About the project

The HGSC is currently sequencing the honey bee, Apis mellifera. The version 4.0 assembly was released in March 2006 and published in October 2006. The genome sequence is being upgraded with additional sequence coverage. The honey bee is important in the agricultural community as a producer of honey and as a facilitator of pollination. It is a model organism for studying the following human health issues: immunity, allergic reaction, antibiotic resistance, development, mental health, longevity and diseases of the X chromosome. In addition, biologists are interested in the honey bee's social instincts and behavioral traits.

Sequencing of the honey bee is jointly funded by National Human Genome Research Institute (NHGRI) and the Department of Agriculture (USDA). Multiples from the same queen (strain DH4) were obtained from Danny Weaver of B.Weaver Apiaries. All libraries were made from DNA isolated from these drones. The honey bee BAC library (CHORI-224) was prepared by Pieter de Jong and Katzutoyo Osoegawa at the Children's Hospital Oakland Research Institute.

Access to the data

Genome Assembly

The genome assembly Amel_4.0 is available for download as linearized scaffolds for each chromosome and as contig files with assembly information (position and orientation on the chromosome). The assembly is described in more detail in the README file.

Comparisons of cDNA sequences to the genome assemblies are available to evaluate assembly completeness and correctness. See alignments for the different assemblies (1.0, 1.1, 1.2, 2.0, 3.0).

BLAST Searches

HGSC

• Assembled linearized scaffolds for each chromosome
• Assembled contigs
• Bin0 reads

Traces are available from the NCBI Trace Archive, which can be searched using NCBI MegaBLAST with a same species or cross species query.

Note on Sequence Traces

BAC-based Data Resources

Individual BAC clones can be searched using the Sequencing Project Browser with a query of:

• an Accession number (AC141790 )
• a Clone name (CH224-59E2)
• or a Project name (AMCL)

in the appropriate query box.

Sequence Read Data

The sequences for Sanger data are in the NCBI Trace Archive.

Use the BAC Fisher to find Whole Genome Shotgun reads that overlap sequencing reads from a clone. This program finds similar sequences where the matches extend to the end of the query sequences . BAC-Fisher is tuned to reject repeat matches without masking repeats in the query.

Additional sequence data generated using the Roche 454 platform can be downloaded from the FTP site or searched using BLAST.

Africanized honey bee SNP Data

Africanized honey bee sequences were aligned to the genome assembly to identify single nucleotide polymorphisms. The sequence reads are available from the NCBI trace archive. The SNP analysis results are available for download. Additional sequence data generated using the Roche 454 platform can be downloaded from the FTP site or searched using BLAST.

Other Resources

For information on related large-scale sequencing projects see the International Genome Consortium Database

For companion publications see:
NCBI Honey Bee Genome Publication and Press Portal

For the honey bee model organism database see: BeeBase

NCBI Taxonomy Browser

Conditions for use

Citations

The Honeybee Genome Sequencing Consortium. Insights into social insects from the genome of the honeybee Apis mellifera. Nature 443, 931-949(26 October 2006)

Christine G. Elsik, Kim C. Worley, Lan Zhang, Natalia V. Milshina, Huaiyang Jiang, Justin T. Reese, Kevin L. Childs, Anand Venkatraman, C. Michael Dickens, George M. Weinstock, and Richard A. Gibbs. Community annotation: Procedures, protocols, and supporting tools Genome Res. 2006 16: 1329-1333.

Joel Savard, Diethard Tautz, Stephen Richards, George M. Weinstock, Richard A. Gibbs, John H. Werren, Herve Tettelin, and Martin J. Lercher. Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects Genome Res. 2006 16: 1334-1338.