Evolution and origin of vomeronasal-type odorant receptor gene repertoire in fishes

Abstract

Background: In teleost fishes that lack a vomeronasal organ, both main odorant receptors (ORs) and vomeronasal receptors family 2 (V2Rs) are expressed in the olfactory epithelium, and used for perception of water-soluble chemicals. In zebrafish, it is known that both ORs and V2Rs formed multigene families of about a hundred copies. Whereas the contribution of V2Rs in zebrafish to olfaction has been found to be substantially large, the composition and structure of the V2R gene family in other fishes are poorly known, compared with the OR gene family.

Results: To understand the evolutionary dynamics of V2R genes in fishes, V2R sequences in zebrafish, medaka, fugu, and spotted green pufferfish were identified from their draft genome sequences. There were remarkable differences in the number of intact V2R genes in different species. Most V2R genes in these fishes were tightly clustered in one or two specific chromosomal regions. Phylogenetic analysis revealed that the fish V2R family could be subdivided into 16 subfamilies that had diverged before the separation of the four fishes. Genes in two subfamilies in zebrafish and another subfamily in medaka increased in their number independently, suggesting species-specific evolution in olfaction. Interestingly, the arrangements of V2R genes in the gene clusters were highly conserved among species in the subfamily level. A genomic region of tetrapods corresponding to the region in fishes that contains the V2R cluster was found to have no V2R gene in any species.

Conclusion: Our results have indicated that the evolutionary dynamics of fish V2Rs are characterized by rapid gene turnover and lineage-specific phylogenetic clustering. In addition, the present phylogenetic and comparative genome analyses have shown that the fish V2Rs have expanded after the divergence between teleost and tetrapod lineages. The present identification of the entire V2R repertoire in fishes would provide useful foundation to the future functional and evolutionary studies of fish V2R gene family.

Figure 1

Phylogenetic relationship and estimated divergence times [25] of zebrafish, medaka, fugu, and pufferfish.

Figure 2

A flow chart of the procedure of V2R gene identification from draft genome sequences.

Figure 3

Phylogenetic relationships of fish V2Rs and related GPCRs. The tree is reconstructed by the neighbor-joining method with protein JTT matrix distances. Bootstrap values are shown on the major internal node only. The triangles and squares at the tips of the tree indicate species: open triangle, zebrafish; solid triangle, medaka; open square, pufferfish; solid square, fugu. Five fugu and two goldfish V2Rs used for constructing the profile HMM are shown in the tree. Solid circles at internal nodes indicate the position of the most recent common ancestor between teleost fishes and tetrapods. Open circles indicate the position of the most recent common ancestor among four fishes. Colors of each vertical bar indicate subfamilies in the fish V2R gene family. Genbank accession numbers of known V2Rs and related GPCRs used in this analysis are as follows: goldfish V2Rs (AF083080, AF083081), fugu V2Rs (AB008858–AB008862), mouse V2Rs (XP_144968, XP_145559, XP_142496), rat V2Rs (NP_775440–NP_775442), a V2R of Xenopus laevis (AB113361), CaSRs (AAF77923, AAT06805, AB008857, A56715, AAD40638, P48442), GPRC6As (AF158963, AY770492, XP_426177, NP_683766, CAD59483), mouse family C V2R (NP_064302, AAC08413).

Figure 4

Chromosomal locations of V2R genes in zebrafish, medaka, pufferfish, and fugu. Each subfamily is indicated in color as in Figure 3. Asterisks indicate pseudogenes. Note that the scale of the V2R cluster is different among species. The length of the V2R cluster region in each species is shown in parentheses. In fugu, only four representative scaffolds that contain V2R genes are shown.

Figure 5

Genomic region around the V2R gene cluster in fishes and the corresponding region in tetrapods. The fish V2R cluster is shown in black. Positions and transcriptional orientations of genes are indicated by arrows. V2R (C) indicates the family C V2R gene.