Evidence of recombination in the Banana bunchy top virus genome

► Sequences of DNA-U3 were analyzed for first time from BBTV population in Pakistan. ► Sequence divergence in DNA-U3 was higher compared to other genomic components. ► Higher variability seems due to be recombination in BBTV genomes. ► Recombination events were detected among and between the isolates of two sub-groups. ► A novel intragenomic recombination mechanism is playing role in BBTV evolution.