Apis mellifera - honey bee genome data and search tips

Revised August 7, 2006

The Map Viewer help document describes how to use the Map Viewer software. This page describes the data available for Apis mellifera (honey bee), and the search tips specific to that organism. You can also return to the Apis mellifera genome view search page. The Map Viewer home page allows you to search the genome data of any organism represented in MapViewer. Scope of Data Honey Bee Genomic Sequence Data Honey Bee BLAST Databases Additional Honey Bee Genome Resources Available Maps Genetic Linkage Solignac_3 Genetic (AmelMap3) Map Hunt v.2 Linkage Map Sequence-Based Maps Ab initio Models Map Anopheles gambiae RNA Map Apis mellifera RNA Map Drosophila melanogaster RNA Map Insecta RNA Map Anopheles gambiae UniGene Clusters Map Apis mellifera UniGene Clusters Map Drosophila melanogaster UniGene Clusters Map Insecta UniGene Clusters Map Assembly Map Component Map Contig Map CpG Island Map GenBank DNA Map Genes On Sequence Map Official Gene Set RNA Map RefSeq Transcripts On Sequence Map STS Map Variation Map Constructing queries Searchable Terms Map Positions or Regions

Scope of Data

Honey Bee Genomic Sequence Data

Honey Bee BLAST Databases

The complete set of honey bee sequence databases available for BLAST searching are shown on the honey bee BLAST page, which includes a link to the database descriptions. In addition, those interested in comparative genomics can utilize the insect genomes BLAST page, which include individual and combined sequence databases for Drosophila melanogaster, Drosophila pseudoobscura, Anopheles gambiae and Apis mellifera.

Additional Honey Bee Genome Resources

In addition to the Apis mellifera data available in the Map Viewer and through BLAST, information is available from the Honey Bee Genome Resources Guide, which includes links to NCBI resources and external resources pertaining to genomic sequence, maps and annotation. The new Entrez database, the Genome Project Database, provides another resource for honey bee genome information. An explanation of the A. mellifera-specific Gnomon gene prediction processing can be found here, along with links to the general Gnomon description. In addition, the NCBI Handbook includes a series of exercises that demonstrate additional questions that can be answered with Map Viewer.

Available Maps

Genetic Linkage Maps

Solignac_3

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 the 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. Solignac_3 (AmelMap3) is an update from the previous linkage map associated with Amel_2.0, Solignac_1700, which was based on 1694 markers.

Hunt Linkage Map

This Hunt v.2, August 2005 release linkage map was constructed by David Schlipalius 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. There are 300 sequenced markers on the map, not including the genes Amtyr1 (tyramine receptor 1), X (=csd), hash1 (honey bee acheate scute homolog 1), Hex (hexokinase) and Per (period gene). Markers were scored in one family of haploid male sons of an F1 queen resulting from a cross between a European-derived stock of Apis mellifera and an African-derived stock (A. m. scutellata). This mapping population was also used to map quantitative trait loci influencing defensive behavior, body size and alarm pheromone production (Hunt et al. 1998; 1999). Linkage groups in the Hunt map, which has its own linkage group designations, were ordered and oriented to the Solignac/bee genome linkage groups based on shared microsatellite markers, between the Hunt map and Solignac map, and shared GenBank accession numbers between the Hunt map and the bee genome. Common markers between the Hunt map and Solignac map/bee genome can be viewed by displaying the Solignac map, Hunt map, and GenBank_DNA map next to each other in Map Viewer using Maps and Options and selecting the option "Show Connections" (see LG4 as an example).

Sequence-Based Maps

Ab initio

Models generated by Gnomon. mRNA alignments were used to segment the genomic sequence by putative gene boundaries, and Gnomon was executed on these segments to predict genes. Specific parameters were developed for Gnomon to run bee-specific gene prediction. Models with a completely-supported CDS are blue, models with a partially-supported CDS are green, and the pure ab initio predictions are brown. Pure ab initio status indicates that the model was built without the support of mRNA or protein alignments, either through failure to align the sequence to the genome or an alignment ignored by Gnomon due to a score falling below a pre-determined threshold.

