Comparative Analysis of Exonic SSR ‐Containing Genes in Three Diving Duck Species Reveals Shared Functional Themes

Simple sequence repeats (SSRs) are ubiquitous components of eukaryotic genomes that contribute to genome evolution, genetic variation, and gene regulation. Although genome‐wide SSR landscapes have been extensively characterized across vertebrates, the cross‐species distribution and functional associations of exonic SSR‐containing genes remain poorly understood, particularly in non‐model birds. To address this knowledge gap, we performed a comparative analysis of chromosome‐level genome assemblies from three diving duck species ( Aythya ferina , Aythya marila , and Netta rufina ) to investigate genome‐wide SSR patterns and the cross‐species sharing and functional characteristics of exonic SSR‐containing genes. Comparative analyses of genome‐wide SSRs revealed pronounced interspecific variation in SSR abundance and repeat composition, whereas exonic SSR abundance showed more similar values after normalization by total annotated exon sequence length. Cross‐species comparison identified 4336 exonic SSR‐containing genes shared among all three species, greatly outnumbering the species‐specific gene sets. Functional enrichment analyses identified four broad functional themes associated with these shared genes: (i) gene transcription and epigenetic regulation, (ii) protein homeostasis and the ubiquitin–proteasome system, (iii) development, differentiation and morphogenesis, and (iv) stress response and cellular maintenance. The most significantly enriched categories were associated with transcriptional regulation, chromatin remodeling, RNA processing, and epigenetic regulation, whereas autophagy‐ and other cellular‐maintenance pathways indicated additional associations with stress‐response processes. These functional associations should be interpreted cautiously because they may be influenced by cross‐species annotation limitations and gene‐architecture differences. Collectively, our results reveal distinct patterns for genome‐wide and exonic SSRs distribution among the three diving duck species and identify shared functional associations of genes containing exonic SSRs. These findings provide a comparative genomic framework for future investigations of exonic SSRs in waterfowl and other non‐model vertebrates.