Circle-Seq Analysis Reveals the Involvement of eccDNAs in Salt Stress Response of Bermudagrass (Cynodon dactylon)

Extrachromosomal circular DNAs (eccDNAs) have been identified in a wide variety of plant species and play a pivotal role in genomic plasticity, emerging as key drivers of stress adaptation. However, the functional roles of eccDNAs under environmental stress remain largely unexplored in plants. As a high-quality turfgrass, bermudagrass ( Cynodon dactylon L.) is a pivotal species for the reclamation and improvement of saline-alkali soils. Therefore, we performed a comprehensive analysis of the eccDNAs profile in bermudagrass under salt stress. A total of 1,068 eccDNAs were identified across all chromosomes. These eccDNAs were characterized by short lengths (ranging from 100 bp to 1 kb) and low GC content. eccDNA was not entirely random but rather exhibited a certain preference in intergenic regions and coding sequences (CDS). The identification of A/T-rich motifs at the junction sites suggests that these eccDNAs likely originate from physically unstable scaffold/matrix attachment regions (S/MARs) and are generated via the microhomology-mediated end joining (MMEJ) pathway. Notably, salt stress specifically enriched eccDNAs derived from DNA transposons, including the CACTA, Harbinger, Helitron, and MITE families. Overall, our findings reveal complex extrachromosomal regulatory mechanisms in bermudagrass, offering novel insights into its genomic adaptation under environmental stress.