Dataset Information

Inventory of the cichlid olfactory receptor gene repertoires: identification of olfactory genes with more than one coding exon.

ABSTRACT:

Background

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. Here, we present the contents of the olfactory receptor (OR) repertoires in the genomes of these five fishes.

Results

We 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.

Conclusions

Cichlid 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.

SUBMITTER: Azzouzi N

PROVIDER: S-EPMC4122780 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature

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Publications

Inventory of the cichlid olfactory receptor gene repertoires: identification of olfactory genes with more than one coding exon.

Azzouzi Naoual N Barloy-Hubler Frederique F Galibert Francis F

BMC genomics 20140711

<h4>Background</h4>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. Here, we present the contents of the olfactory receptor (OR) repertoires in the genomes of these five fishes.<h4>Results</h4>We performed an exhaustive TBLASTN search of the five cichlid genomes to identify their OR repertoires as completely as possibl ...[more]

PMID: 25015101

Similar Datasets

Project description:BACKGROUND: The detection of odorants is mediated by olfactory receptors (ORs). ORs are G-protein coupled receptors that form a remarkably large protein superfamily in vertebrate genomes. We used data that became available through recent sequencing efforts of reptilian and avian genomes to identify the complete OR gene repertoires in a lizard, the green anole (Anolis carolinensis), and in two birds, the chicken (Gallus gallus) and the zebra finch (Taeniopygia guttata). RESULTS: We identified 156 green anole OR genes, including 42 pseudogenes. The OR gene repertoire of the two bird species was substantially larger with 479 and 553 OR gene homologs in the chicken and zebra finch, respectively (including 111 and 221 pseudogenes, respectively). We show that the green anole has a higher fraction of intact OR genes (approximately 72%) compared with the chicken (approximately 66%) and the zebra finch (approximately 38%). We identified a larger number and a substantially higher proportion of intact OR gene homologs in the chicken genome than previously reported (214 versus 82 genes and 66% versus 15%, respectively). Phylogenetic analysis showed that lizard and bird OR gene repertoires consist of group alpha, theta and gamma genes. Interestingly, the vast majority of the avian OR genes are confined to a large expansion of a single branch (the so called gamma-c clade). An analysis of the selective pressure on the paralogous genes of each gamma-c clade revealed that they have been subjected to adaptive evolution. This expansion appears to be bird-specific and not sauropsid-specific, as it is lacking from the lizard genome. The gamma-c expansions of the two birds do not intermix, i.e., they are lineage-specific. Almost all (group gamma-c) OR genes mapped to the unknown chromosome. The remaining OR genes mapped to six homologous chromosomes plus three to four additional chromosomes in the zebra finch and chicken. CONCLUSION: We identified a surprisingly large number of potentially functional avian OR genes. Our data supports recent evidence that avian olfactory ability may be better developed than previously thought. We hypothesize that the radiation of the group gamma-c OR genes in each bird lineage parallels the evolution of specific olfactory sensory functions.

Dataset Information

Inventory of the cichlid olfactory receptor gene repertoires: identification of olfactory genes with more than one coding exon.

Background

Results

Conclusions

Publications

Inventory of the cichlid olfactory receptor gene repertoires: identification of olfactory genes with more than one coding exon.

Similar Datasets

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