Genome-Wide Characterization of the HOX Gene Family: Evolution and Expression Patterns in Donkey

The <i>HOX</i> gene family plays an indispensable role in regulating embryonic development, cell differentiation, and morphogenesis. This study employed bioinformatics approaches for systematic analysis, ultimately identifying 33 <i>HOX</i> gene family members from the donkey genome. Physicochemical property analysis revealed that the number of amino acids encoded ranged from 94 to 444, with 31 members classified as alkaline proteins. Their secondary structure was predominantly composed of random coils and alpha helices, and all members were localized to the nucleus. Conserved motif analysis further demonstrated that all donkey HOX family proteins contained highly conserved motifs 1 and 2. Along with three other species, the 33 donkey <i>HOX</i> genes were clustered into eight phylogenetic subgroups. Furthermore, collinearity analysis indicated a high degree of collinearity between the donkey and horse <i>HOX</i> gene families. Gene Ontology analysis confirmed the significant role of the donkey <i>HOX</i> gene family in regulating embryonic development and skeletal system formation. Tissue expression profile analysis revealed significant differences in the expression levels of the 33 <i>HOX</i> genes across 13 different tissues. This study not only systematically identified and characterized the donkey <i>HOX</i> gene family but also provided valuable insights into the genetic regulation mechanisms of key traits in donkey molecular breeding.