Dramatic variation of the vomeronasal pheromone receptor gene repertoire among five orders of placental and marsupial mammals

Abstract

Pheromones are chemicals emitted and sensed by conspecifics to elicit social and sexual responses and are perceived in terrestrial vertebrates primarily by the vomeronasal organ (VNO). Pheromone receptors in the mammalian VNO are encoded by the V1R and V2R gene superfamilies. The V1R superfamily contains 187 and 102 putatively functional genes in the mouse and rat, respectively. To investigate whether this large repertoire size is typical among mammals with functional VNOs, we here describe the V1R repertoires of dog, cow, and opossum based on their draft genome sequences. The dog and cow have only 8 and 32 intact V1R genes, respectively. Thus, the intact V1R repertoire size varies by at least 23-fold among placental mammals with functional VNOs. To our knowledge, this size ratio represents the greatest among-species variation in gene family size of all mammalian gene families. Phylogenetic analysis of placental V1R genes suggests multiple losses of ancestral genes in carnivores and artiodactyls and gains of many new genes by gene duplication in rodents, manifesting massive gene births and deaths. We also identify 49 intact opossum V1R genes and discover independent expansions of the repertoire in placentals and marsupials. We further show a concordance between the V1R repertoire size and the complexity of VNO morphology, suggesting that the latter could indicate the sophistication of pheromone communications within species. In sum, our results demonstrate tremendous diversity and rapid evolution of mammalian V1R gene inventories and caution the generalization of VNO biology from rodents to all mammals.

Fig. 1.

Variation in the numbers of intact V1R genes (filled bars) and pseudogenes (open bars) among mice, rats, humans, dogs, cows, and opossums with the phylogenetic relationships among the species shown by the tree. Mice have 187 functional V1Rs and 168 pseudogenes (11, 12). Rats have 102 functional V1Rs and at least 50 pseudogenes (ref. and P.S., unpublished data). Humans have 4 V1R ORFs and ≈200 pseudogenes (9, 13). Cows have 32 functional V1Rs and 41 pseudogenes (this study). Dogs have 8 functional V1Rs and 22 pseudogenes (this study). Opossums have 49 functional V1Rs and 53 pseudogenes (this study). The number of pseudogenes in rats is likely an underestimate because there has been no comprehensive study of rat V1R pseudogenes.

Fig. 2.

Phylogeny of intact V1R genes: 8 in dogs, 32 in cows, 4 in humans, 102 in rats, and 187 in mice. Shaded regions group the genes into 18 placental mammalian V1R families previously described in refs. , , and or described here (see Results), with the family names indicated. Black circles mark family groups that contain more than one family as shown in Table 1. Dog branches are in red, cow branches are in black, human branches are in blue, mouse branches are in purple, and rat branches are in green. Bootstrap percentages supporting the family groups are shown if >50. The tree was reconstructed by using the neighbor-joining method with Poisson-corrected protein distances. The arrow points to where the tree is rooted with putative V1Rs of the frog Xenopus tropicalis (W.E.G. and J.Z., unpublished data). (Scale bar: 0.2 amino acid substitutions per site.)

Fig. 3.

Phylogeny of intact V1R genes from the opossum, mouse, rat, dog, and cow. V1R families of placental mammals (V1RA-V1RQ) have been collapsed for better illustration, but all 49 V1Rs of the opossum are shown. Opossum genes are divided into eight families (oV1RA-oV1RH). The tree was reconstructed by using the neighbor-joining method with Poisson-corrected protein distances. Bootstrap percentages are shown if >50. The arrow points to where the tree is rooted with X. tropicalis V1Rs. (Scale bar: 0.2 amino acid substitutions per site.)

Fig. 4.

Correlation between the morphological complexity of VNO and the number of intact V1R genes in the genome. Morphological complexity follows ref. .