Tandem repeat sequence of duck circovirus serves as downstream sequence element to regulate viral gene expression.

•The quadruple tandem repeat sequence (QTR) was firstly found in intergenic region of rep and cap genes of DuCV genome, not in other circoviruses.•The QTR was also obviously different and evolutionarily conserved in genotype 1 and 2 DuCV strains, which could serve as a molecular marker to distinguish DuCV genotypes.•The QTR functioned as downstream sequence element (DSE) of polyadenylation signals to enhance mRNA stability, which depended four copies but not direction of QTR.•The subgenome and reversed genetic models of DuCV demonstrated QTR as DSE played a vital role in regulating viral genes expression and replication.