Apis mellifera
(NHGRI Press Photos)

The January 2005 Apis mellifera genome assembly is based on the Amel_2.0 assembly produced by the Human Genome Sequencing Center (HGSC) at Baylor School of Medicine. To see a list of the assembly's linkage groups, click here. (A linkage group is a large collection of scaffolds that is somewhat equivalent to a chromosome.) For more information about this assembly, see Amel_2.0 in the NCBI Assembly database.

Sample position queries

A genome position can be specified by a linkage group coordinate range, the accession number of an mRNA or EST, a gene name, or keywords from the GenBank description of an mRNA. The following list shows examples of valid position queries for the A. mellifera genome. Note that some position queries (e.g. "huntington") may return matches to the mRNA records of other species. In these cases, the mRNAs are mapped to their homologs in A. mellifera. See the User's Guide for more information.

  Genome Browser Response:
Group1   Displays all 25,433,307 bases of linkage group Group1
Group10:1-50,000   Displays first 50,000 bases of linkage group Group10

BI510436   Displays region of genome aligning to EST with GenBank accession BI510436
AB193550   Displays region of genome aligning to mRNA with GenBank accession AB193550
dock   Displays region of genome aligning to gene with identifier dock (a D. melanogaster gene)

preprosecapin   Lists preprosecapin mRNAs
odorant binding   Lists odorant-binding protein mRNAs
huntington   Lists candidate genes associated with Huntington's disease
robinson   Lists accessions deposited by authors named Robinson
Robinson,G.E.   Lists mRNAs deposited by co-author G.E. Robinson

Use this last format for author queries. Although GenBank requires the search format Robinson GE, internally it uses the format Robinson,G.E.

Assembly details

Amel_2.0 was created using a combination of whole genome shotgun and BAC sequencing methods. The assembly was produced using Baylor HGSC's assembly engine, Atlas. Approximately 2.7 million reads were assembled, representing about 1.8 Gb of sequence and about 7.5x coverage of the (clonable) honeybee genome.

The assembly consists of a set of contigs and scaffolds. Some scaffolds contain ordered and oriented sequence contigs; others contain isolated single contigs that could not be linked. Scaffolds are further grouped into 17 linkage groups. Contigs that could not be placed into groups are contained in GroupUn. The N50 size of the contigs in this assembly is 36 Kb; the N50 size of the scaffolds is 343 Kb. The total contig length in the assembly is 225 Mb, and the total span of the assembly is 229 Mb including gaps. More details about Amel_2.0 can be found here.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data are made available with specific conditions for use. The apiMel2 annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to the success of this release.

GenBank Pipeline Details

For the purposes of the GenBank alignment pipeline, this assembly is considered to be: well-ordered.