Taste perception refers to sensations triggered by taste buds on the surface of the tongue, which sense sweet, salty, sour, bitter and umami flavors. These gustatory senses are closely related to an animal's diet and external environments [1
]. Most taste sensations are triggered via receptor-based sensors expressed in different taste-cell types [4
]. Among these chemical senses, bitter tastes are particularly important because many poisonous substances tend to be bitter, and bitter taste perception can allow animals to detect and avoid toxins in food [7
]. This process is mainly mediated by bitter taste receptors (T2R) which are encoded by T2R genes.
T2R genes belong to one type of G-protein-coupled receptors (GPCR) which are characterized by their seven conserved transmembrane regions [8
]. T2Rs are the largest family of taste receptors, which bind to tastants. T2R genes contain an average of 300 codons, and there are no introns in their coding regions, making them easy to detect in whole-genome sequences. Like olfactory and other chemosensory receptor genes, T2R genes also form a multi-gene family and display high sequence similarity [9
]. T2R genes are not randomly distributed through chromosomes; instead they tend to cluster together in a few specific genomic regions, perhaps corresponding to their generation by tandem gene duplications. For example, human T2R genes are mainly located in chromosomes 7 and 12, and mouse T2R genes are concentrated in chromosomes 6 and 15 [10
In previous studies, T2R gene repertoires have been described in some mammals, chickens, frogs and some teleost fishes [9
]. With the availability of whole-genome sequences of animals, T2R genes can be detected by applying data-mining methods. The nearly complete human and mouse T2R gene repertoires have been reported by Conte et al. [9
] and Shi et al. [10
]. Although these studies used different methods, their results were similar. Conte and colleagues [9
] identified 34 and 40 T2R genes in human and mouse genomes, respectively, and Shi and co-workers [10
] identified 33 and 36 T2R genes, respectively. Other vertebrate T2R gene receptors have also been identified [15
], for example, those of rat, dog, opossum, chicken and some teleost fishes. By analyzing the low-coverage genome sequence, T2R genes have also been identified in the cow. Owing to the different data-mining criteria used for the identification of T2R genes, results have differed among studies. For example, Shi et al [16
] identified 64 T2R genes in the frog, whereas Go [15
] only identified only 54 T2R genes. Furthermore, some studies focused on identification of G-protein-coupled receptors (GPCRs) from genome sequences [19
]; however, not all GPCR-encoding genes are T2R genes, they also include other gene families, such as olfactory receptor (OR) and vomeronasal pheromone (VR) receptor genes. These studies also distinguished T2R genes from non-T2R GPCR genes. In Additional file 1
, we list the sizes of the T2R gene repertoires that have been well documented from a range of species. These results indicate that the number of T2R genes shows extensive variation among taxa. For example, the chicken and zebrafish have only 3 and 4 intact T2R genes, respectively, whereas the frog (Xenopus tropicalis
) has nearly 50 intact T2R genes. The number of intact genes in the frog is therefore about 16 times greater than in the chicken and 12 times greater than in the zebrafish. Furthermore, massive pseudogenization has occurred in some species. These observations indicated that ability to bitter taste might be largely determined by the number of functional genes. Bitter taste perception in animals is tightly coupled with diet and habitats. Differences in gene family size are due to lineage-specific gene duplications and losses in vertebrates, which represents an extreme form of birth-and-death evolution [15
]. Therefore, it is interesting to study the pattern of gains and losses of T2R genes during vertebrate evolution.
Go has previously predicted the numbers of ancestral T2R genes using the linearized tree method [15
], and identified some lineage-specific gene expansions and contractions that occurred throughout vertebrate evolution. However, this method did not characterize the gains and losses of T2R genes in detail, especially in mammals. To gain further insight into the evolutionary dynamics of T2R genes, we identified more T2R gene repertoires in vertebrates, and used the reconciled-tree method to study evolutionary changes in T2R gene families [22
]. In this study, we provide a more comprehensive view of birth-and-death processes involving T2R genes during the evolution of vertebrates, and suggest that this approach might further improve our understanding of bitter taste sensitivities.