On the origin and evolution of vertebrate olfactory receptor genes: comparative genome analysis among 23 chordate species

Abstract

Olfaction is a primitive sense in organisms. Both vertebrates and insects have receptors for detecting odor molecules in the environment, but the evolutionary origins of these genes are different. Among studied vertebrates, mammals have approximately 1,000 olfactory receptor (OR) genes, whereas teleost fishes have much smaller (approximately 100) numbers of OR genes. To investigate the origin and evolution of vertebrate OR genes, I attempted to determine near-complete OR gene repertoires by searching whole-genome sequences of 14 nonmammalian chordates, including cephalochordates (amphioxus), urochordates (ascidian and larvacean), and vertebrates (sea lamprey, elephant shark, five teleost fishes, frog, lizard, and chicken), followed by a large-scale phylogenetic analysis in conjunction with mammalian OR genes identified from nine species. This analysis showed that the amphioxus has >30 vertebrate-type OR genes though it lacks distinctive olfactory organs, whereas all OR genes appear to have been lost in the urochordate lineage. Some groups of genes (theta, kappa, and lambda) that are phylogenetically nested within vertebrate OR genes showed few gene gains and losses, which is in sharp contrast to the evolutionary pattern of OR genes, suggesting that they are actually non-OR genes. Moreover, the analysis demonstrated a great difference in OR gene repertoires between aquatic and terrestrial vertebrates, reflecting the necessity for the detection of water-soluble and airborne odorants, respectively. However, a minor group (beta) of genes that are atypically present in both aquatic and terrestrial vertebrates was also found. These findings should provide a critical foundation for further physiological, behavioral, and evolutionary studies of olfaction in various organisms.

Keywords: amphioxus; chordate; molecular evolution; multigene family; olfactory receptor; vertebrate.

FIG. 1.—

(A) Neighbor-Joining (NJ) phylogenetic tree for 615 OR-like genes and six non-OR GPCR genes as the outgroup. This tree was constructed using 31 functional OR genes in the amphioxus (magenta) and all functional Type 1 and Type 2 genes in the sea lamprey (blue), zebra fish (green), and human (red; see fig. 2). One B. belcheri OR-like gene (GenBank accession number, AB182635; Satoh 2005) and two river lamprey OR genes (AJ012708 and AJ012709; Freitag et al. 1999) were also used (indicated by arrows). Outgroup genes were randomly chosen from non-OR rhodopsin-like GPCR genes in humans (Fredriksson et al. 2003). The following genes were used as the outgroup: alpha-1B-adrenergic receptor (NP_000670.1), cholinergic receptor, muscarinic 1 (NP_000729.2), somatostatin receptor 5 (NP_001044.1), chemokine-binding protein 2 (NP_001287.2), GPCR 35 (NP_005292.2), and GPCR G2A (NP_037477.1). Bootstrap values obtained from 500 resamplings are shown only for major clades. The number of amino acid sites used was 184. The scale bar represents the estimated number of amino acid substitutions per site. (B) NJ phylogenetic tree for all (134) functional Type 2 genes identified in this study with six Type 1 genes as the outgroup. The following genes were used as the outgroup: group α, HsOR1.1.3; β, DareOR15.62; γ, HsOR11.3.2; δ, DareOR15.1; ϵ, DareOR10.29; and ζ, DareOR10.1 (Niimura and Nei 2003; this study). Bootstrap values obtained from 500 resamplings are shown for the clades with >70% bootstrap values. The species names are colored according to the color code. The number of amino acid sites used was 234.

FIG. 2.—

The number of genes belonging to each group in 19 vertebrate species. Red, yellow, and blue bars represent functional genes, truncated genes, and pseudogenes, respectively. The numbers in parentheses below each bar indicate those of functional genes, truncated genes, and pseudogenes. For mammalian OR genes, groups α and β correspond to class I and group γ corresponds to class II (Glusman et al. 2000; Niimura and Nei 2005b, 2006). The numbers of class I and class II (group γ) genes in mammals were reported in Niimura and Nei (2007) and Go and Niimura (2008). The number of group α genes in a mammalian species was obtained by subtracting the number of group β genes (see fig. 3) from that of class I genes. Note that the scales of bar graphs are different among groups because of large variations in the number of genes belonging to each group. Putative functions are also shown at the bottom. “Air” and “Water” represent the detection of airborne and water-soluble odorants, respectively.

FIG. 3.—

Neighbor-Joining phylogenetic tree for 36 group β genes identified in this study with all (387) human functional OR genes. Bootstrap values were obtained from 500 replications and are shown for the clades with >70% bootstrap values (in clade β) and for major clades. Species names are colored in the same manner as figure 1B. The number of amino acid sites used was 232. Names of group β genes are provided in supplementary data set 3 (Supplementary Material online).

FIG. 4.—

Schematic illustration of the evolution of OR gene families in chordates. In the tetrapod lineage, the number of group α and γ genes has dramatically expanded, probably due to the importance of olfactory information in terrestrial life (see Niimura and Nei 2005b).

FIG. 5.—

Numbers of functional OR genes and those of functional TAAR genes in 16 vertebrate species. A dashed line indicates the points in which the number of OR genes and that of TAAR genes are equal. The numbers of TAAR genes in the sea lamprey, zebra fish, stickleback, medaka, fugu, western clawed frog, and chicken were obtained from Hashiguchi and Nishida (2007). Those in the platypus, opossum, cow, and dog were taken from Grus et al. (2007), and those in the mouse, rat, chimpanzee, and human were from Lindemann et al. (2005). The number of TAAR genes in the macaque was obtained from Nei et al. (2008). La, sea lamprey; Ze, zebra fish; St, stickleback; Me, medaka; Fu, fugu; Ch, chicken; Fr, western clawed frog; Pl, platypus; Op, opossum; Co, cow; Do, dog; Mo, mouse; Ra, rat; Ma, macaque; Cp, chimpanzee; and Hu, human.