Abdominal-A

Abdominal-A (abd-A) encodes a product with specific RNA polymerase II transcription factor activity involved in oenocyte development which is localized to the nucleus. It is expressed in the Drosophila embryo and larva (Flybase website). Its amino acid sequence contains a homeobox domain and a 'Homeobox' antennapedia-type domain. It interacts genetically with a number of developmental genes including Ubx , abd-B , Dfd , and lab. The gene consists of three exons: (1) a 5' highly conserved 750 bp exon, (2) a small (36 bp), highly conserved second exon, and (3) a third exon containing a homeobox domain. Similarity between the homeobox domain of abd-A and other homeobox genes (such as Ultrabithorax and Antennapedia) makes this third exon a poor choice for phylogenetic studies. DeMenten et al. (2003, Fig. 2) provide a map of the gene. Complete sequences of the abd-A gene are available on Genbank for Tribolium castaneum [Genbank number AF017415], Drosophila melanogaster [Genbank number X54453], Anopheles gambiae [Genbank number AF080566], and Myrmica rubra [Genbank number AF332515] (Niculita et al. 2001).

Abd-A has been used in phylogenetic studies of ants (Astruc et al. 2004, Ward & Downie 2005) as well as in studies of sex determination (DeMenten et al. 2003). Primers developed initially by DeMenten et al. 2003 span an approximately 700 bp region in the first exon of the abd-A gene (with no introns). Primers were later improved by Ward & Downie 2005 in a phylogenetic study of ants. The utility of this gene relative to the others used by Ward & Downie (2005) was not discussed, although the gene appears to be a highly conserved one (sequence divergence ranged from 7.3% to 19.4%). The gene appears to be a reasonable one for higher-level bee phylogeny. Apis mellifera abd-A sequence is available under Genbank accession number AY703685 (Ward & Downie 2005). Using this fragment to search the honeybee genome, we were able to locate a complete abd-A fragment for the honeybee. Primers developed for ants and bees (Ward & Downie 2005), a map of the gene (from DeMenten et al. 2003), and an alignment of Apis and Myrmica abd-A are provided in the files listed below.

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Gene Information:

Map of Abdominal-A (.pdf file)
Abdominal-A primer information (.pdf file)

Related Papers:
Ward, P.S. & D.A. Downie (2005). The ant subfamily Pseudomyrmecinae (Hymenoptera: Formicidae): phylogeny and evolution of the big-eyed arboreal ants. Syst. Entomol. 30: 310-335.

Excel spreadsheets:
Genbank accession numbers from Ward & Downie (2004) (.xls file)

Data sets:
Ward & Downie (2004) data set (.txt file)
available from TREEBASE: M1940)

Alignments:
Apis + Myrmica alignment (.doc file)
Contains longer Myrmica and Apis reference sequences and the Apis fragment used in Ward & Downie (2004).