Molecular diversity, recombination and population structure of alphasatellites associated with begomovirus disease complexes

The genus, begomovirus (family Geminiviridae) includes a large number of viruses infecting a wide range of plant species worldwide. The majority of monopartite begomoviruses are associated with satellites (betasatellites) and/or satellite-like molecules (alphasatellites). In spite of the Indo-China region being regarded as the centre of origin of begomoviruses and satellites, a detailed study on the emergence and evolution of alphasatellites in India has not yet conducted. Our present analysis indicated the association of 22 alphasatellites with monopartite and bipartite begomovirus-betasatellite complexes in India. Based on sequence pairwise identity, these alphasatellites were categorized into five distinct groups: Cotton leaf curl alphasatellite, Gossypium darwinii symptomless alphasatellite, Gossypium mustelinum symptomless alphasatellite, Okra leaf curl alphasatellite and an unreported Chilli leaf curl alphasatellite (ChiLCA). Furthermore, infectivity analysis of the cloned ChiLCA along with the viral components of either cognate or non-cognate chilli-infecting begomoviruses on Nicotiana benthamiana suggested that ChiLCA is dispensable for leaf curl disease development. It is noteworthy that in the presence of ChiLCA, a marginal decrease in betasatellite DNA level was noticed. Additionally, high genetic variability and diverse recombination patterns were detected among these alphasatellites, and the nucleotide substitution rate for the Rep gene of ChiLCA was determined to be 2.25 × 10− 3 nucleotides/site/year. This study highlights the genetic distribution, and likely contribution of recombination and nucleotide diversity in facilitating the emergence of alphasatellites.