Abstract
BackgroundTAARs (trace amine-associated receptors) are among the principal receptors expressed by the olfactory epithelium. We used the recent BROAD Institute release of the genome sequences of five representative fishes of the cichlid family to establish the complete TAAR repertoires of these species and to compare them with five other fish TAAR repertoires.ResultsThe genome sequences of O. niloticus, P. nyererei, H. burtoni, N. brichardi and M. zebra were analyzed by exhaustive TBLASTN searches with a set of published TAAR gene sequences used as positive bait. A second TBLASTN analysis was then performed on the candidate genes, with a set of non-TAAR class A GPCR (G protein-coupled receptors) used as negative bait. The resulting cichlid repertoire contained 44 complete TAAR genes from O. niloticus, 18 from P. nyererei, 23 from H. burtoni, 12 from N. brichardi and 20 from M. zebra, plus a number of pseudogenes, edge genes and fragments. A large proportion of these sequences (80%) consisted of two coding exons, separated in all but two cases by an intron in the interloop 1 coding sequence. We constructed phylogenetic trees. These trees indicated that TAARs constitute a distinct clade, well separated from ORs (olfactory receptors) and other class A GPCRs. Also these repertoires consist of several families and subfamilies, a number of which are common to fugu, tetraodon, stickleback and medaka. Like all other TAARs identified to date, cichlid TAARs have a characteristic two-dimensional structure and contain a number of amino-acid motifs or amino acids, such cysteine, in particular conserved positions.ConclusionsLittle is known about the functions of TAARs: in most cases their ligands have yet to be identified, partly because appropriate methods for such investigations have not been developed. Sequences analyses and comparisons of TAARs in several animal species, here fishes living in the same environment, should help reveal their roles and whether they are complementary to that of ORs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1478-4) contains supplementary material, which is available to authorized users.
Highlights
Trace amine-associated receptor (TAAR) are among the principal receptors expressed by the olfactory epithelium
Cichlid TAAR repertoires We carried out a TBLASTN search of the five cichlid genome sequences determined by the BROAD Institute [23], with a set of 199 sequences corresponding to 109 zebrafish, 27 medaka, 50 stickleback and 13 fugu annotated TAAR genes retrieved from the GenBank and ENSEMBL databases [8] (Additional file 1)
This initial search, with a cut-off of 1e−50, identified a number of candidate receptors; false candidates were identified by a second TBLASTN search with 247 fish class A nonTAAR G protein-coupled receptor (GPCR) sequences (Additional file 2) and were excluded
Summary
TAARs (trace amine-associated receptors) are among the principal receptors expressed by the olfactory epithelium. Trace amine-associated receptors (TAARs) are a class of chemoreceptors belonging to the G protein-coupled receptor (GPCR) superfamily [1,2,3]. They have been found in the olfactory epithelium, where, unlike human and zebrafish TAAR1, they are expressed together with the main olfactory receptors (ORs), each by a specific subset of neurons [4]. It is difficult to interpret and explain the very different numbers of receptors and OR/TAAR ratios in mammals and fishes These differences reflect differences in physiology and/or environment or different agonist distributions. It is possible that some ligands are recognized by TAARs in fish and Azzouzi et al BMC Genomics (2015) 16:335
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