Evolutionary dynamics of olfactory receptor genes in fishes and tetrapods

Abstract

Olfaction, which is an important physiological function for the survival of mammals, is controlled by a large multigene family of olfactory receptor (OR) genes. Fishes also have this gene family, but the number of genes is known to be substantially smaller than in mammals. To understand the evolutionary dynamics of OR genes, we conducted a phylogenetic analysis of all functional genes identified from the genome sequences of zebrafish, pufferfish, frogs, chickens, humans, and mice. The results suggested that the most recent common ancestor between fishes and tetrapods had at least nine ancestral OR genes, and all OR genes identified were classified into nine groups, each of which originated from one ancestral gene. Eight of the nine group genes are still observed in current fish species, whereas only two group genes were found from mammalian genomes, showing that the OR gene family in fishes is much more diverse than in mammals. In mammals, however, one group of genes, gamma, expanded enormously, containing approximately 90% of the entire gene family. Interestingly, the gene groups observed in mammals or birds are nearly absent in fishes. The OR gene repertoire in frogs is as diverse as that in fishes, but the expansion of group gamma genes also occurred, indicating that the frog OR gene family has both mammal- and fish-like characters. All of these observations can be explained by the environmental change that organisms have experienced from the time of the common ancestor of all vertebrates to the present.

Fig. 1.

Phylogenetic trees of vertebrate OR genes. (A) NJ tree for 1,026 functional OR genes. This tree contains 102 zebrafish, 44 pufferfish, 410 X. tropicalis, 82 chicken, and 388 human (5) OR genes. The number of amino acid sites used was 173 after deletion of all alignment gaps. A branch specific to each species is colored according to the color code at the bottom left. “Frog” indicates X. tropicalis. The scale bar indicates the estimated number of amino acid substitutions per site. The name of each OR gene group, defined in B, is shown. The bootstrap value obtained from 1,000 replications is shown for the clade determining each group. The arrow indicates the zebrafish group γ gene (Dr3OR5.4). Clade a and b and clade c indicate the rapid expansion of group γ genes in the X. tropicalis and chicken lineages, respectively. The GenBank accession numbers of the genes not assigned to the genome sequences are U42392, U42394, and AF283560-AF283561 for zebrafish genes; AB031380 and AB031383-AB031385 for pufferfish genes; and Z79585 and Z79587-Z79589 for chicken genes. (B) Condensed phylogenetic tree (31) at the 70% bootstrap value level for 310 functional OR genes and two outgroup non-OR GPCR genes. This condensed tree was produced from the NJ tree shown in Fig. 4 by assuming that all of the interior branches showing <70% bootstrap values had branch length 0. Bootstrap values obtained from 1,000 replications are shown for major clades. Black and white dots at nodes indicate the branches supported by >90% and >80% bootstrap values, respectively. (I) or (II) after the name of an OR gene group (α-ζ) indicates class I or II in the currently accepted classification of vertebrate OR genes. As the outgroup (Outgp), the bovine adenosine A1 receptor (GenBank accession no. X63592) and rat α2B-adrenergic receptor (AF366899) were used. As for group γ genes, four representative genes from zebrafish (Dr3OR5.4), X. tropicalis (Xt1OR1178.1), chickens (Gg2OR5.8), and humans (HsOR11.18.9, OR10G6) were used. Fish and amphibian OR genes found in the DDBJ database were also included. The color code for each bar showing the species is the same as in A. Four X. laevis genes (AJ249404 and AJ250750-AJ250752) are indicated by the same color (green) as X. tropicalis. Fish genes from the species other than zebrafish and pufferfish are shown by gray bars with their names: Carp, common carp (Cyprinus carpio, AB038166); Catfish, channel catfish (Ictalurus punctatus, L09217-L09225); Goldfish, goldfish (Carassius auratus, AF083076-AF083079); Lamp, European river lamprey (Lampetra fluviatilis, AJ012708-AJ012709); Loach, Japanese loach (Misgurnus anguillicaudatus, AB115055-AB115078); Medaka, Japanese medaka (Oryzias latipes, AB022646-AB022647 and AB029474-AB029480); Salmon, Atlantic salmon (Salmo salar, AY007188).

Fig. 2.

Evolutionary dynamics of vertebrate OR genes. The MRCA between jawed and jawless vertebrates had at least two ancestral OR genes, type 1 (gray circle) and type 2 (gray triangle). In the jawed vertebrate lineage, the ancestral type 1 genes had diverged to group α-ζ genes (colored circles), whereas ancestral type 2 genes became group η, θ, and κ genes (colored triangles). The MRCA between fishes and tetrapods had at least nine ancestral genes corresponding to the nine groups. At present, some extant fish species retain OR genes belonging to eight different groups except group α, which is illustrated by five colored circles and three triangles. In the mammalian lineage, seven groups of genes have been lost, but the number of group α (a red circle) and γ genes (a blue circle) have greatly increased to generate an enormous OR gene family. Expansion of group γ genes is also observed in amphibians, but they have genes belonging to eight different groups. The OR gene repertoire in birds (not shown) is similar to that in mammals. The divergence times between jawed and jawless vertebrates and between fishes and tetrapods were obtained from ref. .