Table 1.
The number of TAAR genes identified in the 30 animal genomes.
Fig 1.
Syntenic relationship of the TAAR genes in nine vertebrate genomes.
Only genomes in which all TAAR genes are located in one chromosome or no more than two scaffolds were examined (Xenopus genes are found in two scaffolds). TAAR and adjacent non-TAAR genes are depicted by the closed and open boxes, respectively (pseudogenes are not included). TAAR genes are shown in different colors based on their taxonomic distributions as follows: TAAR1 found in jawed vertebrates in red, amniote-specific TAAR2 and TAAR5 in purple, mammalian-specific TAAR3 in orange, tetrapod-specific TAAR4 in dark blue, eutherian-specific TAAR6, 7, and 8 in light green, therian-specific TAAR9 in cyan, and metatherian-specific TAARM1-M3 in dark green. Note that the same color scheme is used in Figs 2 and 3. When tandemly duplicated functional copies exist for a TAAR gene, the copy number is also shown. Gene locations are not in scale (see S2 Table for the actual positional information). Black arrows indicate transcriptional directions. A current consensus of the tetrapod phylogeny with their approximate divergence times (million years ago; MYA) is illustrated at the top [33, 34]. The chromosome or scaffold numbers are shown below the genus names.
Fig 2.
The maximum-likelihood phylogeny of TAAR proteins from ten representative vertebrate species.
Only representative TAAR proteins are included for each species. Four biogenic amine receptors (5HT4R: serotonin receptors, and H2R: histamine receptors) are used as the outgroup. The genes newly identified in this study are shown in italics. The numbers at internal branches show the bootstrap support values (%) for the maximum-likelihood and neighbor-joining phylogenies and the posterior probability (%) for the Bayesian phylogeny in this order. Supporting values are shown only for the internal branches that have at least one method supporting higher than 70%. For TAAR V, teleost TAARs, and lamprey TAAR-like, we followed the gene names given by Hashiguchi and Nishida [26]. The inset illustrates a current consensus of the vertebrate phylogeny with their approximate divergence times (MYA) [33, 34].
Fig 3.
The maximum-likelihood phylogeny of TAAR proteins from 24 gnathostome genomes.
All functional proteins in tetrapods, nine representative teleost proteins, and two elephant shark TAARs are included in the analysis. TAAR V as well as the lamprey TAAR-like sequences are used as the outgroup. The genes newly identified in this study are shown in italics. The numbers at internal branches show the bootstrap support values (%) for the maximum-likelihood and neighbor-joining phylogenies and the posterior probability (%) for the Bayesian phylogeny in this order. Supporting values are shown only for the major internal branches that have at least one method supporting higher than 70%. Blue-colored branches indicate the species-specific gene duplications within a cluster supported by higher than 80% of bootstrap values or posterior probability for all methods. Red-colored branches and arrows indicate those identified to be under positive selection by the branch-site models of PAML analysis (see S4 Table). Brown-colored branches indicate nine representative teleost TAARs, elephant shark TAARs, and lamprey TAAR-like proteins. The inset illustrates the evolution of vertebrate TAARs with approximate timing of various gain (green) and loss (blue) events. The vertebrate phylogeny is based on Blair and Hedges [33].
Fig 4.
The number of TAAR genes within each TAAR subfamily for each therian species.
The size of bubbles denotes the number of species where the corresponding TAAR genes are found. The average ω (dN/dS) calculated by the PAML M0 model for each TAAR subfamily is also plotted (open squares).
Fig 5.
The 3D-structural model of the elephant TAAR7a protein (cyan) superimposed with the turkey β1-adrenergic receptor (β1AR, gray).
The ligand of the β1AR, dobutamine, is shown with the stick model. Positively selected sites are indicated by red (detected by the site model in TAAR7), green (detected by the branch-site model in flying fox TAAR7c and elephant TAAR7a), purple (detected by the site model in TAAR8), and brown (detected by the branch-site model in mouse TAAR8a). The transmembranes (TM) and internal/external loop (IC1-3 and EC1-3) regions as well as N-terminal (N) are labeled. The C-terminal is invisible locating behind TM1. See S6 Fig for more details.