The honey bee was selected as a high priority organism for sequencing by the National Human Genome Research Institute (NHGRI) based on its importance to (1) the agricultural community, (2) those studying social instincts and behavioral traits and (3) those conducting medical research. The Honey Bee Genome Sequencing Project (HBGSP) Consortium, lead by the Human Genome Sequencing Center at Baylor College of Medicine (BCM-HGSC), published the culmination of their work, the generation and analysis of the genome sequence of the honey bee Apis mellifera, in the journal Nature. Additional information and resources are available at the Honey Bee Genome Resources guide page and in the Entrez Genome Project Database.

The fifth release of the draft honey bee genome assembly (Amel_4.0) was released by Baylor College of Medicine on March 10, 2006. This is the current version of the sequence and assembly displayed in Map Viewer. Amel_4.0 was created by adding reads generated by shotgun sequencing of purified AT-rich genomic DNA, Fosmid clone ends, BAC reads and repetitive reads to the whole genome shotgun (WGS) reads from Amel_2.0. The improved Solignac microsatellite linkage map (AmelMap3) was used to make the best placement of genome sequence on chromosomes. Amel_4.0 is based on version 5 of the WGS project AADG00000000 and includes the reference assembly and a partial haplotype represented as an alternate assembly. NCBI has annotated Baylor assembly Amel_4.0 using Gnomon and these bee-specific gene predictions, along with the Official Gene Set and additional map data, can be viewed in the Map Viewer display. This release includes a major change to the Map Viewer in that the previous build (Amel_2.0)) can still be accessed for Map Viewer display. For additional information on this change and other updates for Amel_4.0, please refer to the Release Notes.

The Solignac_3 microsatellite-based linkage map (AmelMap3) was generated by localizing each marker in the position of the chromosome which contains that marker using the data provided by Michel Solignac and his colleagues at the Laboratory Evolution, Genomes and Speciation, CNRS, France. The linkage map for honey bee was constructed mainly from the progeny of two hybrid queens (A. m. ligustica x A. m. mellifera). These are distinguished as follows: b: queen blanche, v: queen verte, d: les deux (both). The sixteen linkage groups displayed in Map Viewer are comprised of 2008 markers, the majority of which are microsatellite markers with a smaller number of RAPD markers and markers generated by PCR from primer pairs.

The Hunt linkage map was constructed from data generated in the lab of Greg Hunt in the Department of Entomology, Purdue University, Indiana. The map was constructed with about one third RAPD and two thirds AFLP markers, along with 42 microsatellites. There are 1110 markers covering over 4996 cM in 25 linkage groups. Additional information on the Hunt linkage map and its markers is available here.

The University of Illinois at Urbana-Champaign's Bioinformatics Unit conducted a sequencing program to study gene expression in Apis mellifera. 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. 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 project site allows for various sequence searches (BLAST, keywords) and downloading. Additional information about the project can be found here.

Available Documentation:

• NCBI Handbook: Map Viewer chapter - resource description
• NCBI Handbook: Map Viewer Exercises - tutorials and examples
• Map Viewer Help - details about navigation and customizing your display
• Genome Assembly - description of genome assembly and annotation process
• Gnomon - description of NCBI's Hidden Markov Model (HMM) ab initio prediction program