Characterization and phylogeny of bitter taste receptor genes (Tas2r) in Squamata.

The perception of bitter taste is linked to the detection of toxins. Therefore, it facilitates avoiding the consumption of potential toxins in the diet. At the molecular level, bitter taste is mediated by taste 2 receptors (Tas2rs). Studies on Tas2r have made major advances in recent years. However, little is known about Tas2rs in Squamata, the second largest order of extant vertebrates. To explore the repertoire and phylogenetic relationships among Tas2r genes in Squamata, we identified and characterized Tas2rs from genome assemblies of 15 Squamata species. We observed considerable Tas2r contraction and expansion in the suborders Serpentes and Lacertilia, respectively. Phylogenetic and reconciliation analysis suggested that lineage-specific gene gains and losses could have led to the Tas2r contraction and expansion in Squamata. Different Tas2r repertoires in Serpents and Lacertilia also reflect their oral anatomical features and taste behaviors. Our findings offer novel perspectives into the study of taste and dietary protection in Squamata species.

The repertoire of bitter taste receptor genes in canids.

Bitter taste receptors (Tas2rs) play important roles in mammalian defense mechanisms by helping animals detect and avoid toxins in food. Although Tas2r genes have been widely studied in several mammals, minimal research has been performed in canids. To analyze the genetic basis of Tas2r genes in canids, we first identified Tas2r genes in the wolf, maned wolf, red fox, corsac fox, Tibetan fox, fennec fox, dhole and African hunting dog. A total of 183 Tas2r genes, consisting of 118 intact genes, 6 partial genes and 59 pseudogenes, were detected. Differences in the pseudogenes were observed among nine canid species. For example, Tas2r4 was a pseudogene in the dog but might play a functional role in other canid species. The Tas2r42 and Tas2r10 genes were pseudogenes in the maned wolf and dhole, respectively, and the Tas2r5 and Tas2r34 genes were pseudogenes in the African hunting dog; however, these genes were intact genes in other canid species. The differences in Tas2r pseudogenes among canids might suggest that the loss of intact Tas2r genes in canid species is species-dependent. We further compared the 183 Tas2r genes identified in this study with Tas2r genes from ten additional carnivorous species to evaluate the potential influence of diet on the evolution of the Tas2r gene repertoire. Phylogenetic analysis revealed that most of the Tas2r genes from the 18 species intermingled across the tree, suggesting that Tas2r genes are conserved among carnivores. Within canids, we found that some Tas2r genes corresponded to the traditional taxonomic groupings, while some did not. PIC analysis showed that the number of Tas2r genes in carnivores exhibited no positive correlation with diet composition, which might be due to the limited number of carnivores included in our study.

Characteristics of Microbiota in Different Segments of the Digestive Tract of Lycodon rufozonatus.

The gastrointestinal tract of animals contains microbiota, forming a complex microecosystem. Gut microbes and their metabolites can regulate the development of host innate and adaptive immune systems. Animal immune systems maintain intestinal symbiotic microbiota homeostasis. However, relatively few studies have been published on reptiles, particularly snakes, and even fewer studies on different parts of the digestive tracts of these animals. Herein, we used 16S rRNA gene sequencing to investigate the microbial community composition and adaptability in the stomach and small and large intestines of Lycodon rufozonatus. Proteobacteria, Bacteroidetes, and Firmicutes were most abundant in the stomach; Fusobacteria in the small intestine; and Proteobacteria, Bacteroidetes, Fusobacteria, and Firmicutes in the large intestine. No dominant genus could be identified in the stomach; however, dominant genera were evident in the small and large intestines. The microbial diversity index was significantly higher in the stomach than in the small and large intestines. Moreover, the influence of the microbial community structure on function was clarified through function prediction. Collectively, the gut microbes in the different segments of the digestive tract revealed the unique features of the L. rufozonatus gut microbiome. Our results provide insights into the co-evolutionary relationship between reptile gut microbiota and their hosts.

The complete mitochondrial genome of the Riparia riparia (Passeriformes: Hirundinidae).

