Occurrence of a recombinant molecule carrying sequences derived from an alphasatellite and the helper virus in cotton affected with cotton leaf curl disease

Abstract

Cotton leaf curl disease (CLCuD), a serious constraint to cotton production across Pakistan and northwestern India, is caused by begomoviruses in association with a specific betasatellite, Cotton leaf curl Multan betasatellite (CLCuMB). Begomovirus-betasatellite complexes are also frequently associated with satellite-like components known as alphasatellites, the most commonly identified of which, in cotton, is Cotton leaf curl Multan alphasatellite (CLCuMA). In Pakistan, the Burewala strain of Cotton leaf curl Kokhran virus (CLCuKoV-Bu) is the only begomovirus consistently identified in CLCuD affected cotton. Analysis of a CLCuD-affected cotton plant originating from Bhakkar (Punjab province, Pakistan) showed the presence of CLCuKoV-Bu, CLCuMB and CLCuMA, which were all cloned. However, a further clone obtained was shown to be a recombinant molecule consisting of sequences derived from CLCuMA, a small amount of sequence derived from a second alphasatellite and sequence derived from CLCuKoV-Layyah, another strain of the virus that is less frequently encountered. This study highlights the ease with which sequences can be exchanged between components of begomovirus-betasatellite-alphasatellite complexes.