,000 cDNA clones were partially sequenced from the normalized and subtracted libraries at the Keck Center, resulting in 15,311 vector-trimmed, high-quality, sequences with an average read length of 494 bp. and average base-quality of 41. These sequences were assembled into 8966 putatively unique sequences, which were tested for similarity to sequences in the public databases with a variety of BLAST searches. Apis ESTs were tentatively assigned molecular function and biological process using the Gene Ontology (GO) classification system.

The University of Illinois Bee-ESTdb integrates data from the bee brain EST sequencing project with data from sequencing and gene research projects from other organisms, primarily the fruit fly Drosophila melanogaster.The goal of Bee-ESTdb is to provide updated information on the genes of the honey bee, currently using annotation primarily from flies to suggest cellular roles, biological functions, and evolutionary relationships. All data in this database are freely available. The Clemson University Genomics Institute is the distributor of these public domain cDNA clones. For information on how to purchase an individual clone or the entire collection, please contact www.genome.clemson.edu/orders/ or generobi@life.uiuc.edu.

A paper describing this project is in preparation. This research was funded by the University of Illinois Critical Research Initiatives Fund and a Burroughs-Wellcome Trust Innovation Award in Functional Genomics. 
Cover of April 2002 edition of Genome Research.  Feature publishing of "Annotated Expressed Sequence Tags and cDNA Microarrays for Studies of Brain and Behavior in the Honey Bee" available in full text, pdf and abstract versions.  Follow newslink for more information.
EST Data summary statistics

The EST data can be searched and retrieved using the following search criteria: *
(For basic information on bioinformatics and the kinds of analyses you can perform, see the NCBI website).

Search by BLAST  The user can cut and paste one or more sequences to BLAST against three Honey Bee EST data sets from the normalized and subtracted libraries. The data sets comprise the unique sequence set generated by CAP3 assembly program (BeeEST.assembled); the high quality EST set (BeeEST.trim) that contains vector-free, high-quality sequence at least 200 bp in length; and the raw data set which includes low quality sequences and vector sequences (BeeEST.raw).

Search by Keyword  Search the database by entering a keyword to retrieve Gene Ontology recognized terms, and retrieve Bee EST annotation for each of those terms. EST's can have multiple GO terms. To see all possible terms for a particular EST, use the 'Search the Gene Association Database by Id' below. The Gene Ontology Consortium documentation is available at GO documentation

Search by Sequence ID  The user can enter EST ID, GENBANK accession ID (not available yet), or Contig ID to retrieve and download the sequences, view the sequence chromatograph and quality, view contig structure and the consensus sequence.

Search the Gene Association Database by Id  Search the database by entering a Contig ID or Flybase Gene Number or Gene Symbol to retrieve annotated ESTs for that ID.

*This website is best viewed using Internet Explorer 4.0 or above, or Netscape Navigator 4.x

 

The assembled sequences analyzed in Whitfield et al. 2002 Gen. Res. can be downloaded here.


This site is maintained by the Bioinformatics Unit
of the W.M. Keck Center for Comparative and Functional Genomics
at the University of Illinois