The Sand Martin (Riparia riparia) belongs to Hirundinidae. In this study, the complete mitochondrial genome of R. riparia was sequenced and characterized. The genome was 17,963 bases in length (GenBank accession no. OK537984) including 13 protein-coding genes, two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and two control regions. The overall base composition of R. riparia mitogenome was 30.5% for A, 31.8% for C, 14.5% for G, and 23.2% for T. Phylogenetic analysis revealed that R. riparia was genetically closest to the species of genus Tachycineta. R. riparia mitogenome could contribute to our understanding of the phylogeny and evolution of this species.

Evolutionary insights into umami, sweet, and bitter taste receptors in amphibians.

Umami and sweet sensations provide animals with important dietary information for detecting and consuming nutrients, whereas bitter sensation helps animals avoid potentially toxic or harmful substances. Enormous progress has been made toward animal sweet/umami taste receptor (Tas1r) and bitter taste receptor (Tas2r). However, information about amphibians is mainly scarce. This study attempted to delineate the repertoire of Tas1r/Tas2r genes by searching for currently available genome sequences in 14 amphibian species. This study identified 16 Tas1r1, 9 Tas1r2, and 9 Tas1r3 genes to be intact and another 17 Tas1r genes to be pseudogenes or absent in the 14 amphibians. According to the functional prediction of Tas1r genes, two species have lost sweet sensation and seven species have lost both umami and sweet sensations. Anurans possessed a large number of intact Tas2rs, ranging from 39 to 178. In contrast, caecilians possessed a contractive bitter taste repertoire, ranging from 4 to 19. Phylogenetic and reconciling analysis revealed that the repertoire of amphibian Tas1rs and Tas2rs was shaped by massive gene duplications and losses. No correlation was found between feeding preferences and the evolution of Tas1rs in amphibians. However, the expansion of Tas2rs may help amphibians adapt to both aquatic and terrestrial habitats. Bitter detection may have played an important role in the evolutionary adaptation of vertebrates in the transition from water to land.

Genome-wide analysis of the Aquaporin gene family in reptiles.

Aquaporin (AQP) genes are widely distributed in plants, unicellular organisms, invertebrates and vertebrates. They play a critical role in the transport of water and other solutes across cell membranes. AQP genes have been identified and studied in many species but the AQPs of reptiles are unknown. Newly obtained genome assemblies provide an opportunity to identify the complete AQPs set and explore the evolutionary relationship of these genes. A total of 212 putative AQP genes were identified from 18 reptile species, including 20 partial genes and 192 intact genes. Phylogenetic results showed that 193 AQP genes could be classified into three major clades according to their subfamily. The divergence or phylogenetic distance between reptile AQP genes was closely related to traditional taxonomic groupings. Evolutionary analysis indicated the presence of positively selected sites in the AQP3 (P = 0.0104⁎⁎) and AQP7 (P = 0.0202⁎⁎) among land reptiles, suggesting their relationship to terrestrial environment adaptation.

Genomic analysis and adaptive evolution of the RIG-I-like and NOD-like receptors in reptiles.

Pattern recognition receptors (PRRs) play a crucial role in the host's innate immune system. Among the PPRs, the RIG-I-like (RLRs) and NOD-like receptors (NLRs) are two important subgroups. To understand the role of RLRs (RIG-I, MDA5, LGP2) and NLRs (NOD1, NLRC3, NLRX1, NOD2) in reptilian evolution, we identified six genes from reptilian genomes. A total of 168 putative genes were identified from 28 reptile species, including 141 intact genes, 25 partial genes and two pseudogenes. Interestingly, the NOD2 gene was absent in all reptile species. Phylogenetic results showed that all genes were divided into four major clades corresponding to their traditional taxonomic groups, indicating that these genes are conserved in reptiles. Evolutionary analyses detected positive selection in six genes. Most of the positively selected sites (50/76) were located in known functional domains, reflecting their critical and particular contributions to host defense during reptilian evolution. Branch model analysis showed that NLRs were under different evolutionary forces, while the RLRs were not, suggesting that semiaquatic species and terrestrial species faced different environmental pathogens, leading to different adaptations. Moreover, the positively selected sites identified in MDA5 using the branch-site model among semiaquatic reptiles, suggested their involvement in adaptation to semiaquatic environments.

