Tandem duplicate genes preferentially contribute to the resistance of abiotic stress in sunflowers

Plant ability to evolve and maintain tandem duplicate genes (TDGs) is crucial for adapting to dynamic environments and maintaining strong adaptability. Despite sunflower's robust resistance to abiotic stresses, systematic reporting on its TDGs is still lacking. In this study, we identified 8791 TDGs in sunflower genome and the TDG events tend to occur independently after species divergence. The timing of duplication events was estimated by analyzing the number of substitutions per synonymous site ( Ks ) values of TDG pairs, occurring approximately 2.10–4.19 and 17.28–19.38 million years ago. Functional enrichment analysis revealed that sunflower TDGs were primarily associated with secondary metabolite biosynthesis and environmental adaptation. Through the transcriptomics analysis of sunflowers under various abiotic stresses, we found that sunflower TDGs preferentially exhibited differential expression under salt, drought and cold stresses rather than heat stress, implying that sunflower TDGs function in responding to certain abiotic stresses. The significantly positive correlation between expression divergent distance and Ka (number of substitutions per nonsynonymous site), Ks , Ka/Ks , or π (the average number of pairwise nucleotide differences) in TDG pair indicated that earlier occurrence of TDGs led to relaxed selection pressure and increased sequence divergences among the retained TDGs, hence accelerating greater expression divergence among TDGs. Our study may provide insights into the genetic basis of sunflower stress resistance and also identify candidate genes for molecular breeding. • Genome-wide identification and distribution of tandem duplicate genes (TDGs) in sunflower. • Sunflower TDGs play key roles in secondary metabolite biosynthesis and environmental adaptation. • Sunflower TDGs preferentially exhibited differential expression under certain abiotic stresses.