International Journal of Molecular Veterinary Research, 2025, Vol.15, No.1, 22-31 http://animalscipublisher.com/index.php/ijmvr 24 genomic studies have shown transcriptional flexibility with support maintenance among a series of hosts. Leishmania infantum, the causative agent of zoonotic visceral leishmaniasis, uses dogs as its main reservoir; genomic studies reveal genes of resistance to oxidative stress and antigenic variation that facilitate chronic infection. Toxocara canis, a dog nematode, can infect humans to cause visceral larva migrans, with higher gene families for cuticular antigens and immunomodulatory proteins regarding host invasion. Fungal pathogens such as Microsporum canis are also transmitted between human beings and dogs, and their genomes possess keratin-degrading enzymes with functions in interspecies infection. 2.4 Comparison of host adaptation and transmission modes among pathogens Among various pathogen lineages, common convergent mechanisms regulate successful transmission and adaptation in dogs, free-ranging canids, and human populations. Comparative genomics identifies general mechanisms of evolution such as host-compatible receptor-binding mutations, antigenic variation for enhanced immune evasion, and environmental persistence genes for indirect transmission. For instance, viral surface protein variants (i.e., RABV G and CDV H proteins) and bacterial adhesins facilitate infection between species, whereas parasitic and fungal pathogens employ immunomodulatory molecules for chronic colonization. Niche overlap in domestic and wildlife canid niches also facilitates the prospect of interspecies transmission of pathogens, where the application of integrated genomic surveillance to preemption of future zoonotic danger is emphasized (Ricardo et al., 2024). 3 Comparative Genomics in Pathogen Evolution and Host Adaptation Studies 3.1 Advances in genome sequencing and annotation of canine-associated pathogens Advancements in next-generation sequencing (NGS) and metabarcoding have enabled comprehensive, assumption-free characterization of the affluent and intricate pathogen communities in domestic dogs and free-ranging canids. The technology has revealed high prevalence and richness of bacterial, protozoan, and viral pathogens, and detection of previously undscribed and uncharacterized species, and enabled large-scale genomic surveillance and annotation of canine-associated pathogens (Lewin et al., 2020; Weber et al., 2020). 3.2 Insights from core and accessory genome analyses on evolutionary dynamics Comparative genomics has shown that both core and accessory genomes play important roles in the evolution and adaptation of pathogens. Host-specific adaptation in Campylobacter jejuni, for example, is due both to the presence/absence of accessory genes and to allelic variation in core genes, suggesting multifactorial evolutionary processes. These analyses allow the identification of genetic markers for host specificity and the informing of surveillance and intervention strategies (Epping et al., 2021). Similarly, comparisons of Streptococcus agalactiae and Rhodococcus equi show that gene acquisition/loss and a large, open pangenome facilitate adaptation to diverse hosts and environmental niches (Richards et al., 2019). 3.3 Gene family expansion/contraction and host-specific adaptation Gene family expansion and contraction, combined with allelic variation specific to the host, are significant host adaptation mechanisms. In C. jejuni, specific allelic variants of central genes (e.g., dnaE, rpoB, ftsX, pycB) are associated with adaptation in particular host species, while in vector-borne helminths, mitochondrial and nuclear gene research reports haplotype variation in correlation with host and geographic origin (Epping et al., 2021; Laidoudi et al., 2022; Gabrielli et al., 2023). Such genomic changes can induce the evolution of host-adapted pathogen lineages. 3.4 Roles of horizontal gene transfer and recombination in adaptive evolution Horizontal gene transfer (HGT) and recombination are the forces driving adaptive evolution in the bacterial pathogens. HGT supports rapid uptake of new traits, such as antibiotic resistance and virulence factors, and can lead to gene spillover among populations that exist in separate niches (Richards et al., 2019; Arnold et al., 2021). Recombination reactions, as in the case of canid alphaherpesvirus 1 and other pathogens, are responsible for genetic variation and the development of new strains with a modified host range or virulence (Lewin et al., 2020; Arnold et al., 2021).
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