Genomic evidence of gene duplication and adaptive evolution of Toll like receptors (TLR2 and TLR4) in reptiles.

Toll-like receptors (TLRs) encoded by the TLR multigene family play an important role in initial pathogen recognition in vertebrates. Among the TLRs, TLR2 and TLR4 may be of particular importance to reptiles. In order to study the evolutionary patterns and structural characteristics of TLRs, we explored the available genomes of several representative members of reptiles. 25 TLR2 genes and 19 TLR4 genes from reptiles were obtained in this study. Phylogenetic results showed that the TLR2 gene duplication occurred in several species. Evolutionary analysis by at least two methods identified 30 and 13 common positively selected codons in TLR2 and TLR4, respectively. Most positively selected sites of TLR2 and TLR4 were located in the Leucine-rich repeat (LRRs). Branch model analysis showed that TLR2 genes were under different evolutionary forces in reptiles, while the TLR4 genes showed no significant selection pressure. The different evolutionary adaptation of TLR2 and TLR4 among the reptiles might be due to their different function in recognizing bacteria. Overall, we explored the structure and evolution of TLR2 and TLR4 genes in reptiles for the first time. Our study revealed valuable information regarding TLR2 and TLR4 in reptiles, and provided novel insights into the conservation concern of natural populations.

Genomic evidence of bitter taste in snakes and phylogenetic analysis of bitter taste receptor genes in reptiles.

As nontraditional model organisms with extreme physiological and morphological phenotypes, snakes are believed to possess an inferior taste system. However, the bitter taste sensation is essential to distinguish the nutritious and poisonous food resources and the genomic evidence of bitter taste in snakes is largely scarce. To explore the genetic basis of the bitter taste of snakes and characterize the evolution of bitter taste receptor genes (Tas2rs) in reptiles, we identified Tas2r genes in 19 genomes (species) corresponding to three orders of non-avian reptiles. Our results indicated contractions of Tas2r gene repertoires in snakes, however dramatic gene expansions have occurred in lizards. Phylogenetic analysis of the Tas2rs with NJ and BI methods revealed that Tas2r genes of snake species formed two clades, whereas in lizards the Tas2r genes clustered into two monophyletic clades and four large clades. Evolutionary changes (birth and death) of intact Tas2r genes in reptiles were determined by reconciliation analysis. Additionally, the taste signaling pathway calcium homeostasis modulator 1 (Calhm1) gene of snakes was putatively functional, suggesting that snakes still possess bitter taste sensation. Furthermore, Phylogenetically Independent Contrasts (PIC) analyses reviewed a significant correlation between the number of Tas2r genes and the amount of potential toxins in reptilian diets, suggesting that insectivores such as some lizards may require more Tas2rs genes than omnivorous and carnivorous reptiles.

Complete Mitochondrial Genome of the Red Fox (Vuples vuples) and Phylogenetic Analysis with Other Canid Species.

The whole mitochondrial genome sequence of red fox (Vuples vuples) was determined. It had a total length of 16 723 bp. As in most mammal mitochondrial genome, it contained 13 protein coding genes, two ribosome RNA genes, 22 transfer RNA genes and one control region. The base composition was 31.3% A, 26.1% C, 14.8% G and 27.8% T, respectively. The codon usage of red fox, arctic fox, gray wolf, domestic dog and coyote followed the same pattern except for an unusual ATT start codon, which initiates the NADH dehydrogenase subunit 3 gene in the red fox. A long tandem repeat rich in AC was found between conserved sequence block 1 and 2 in the control region. In order to confirm the phylogenetic relationships of red fox to other canids, phylogenetic trees were reconstructed by neighbor-joining and maximum parsimony methods using 12 concatenated heavy-strand protein-coding genes. The result indicated that arctic fox was the sister group of red fox and they both belong to the red fox-like clade in family Canidae, while gray wolf, domestic dog and coyote belong to wolf-like clade. The result was in accordance with existing phylogenetic results.