A Comparative Genomics Analysis Of The Loss Of Whale Taste And The Adaptability Of Cetaceans

Five basic taste modalities (sour, sweet, bitter, salt and umami) can be distinguished by humans and are fundamental for physical and ecological adaptations in mammals. Molecular genetic studies of the receptor genes for these tastes have been conducted in terrestrial mammals; however, little is known about the evolution and adaptation of these genes in marine mammals. Here, all the five basic taste modalities, sour, sweet, bitter, salt and umami, were investigated in cetaceans. Based on sequence characteristics of taste receptor genes, we found multiple indels and/or premature stop codons located on the receptors of sour, sweet, umami and bitter tastes in almost all cetaceans amplified. By mapping the first premature stop codon on secondary structure of each taste receptor, we found all these mutations lead to the truncation of each protein, thus leading to the loss of their function. Furthermore, our selective pressure analysis revelas that functional constraints on sweet, umami and sour taste receptors have not completely removed, suggesting that their pseudogenization may have happened recently, while selective pressures located on bitter taste receptors are almost completely removed, suggesting that their pseudogenization may happen earlier. The integrity of the candidate salt taste receptor genes in all the cetaceans examined may be because of their function in Na+reabsorption, which is key to osmoregulation and aquatic adaptation. Whether cetaceans can taste salt is still unknown, the answer to this question awaits further investigation.To further investigate cetaceans’adaptation to full water environment, we preformed inter-species and intra-species analyses of published cetacean genomes as well as three common bottlenose dolphin genomes. Based on one-to-one orthologous among baiji, minke whale, cow, dog, human and mouse, our PAML analysis reveals pervasively adaptive evolution in innate immune system since the origin of crown cetaceans and their subsequent diversification. And, positively selected genes in both minke whale and baiji are associated with transport, activation, and synthesis of fatty acids, which is consistent with their thicker blubber. Besides, genes involved in osmoregulation, bone density regulation and hypoxia tolerance are also positively selected in cetaceans, which is consistent with the fact that cetaceans are faced with divergent osmotic pressures and possessing fast-swimming and diving behaviors. Furthermore, in order to investigate cetaceans’adaptation to sea water and fresh water, we picked out single nucleotide polymorphisms between oceanic cetaceans (minke whale and common bottlenose dolphin) and fresh water lived baiji using their re-sequencing data, and then used PROVEAN software to predict their effects on protein function. Our PROVEAN analysis reveals that fresh and oceanic lived dolphins had been found harbored different substitutions, which are involved in olfactory and visual system, DNA damage repair, and pigmentation. Demographic reconstructions validated the functional extinction of Yangtze River dolphin may be the consequence of habitat destruction and persecution by humans, and this is consistent with previous baiji genome analysis.