Abstract
BackgroundTo help understand the molecular mechanisms underlying the remarkable phenotypic diversity displayed by cichlids, the genome sequences of O. niloticus, P. nyererei, H. burtoni, N. brichardi and M. zebra were recently determined. Here, we present the contents of the olfactory receptor (OR) repertoires in the genomes of these five fishes.ResultsWe performed an exhaustive TBLASTN search of the five cichlid genomes to identify their OR repertoires as completely as possible. We used as bait a set of ORs described in the literature. The cichlid repertoires thereby extracted contained large numbers of complete genes (O. niloticus 158; H. burtoni 90; M. zebra 102; N. brichardi 69; P. nyererei 88), a small numbers of pseudogenes and many “edge genes” corresponding to incomplete genes located at the ends of contigs. A phylogenetic tree was constructed and showed these repertoires include a large number of families and subfamilies. It also allowed the identification of a large number of OR analogues between cichlids with very high amino-acid identity (≥99%). Nearly 9% of the full-length cichlid OR genes are composed of several coding exons. This is very unusual for vertebrate OR genes. Nevertheless, the evidence is strong, and includes the donor and acceptor splice junction sequences; also, the positions of these genes in the phylogenetic tree indicate that they constitute subfamilies well apart from non-OR G protein-coupled receptor families.ConclusionsCichlid OR repertoires are made up of a larger number of genes and fewer pseudogenes than those in other teleosts except zebrafish. These ORs share all identified properties common to all fish ORs; however, the large number of families and subfamilies, each containing few ORs implies that they have evolved more rapidly. This high level of OR diversity is consistent with the substantial phenotypic diversity that characterizes cichlids.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-586) contains supplementary material, which is available to authorized users.
Highlights
To help understand the molecular mechanisms underlying the remarkable phenotypic diversity displayed by cichlids, the genome sequences of O. niloticus, P. nyererei, H. burtoni, N. brichardi and M. zebra were recently determined
(33/54) of the pseudogenes we found in the cichlid genomes are due to frameshift mutations, whereas the others are due to a nucleotide misincorporation, changing a sense codon into a stop codon (Table 2)
A comprehensive search of the genome sequences of five fishes belonging to the cichlid family (Oreochromis niloticus, Pundamilia nyererei, Haplochromis (Astatotilapia) burtoni, Neolaprologus brichardi, Mitriaclima zebra) was undertaken in order to identify their olfactory receptor (OR) gene repertoires
Summary
We performed an exhaustive TBLASTN search of the five cichlid genomes to identify their OR repertoires as completely as possible. The cichlid repertoires thereby extracted contained large numbers of complete genes A phylogenetic tree was constructed and showed these repertoires include a large number of families and subfamilies. It allowed the identification of a large number of OR analogues between cichlids with very high amino-acid identity (≥99%). 9% of the full-length cichlid OR genes are composed of several coding exons. This is very unusual for vertebrate OR genes. The evidence is strong, and includes the donor and acceptor splice junction sequences; the positions of these genes in the phylogenetic tree indicate that they constitute subfamilies well apart from non-OR G protein-coupled receptor families
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