International Journal of Molecular Veterinary Research, 2025, Vol.15, No.1, 1-12 http://animalscipublisher.com/index.php/ijmvr 3 positive selection, that is, these are involved in defending the host (Figure 1) (Jax et al., 2022). In addition, RNA-seq application has made it possible for infection-regulated transcriptomes to be extensively explored and has provided insight into the differential immune response mounted by various pathogens (Sackton, 2019). All this extensive cataloging of immune genes is required so that canid immunologic molecular mechanisms may be unraveled and their evolutionary history understood. Figure 1 Ratio of nonsynonymous to synonymous changes (dN/dS) mapped on the Toll-like receptor signaling pathway from the KEGG database (Kanehisa 2019; Kanehisa and Goto 2000; Kanehisa et al. 2021). Each box represents one gene in the pathway and the color within the box shows dN/dS for that particular gene. dN/dS was estimated from a total of 26 species of waterfowl using PAML. Small boxes without a color indication were not included in the hybrid capture, usually because they were not annotated in the mallard genome at the start of the study (Adopted from Jax et al., 2022) 3.3 Limitations and challenges in canid genomics Despite the huge advances in canid genomics, challenges and limitations remain. One among them is the quality and completeness of genomic data, which may be undermined by errors in sequencing and gaps in genome assemblies (Sackton, 2020). In addition, immune gene annotation tends to be complicated because of their rapid evolutionary rate and the prevalence of species-specific adaptations, thus leading to incomplete or erroneous annotations (Clark and Greenwood, 2016). A further complication is that additional, larger population resequencing data are required to fully resolve the evolutionary pressures acting on immune genes and uncover rare variants with potentially significant roles in immunity (Sackton, 2020). These challenges will be met by the application of increasingly sophisticated bioinformatic software and the generation of high-quality genomic data from a broader array of canid species. 4 Evolutionary Mechanisms Shaping Immune Genes 4.1 Natural selection and immune gene variability Natural selection is also a significant force that drives canid immune gene diversity. Positive selection, in particular, has been identified as one of the key forces shaping the evolution of immune system genes in species. For instance, it is already established by research that immunity genes and pathogen recognition genes, such as the major histocompatibility complex (MHC) genes, experience diversifying selection of high intensity since they are engaged in host-pathogen interactions (Fornůsková et al., 2013; Dearborn et al., 2022). This selective pressure
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