Aga RNA

Alignment of individual Anopheles gambiae (mosquito) RNAs to the assembled genomic sequence. The corresponding alignment of EST clusters is shown in the Aga UniG map, described below.

Ame RNA

Alignment of individual Apis mellifera (honey bee) RNAs to the assembled genomic sequence. The corresponding alignment of EST clusters is shown in the Ame UniG map, described below.

Dm RNA

Alignment of individual Drosophila melanogaster (fruit fly) RNAs to the assembled genomic sequence. The corresponding alignment of EST clusters is shown in the Dm UniG map, described below.

Ins RNA

Alignment of individual Insecta (true insects) RNAs to the assembled genomic sequence. The corresponding alignment of EST clusters is shown in the Ins UniG map, described below.

Aga UniG

Alignment of Anopheles gambiae (mosquito) EST clusters to the assembled genomic sequence. ESTs are clustered based on shared introns and alignment to a common position on the genome. Co-aligning ESTs can come from one or more UniGene clusters, whose IDs are noted by the EST cluster. (UniGene clusters are made with a different build procedure, so there is not necessarily a one-to-one correspondence between EST clusters on the Aga UniG map and clusters in the UniGene resource.)

Ame UniG

Alignment of Apis mellifera (honey bee) EST clusters to the assembled genomic sequence. ESTs are clustered based on shared introns and alignment to a common position on the genome. Co-aligning ESTs can come from one or more UniGene clusters, whose IDs are noted by the EST cluster. (UniGene clusters are made with a different build procedure, so there is not necessarily a one-to-one correspondence between EST clusters on the Ame UniG map and clusters in the UniGene resource.)

Dm UniG

Alignment of Drosophila melanogaster (fruit fly) EST clusters to the assembled genomic sequence. ESTs are clustered based on shared introns and alignment to a common position on the genome. Co-aligning ESTs can come from one or more UniGene clusters, whose IDs are noted by the EST cluster. (UniGene clusters are made with a different build procedure, so there is not necessarily a one-to-one correspondence between EST clusters on the Dm UniG map and clusters in the UniGene resource.)

Ins UniG

Alignment of Insecta (true insects) EST clusters to the assembled genomic sequence. ESTs are clustered based on shared introns and alignment to a common position on the genome. Co-aligning ESTs can come from one or more UniGene clusters, whose IDs are noted by the EST cluster. UniGene clusters are made with a different build procedure, so there is not necessarily a one-to-one correspondence between EST clusters on the Ins UniG map and clusters in the UniGene resource.

Assembly

The Assembly map allows users to visualize all of the sequence data available for a given region of the genome, and separates the data by assembly. Version 5 of the whole genome shotgun (WGS) project represents the reference genome and identified haplotype contigs, which were omitted from the assembly. By default, the other sequence maps that are available for an organism display the features that have been annotated on the reference assembly.

Component

The component map provides the tiling path of GenBank AADGxxxxxxxx accessions from the A. mellifera whole genome shotgun project (AADG00000000.5) used to build the NW_xxxxxx WGS contigs, which are described below.

Contig

Shows the chromosomal placement of NW_xxxxxx contigs on the honey bee Amel_4.0 assembly of whole genome shotgun (WGS) data. The individual GenBank records used to assemble the contigs are shown on the Component map, described above.

CpG Island

Shows regions of high G + C content on the assembled genome sequence. Two sets of criteria were used for finding CpG islands: "strict" and "relaxed," described below. The algorithm (and cutoffs) were taken from Takai and Jones, 2002. relaxed (shown with light blue shading on the map) 200 bp min length 50% or higher G + C content 0.60 or higher observed CpG / expected CpG post-processing:  merge islands that are <= 100 bp apart strict (shown with dark blue shading on the map) 500 bp min length 50% or higher GC content 0.60 or higher observed CpG / expected CpG

GenBank DNA

Shows the placement of honey bee genomic DNA sequences from GenBank that were not used in the assembly of contigs. The placement is based on the alignment of the sequences to the components of the contigs. The length of a line represents the upper and lower-most points on the genome assembly to which sequence fragments from a single GenBank record were aligned. Thick parts of a line represent fragments of sequence from a GenBank record that have been aligned to the assembled genomic sequence, and the thin parts of a line connect the fragments that come from a single GenBank record.

