High-Copy SINE Transposons Facilitate Broad Ecological Adaptation in White Clover (Trifolium repens)

Recent advances in plant genomics have characterized transposable elements (TEs) as key contributors to genome structure and gene regulation. This study focuses on the remarkably high abundance of short interspersed nuclear elements (SINEs) in the genus Trifolium. Using the allotetraploid horticultural plant white clover (Trifolium repens L.) as the study organism, we systematically investigate lineage-specific SINE amplification, genomic distribution, insertional preferences, and their regulatory effects on gene expression. Our analyses reveal that SINEs are significantly more abundant in Trifolium than in other angiosperms. Comparative genomic analyses further indicate that SINE accumulation is closely associated with polyploidization and domestication. Gene Ontology (GO) enrichment analyses demonstrate that SINEs are preferentially enriched in stress responsive genes. Expression analyses further showed that, within duplicated gene pairs, genes with SINE insertions in their upstream promoter regions exhibit significantly higher transcript levels compared with genes without such insertions. Under drought, cold, and cadmium stress, these SINE-associated genes exhibit upregulation, and our data analysis shows a strong correlation between the presence of SINE insertions and stress-induced upregulation of gene expression. This study demonstrates that SINE insertions in upstream promoter regions modulate transcriptional regulatory networks involved in stress responses, contributing to broad ecological adaptation in white clover.