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. 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 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. A 6-fold coverage WGS, BAC sequence from pooled arrays, and an initial genome assembly (Amel_v1.0) were released beginning in 2003. This has been a challenging project with difficulty in recovering AT-rich regions. The WGS data had lower coverage in AT-rich regions and BAC data from clones showed evidence of internal deletions. Additional reads from AT enriched DNA addressed these underrepresented regions. The current assembly Amel_4.0 was produced with Atlas and includes 2.7 million reads (1.8 Gb) or 7.5x coverage of the (clonable) genome. About 97% of STSs, 98% of ESTs, and 96% of cDNAs are represented in the 231 Mb assembly.
About 2,500 reads were also produced from a strain of Africanized honey bee and SNPs were extracted. These were released in dbSNP and the NCBI Trace Archive. Analysis of the genome by a consortium of 20 labs has been completed. This produced a gene list derived from five different methods melded through the GLEAN software. 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_4.0 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).
The BLAST link is located in the sidebar.
Traces are available from the NCBI Trace Archive by using the link, which can be searched using NCBI MegaBLAST with a same species or cross species query.
Additional sequence data generated using the Roche 454 platform can be downloaded from the 454 Sequence Data site or searched using BLAST.
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 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 |
|---|---|---|---|
| 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
Selected PubMed Citations
Aronstein, KA, Murray, KD, de Leon, JH, Qin, X, Weinstock, GM. High mobility group (HMG-box) genes in the honeybee fungal pathogen Ascosphaera apis. Mycologia ; 99(4):553-61. [PubMed]
Solignac, M, Zhang, L, Mougel, F, Li, B, Vautrin, D, Monnerot, M, Cornuet, JM, Worley, KC, Weinstock, GM et al. The genome of Apis mellifera: dialog between linkage mapping and sequence assembly. Genome Biol. 2007; 8(3):403. [PubMed]
Elsik, CG, Worley, KC, Zhang, L, Milshina, NV, Jiang, H, Reese, JT, Childs, KL, Venkatraman, A, Dickens, CM et al. Community annotation: procedures, protocols, and supporting tools. Genome Res. 2006 Nov; 16(11):1329-33. [PubMed]
Savard, J, Tautz, D, Richards, S, Weinstock, GM, Gibbs, RA, Werren, JH, Tettelin, H, Lercher, MJ. Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects. Genome Res. 2006 Nov; 16(11):1334-8. [PubMed]
Robinson, GE, Evans, JD, Maleszka, R, Robertson, HM, Weaver, DB, Worley, K, Gibbs, RA, Weinstock, GM. Sweetness and light: illuminating the honey bee genome. Insect Mol. Biol. 2006 Oct; 15(5):535-9. [PubMed]
Qin, X, Evans, JD, Aronstein, KA, Murray, KD, Weinstock, GM. Genome sequences of the honey bee pathogens Paenibacillus larvae and Ascosphaera apis. Insect Mol. Biol. 2006 Oct; 15(5):715-8. [PubMed]
Honeybee Genome Sequencing Consortium, Insights into social insects from the genome of the honeybee Apis mellifera. Nature 2006 Oct 26; 443(7114):931-49. [PubMed]
Photo copyright B. Weaver Apiaries
| 2006 Oct 26 |
| Apis mellifera genome published |
| Nature 443, 931-949(26 Oct 2006) |