Gene

Genes that have been annotated on the genomic contigs. This includes known and putative genes placed as a result of alignments of mRNAs to the contigs. If multiple models exist for a single gene, corresponding to splicing variants, the Gene map presents a flattened view of all the exons that can be spliced together in various ways. For example, if one splice variant uses exons 1, 3, 4, and another splice variant uses exons 2, 3, 4, the Genes_seq map shows exons 1, 2, 3, 4. Genes shown on the left of the grey line are transcribed in the - orientation (from bottom up), and those on the right in the + orientation (from top down). Models with Interim GeneIDs (LOC######) may be paralogs, genes not yet curated, duplications because of assembly errors, or pseudogenes. The genome assembly and annotation pipeline assigns interim IDs when there is no unambiguous solution to what they should be. Interim GeneIDs are associated with RefSeq XM_* accessions (model mRNAs),

Official Gene Set

The Official Gene Set (OGS) is a set of gene predictions by various research groups in the Honey Bee Genome Sequencing Consortium using the Baylor honey bee genome assembly version 2 (Amel_2.0). Sets of predictions from all groups were combined using GLEAN to create a non-redundant, consensus set of genes. This consensus set was aligned to assembly 4 (Amel_4.0) using Splign. Gene predictions aligning unambiguously to the assembly represent the preliminary Official Gene Set, which was released at NCBI to coincide with the honey bee genome Nature paper (map and BLAST databases). For about 40 genes, Splign produced more than one plausible alignment to the assembly. For those cases, manual inspection will be done to choose the best alignments. The addition of these final genes will complete the Official Gene Set, at which time an update will be done to finalize the OGS map and BLAST databases at NCBI.

STS	Placement of STSs from a variety of sources onto the assembled genomic sequence (the NW_xxxxxx contigs, described above) using Electronic-PCR (e-PCR).

RefSeq Transcripts

Diagrams of the RNAs that are predicted on the genomic contigs. The RefSeq Transcript map and Gene map are built in the same way; however, the Genes_seq map shows a view of all the exons in a gene, while the RefSeq RNA map could potentially show the combinations of exons (i.e., splice variants) that are valid, if mRNA sequences indicate alternative splice variants.

Variation

Alignment of genetic variation data from dbSNP onto the genomic sequence. Calculation of variation annotation is no longer synchronized with the whole genome annotation pipeline. The Variation map will be updated for Amel_4.0 as soon as it's available. more...

Constructing queries

Searchable Terms

The Apis mellifera data are searchable with the following types of terms: GenBank accessions (e.g., AADGxxxxxxxx) UniGene cluster When searching UniGene clusters, use the numerical value only as the query term, dropping the organism prefix. For example, using the search query 2250 versus Amel_4.0 will return Ame.2250 and Dm.2250 in the Ame UniG and Ins UniG maps, respectively. marker name marker alias Sometimes two or more marker names refer to the same primer pair, and are therefore considered synonyms or "aliases." In such cases, any one of the terms will retrieve the marker. text words e.g., a search for apidaecin will retrieve map objects containing that word in their descriptions. If multiple terms are entered, they will automatically be combined with a Boolean AND.  Also, adjacency searches are not supported at present. For example, a query entered as "cell adhesion" will be processed as cell AND adhesion and will retrieve records with descriptions that contain cell matrix adhesion as well as cell adhesion. The system will retrieve mapped objects containing the search terms in their descriptions.

Map Positions

As noted in the Search By Position section of the Entrez Map Viewer general help document, there are three main ways to search by map position from the Map View of a chromosome: enter a range of interest in the Region text boxes in side bar click on the region of interest in the chromosome thumbnail graphic in the sidebar click on a region of interest in the enlarged Map View of the chromosome For Apis mellifera, the following types of map positions can be entered in option 1: marker names numerical positions - It is not necessary to specify units. The Map Viewer will interpret the range in the units of the Solignac genetic map (centiMorgans). For example: cM - Since the master map is a genetic linkage map, the search program interprets the region number as a centiMorgan (cM) unit (e.g., 1 or 12 or 12.5) Questions or Comments? Write to the NCBI Service Desk