The Gobiidae family occupy one of the most diverse habitat ranges of all fishes. One key reason for their successful colonization of different habitats is their ability to adapt to different energy demands. This energy requirement is related to the ability of mitochondria in cells to generate energy via oxidative phosphorylation (OXPHOS). Here, we assembled three complete mitochondrial genomes of Rhinogobius shennongensis, Rhinogobius wuyanlingensis, and Chaenogobius annularis. These mitogenomes are circular and include 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs, and one non-coding control region (CR). We used comparative mitochondrial DNA (mtDNA) genome and selection pressure analyses to explore the structure and evolutionary rates of Gobiidae mitogenomics in different environments. The CmC model showed that the ω ratios of all mtDNA PCGs were <1, and that the evolutionary rate of adenosine triphosphate 8 (atp8) was faster in Gobiidae than in other mitochondrial DNA PCGs. We also found evidence of positive selection for several sites of NADH dehydrogenase (nd) 6 and atp8 genes. Thus, divergent mechanisms appear to underlie the evolution of mtDNA PCGs, which might explain the ability of Gobiidae to adapt to diverse environments. Our study provides new insights on the adaptive evolution of Gobiidae mtDNA genome and molecular mechanisms of OXPHOS.

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.

Many mammals risk damage from virus invasion due to frequent environmental changes. The oligoadenylate synthesis (OAS) gene family, which is an important component of the immune system, provides an essential response to the antiviral activities of interferons by regulating immune signal pathways. However, little is known about the evolutionary characteristics of OASs in Laurasiatherian mammals. Here, we examined the evolution of the OAS genes in 64 mammals to explore the accompanying molecular mechanisms of the antiviral ability of Laurasiatherian mammals living in different environments. We found that OAS2 and OAS3 were found to be pseudogenes in Odontoceti species. This may be related to the fact that they live in water. Some Antilopinae, Caprinae, and Cervidae species lacked the OASL gene, which may be related to their habitats being at higher altitudes. The OASs had a high number of positive selection sites in Cetartiodactyla, which drove the expression of strong antiviral ability. The OAS gene family evolved in Laurasiatherian mammals at different rates and was highly correlated with the species’ antiviral ability. The gene evolution rate in Cetartiodactyla was significantly higher than that in the other orders. Compared to other species of the Carnivora family, the higher selection pressure on the OAS gene and the absence of positive selection sites in Canidae may be responsible for its weak resistance to rabies virus. The OAS gene family was relatively conserved during evolution. Conserved genes are able to provide better maintenance of gene function. The rate of gene evolution and the number of positively selected sites combine to influence the resistance of a species to viruses. The positive selection sites demonstrate the adaptive evolution of the OAS gene family to the environment. Adaptive evolution combined with conserved gene function improves resistance to viruses. Our findings offer insights into the molecular and functional evolution of the antiviral ability of Laurasian mammals.

Bats are reservoirs for many emerging viruses, yet broad-scale spatial patterns of bat viromes and their ecological determinants remain unclear, limiting spillover risk assessment. To address this, we conducted a standardized survey across central to southern China. During 2022–2023, fecal samples were collected from 527 bats representing 17 species at 21 caves in seven provinces. Using each cave as the analytical unit, samples from all species at a site were pooled to construct 21 fecal RNA virome libraries for metatranscriptomic sequencing; viral-like contigs were annotated, and viral alpha/beta diversity was quantified at the genus level. Sites were grouped by geographic distance and latitude to evaluate spatial differentiation and to relate virome patterns to host community attributes and environmental factors. We annotated 56 viral families, including 19 vertebrate-associated families, with multiple families and genera shared across geographic groupings. Vertebrate-associated viral diversity showed limited evidence of geographic isolation within the study region but suggested gradual turnover with latitude. Host species richness was the strongest correlate of virome diversity, exceeding the effects of evaluated environmental variables (e.g., climate and human activity). These results support prioritization of species-rich bat habitats for surveillance and risk assessment.

Bats, as the world’s second-largest mammalian order, have garnered significant attention for their ability to harbor numerous viruses without exhibiting disease symptoms. Nucleotide-binding domain and leucine-rich repeat-containing receptors (NLRs) are crucial components of the immune system. This study conducted an evolutionary analysis of the NLR gene family across 26 bat species to investigate the molecular mechanisms underlying their role in viral resistance under high viral load pressure. We identified gene duplication events in multiple genes. The NLR gene family exhibited high conservation throughout evolution, which may contribute to the occurrence of gene duplication. This conserved genomic structure also ensures functional stability, safeguarding bats’ antiviral resistance. Most NLR genes primarily function within the type I interferon (IFN) signaling pathway and the NF-κB signaling pathway. The NLR gene family enhances the innate immune capacity of bats through the adaptive evolution of some genes, combining enhanced gene functionality with the maintenance of gene conservation at a low evolutionary rate. Moreover, bats employ diverse innate immune strategies, where multiple immune pathways collectively establish the innate immune barrier. The molecular evolution of this gene family provides new insights into the molecular mechanisms and functional pathways involved in the innate immune response of bats.