Biodiversity, Geographical Distribution and Phylogenetic Analysis of Geminivirus Associated Alphasatellites from Cotton Crop in Pakistan

The complete nucleotide sequence of alpha satellite associated with monopartite begomoviruses complex isolated from cotton from Pakistan was determined and evaluated. The present study represent new complexes of these satellite molecules present in nature. Isolation of 8 alpha satellite molecules including 6 from cotton were identified as strains of PaLCuA (Papaya leaf curl alpha satellite) with 90 % homology, one with 98 % similarity score being an isolate of CLCuMA (Cotton leaf curl Multan alpha satellite) and a new strain of GDSA (Gossypium dawanii symptomless alpha satellite) with 93 % similarity. These sequences could be a new strains of PaLCuA first time reported from cotton plants in Pakistan. As they were only recently discovered so knowledge about these satellite molecules, their structure and function is limited. Further study could reveal their impact on the host and their role in evolution, survival and diversification of begomoviruses.