About the Project
The HGSC has sequenced the honey bee, Apis mellifera. The version 4.0 assembly was released in March 2006 and published in October 2006. An upgrade, version 4.5 with additional sequence coverage, was released in 2011. 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 organization and behavioral traits.
This project was proposed to the HGSC by a group of dedicated insect biologists, headed by Gene Robinson. Following a workshop at the HGSC and a honey bee white paper, the HGSC began the project in 2002.
Publications include a main paper in Nature and up to forty companion papers in Genome Research and Insect Molecular Biology.
Sequencing of the honey bee is jointly funded by National Human Genome Research Institute (NHGRI) and the Department of Agriculture (USDA). Multiple drones 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
The genome assembly Amel_4.5 is available for download as linearized scaffolds for each chromosome and as contig files with assembly information (position and orientation on the chromosome). Use the FTP Data link in the sidebar. 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 by using the FTP Data link in the sidebar. See the alignments for the different assemblies (1.0, 1.1, 1.2, 2.0, 3.0).
Honey Bee SNP Data
Africanized honey bee sequences were aligned to the Amel_3.0 genome assembly to identify single nucleotide polymorphisms. The sequence reads are available from the NCBI Trace Archive link in the sidebar. The SNP analysis results are also available for download using the FTP Data link.
Single nucleotide polymorphisms were also identified in the haplotypes present in the genome assembly.
Assemblies
| Date Released | Release Name | Coverage | Comments |
|---|---|---|---|
| 2011 Jan | Amel_4.5 | ~30x | Improved scaffolding and gapfilling using SOLiD and 454 sequence data. |
| 2006 Mar 10 | Amel_4.0 | 7.5x | Mapped to chromosomes using improved genetic map. |
| 2005 May 1 | Amel_3.0 | 7.5x | Created by adding repetitive reads generated by shotgun sequencing to the previous whole genome shotgun (WGS) reads. In addition, small contigs from contaminated sequences and unmerged contigs from the second potential haplotype were excluded from this assembly. |
| 2005 Jan 20 | Amel_2.0 | 7.5x | A new assembly created by adding reads generated by shotgun sequencing of purified AT-rich genomic DNA, Fosmid clone ends, and BAC reads to the previous whole genome shotgun(WGS) reads. |
| 2004 Jul 20 | Amel_1.2 | 6x | A new assembly created by adding reads generated by shotgun sequencing of purified AT-rich genomic DNA to the previous whole genome shotgun (WGS) reads. In earlier assemblies, some AT-rich regions of the genome had lower coverage, and this new set of reads addressed this issue. |
Other Resources
Honey bee genome sequencing whitepaper
Honey bee sequencing upgrade whitepaper
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
Photo copyright B. Weaver Apiaries