Enhancing the Plant Virus Surveillance Toolbox

Abstract

Plant viruses are economically important pathogens of crops. Viruses exhibit extreme adaptive potential due to their quick mutation rates, extensive recombination, and horizontal gene transfer. This can lead to emergence of new viruses into our cropping systems, or the shifting of viral populations to overcome resistance bred into crops. Because of this, surveillance programs have been established to continually monitor the cropping systems for new viruses as they emerge and populations as the adapt to resistance plant genetics. In this work, three chapters detail two different surveillance methods. First, an established method for linking causality of virus infection to disease symptoms was used to characterize symptoms of an emergent Theobroma cacao infecting badnavirus (Family: Caulimoviridae), Cacao swollen shoot virus Ghana M virus. Second, a bioinformatics pipeline was written to handle target enrichment high throughput sequencing data for an endemic complex of begomoviruses (Family: Geminiviridae) infecting Gossypium spp in Southeast Asia, Cotton leaf curl disease (CLCuD). The pipeline, Virus Community Assembly Tool (ViCAT) was validated on simulated mock communities, spiked mock communities consisting of known concentrations of clones, and three plant samples harboring mixed infections of begomoviruses. Lastly, the ViCAT pipeline was used to characterize community differences of the CLCuD begomoviruses in differentially susceptible/resistant cotton lines. Together the chapters attempt to expand on the current tools in the plant virus surveillance toolbox.