Lineage-Specific WGD and SINEs Are Associated with Gene Family Dynamics and Stress Responsiveness in White Clover (Trifolium repens)

Gene family expansion and contraction are key processes underlying functional innovation and genome evolution in plants, yet their roles in the horticultural plant white clover (Trifolium repens) remain poorly understood. In this study, we systematically investigated the association between lineage-specific whole-genome duplication (WGD) and short interspersed nuclear elements (SINEs) with gene family dynamics and stress-responsive transcription. Our results indicate that white clover underwent a lineage-specific WGD, which is associated with increased gene family expansion. SINE copy number was strongly correlated with the proportion of significantly expanded genes (r = 0.637, p = 0.0259, n = 12), but not with the proportion of significantly contracted genes. This result suggests a potential association between SINE insertions and gene family expansion. GO enrichment analyses indicated that expanded gene families are predominantly involved in metabolic processes, environmental stress responses, defense mechanisms, and floral organ development, whereas contracted gene families were mainly enriched in core housekeeping functions, such as ubiquitin-dependent protein catabolism and mitochondrial organization. Transcriptome analyses further showed that genes within expanded families were broadly upregulated under drought, cadmium, and cold stress, while generally upregulated in floral tissues compared with other organs. Collectively, these findings reveal the relationships among WGD, SINE elements, and gene family dynamics in environmental adaptation and flower development, providing a molecular framework for understanding adaptive regulation associated with gene family expansion.