The single-stranded DNA, whitefly-transmitted begomoviruses are among the most serious emerging crop pathogens worldwide. To enhance current knowledge of begomovirus diversity, evolution, and biogeography, this project utilizes a novel approach of identifying begomoviruses directly from the Bemisia tabaci whitefly vector. This approach exploits the natural ability of whiteflies to concentrate viruses from the many plants they feed upon, and leverages the capability of metagenomic tools for discovering new viruses. Whitefly samples will be collected from tomato and squash fields from eight countries on six continents. Metagenomic sequencing will yield numerous complete begomovirus genome sequences, which will be used to improve our knowledge of begomovirus phylogeny and evolution. Deep sequencing of the begomovirus core coat protein region will enable direct comparisons of begomovirus diversity between crops and geographic locations.
This global vector-based survey will substantially increase our understanding of begomovirus diversity, recombination, biogeography, and emergence. Since begomoviruses are dangerous plant pathogens that pose a significant threat to global food biosecurity, this project has significant implications for agriculture. A graduate student and a postdoctoral researcher will be trained in cutting-edge molecular biology and bioinformatics techniques through this project. In addition, a Girl Scout "Virus Hunter" patch program will be developed to introduce young women to research in the detection and control of emerging viruses.
Sometimes the biggest threat isn’t one you already know, it’s one you don’t know yet. Certainly this has been the case in crop disease, where once agronomists and plant breeders get a handle on one disease, others emerge, often caused by new viruses that we haven’t seen before. In order to help global agriculture feed the seven billion people on this planet, we need to anticipate what diseases will affect our crops, and be able to track the movement of plant viruses around the world as accurately as possible. To this end, we developed a new method for testing what DNA plant viruses (begomoviruses) are present in tomato, squash and other crop fields in multiple countries (Brazil, Guatemala, Israel, Spain, United States, including Puerto Rico). We focused on begomoviruses because they are the most economically damaging plant viruses throughout tropical and subtropical countries, and they are the most frequently emergent plant pathogens. Begomoviruses move between plants by small insect vectors, the Bemisia tabaci whitefly. Therefore, we sampled whiteflies in fields, killed the flies, isolated viruses from these samples and sequenced all of the viruses contained within the samples. We found begomoviruses in all agricultural fields. While we were able to find out which viruses were present in fields before any plants were showing symptoms of disease, we only found a few species of begomoviruses that had never been seen by scientists before. This suggests that we have a pretty good handle on what viruses are moving around in crop fields currently, though we would have to monitor the viruses in whiteflies in future years to have a stronger sense of that. Importantly, this project did not stop at sensing what viruses are present around crop fields. Begomoviruses are unusual viruses, and for decades researchers thought they primarily evolved by recombination – mixing up their genes with other begomoviruses. We developed a new method to assess how many of the differences we see in begomovirus genomic sequences were due to recombination, and how many were more likely due to mutation. We found that mutation is the dominant way begomoviruses change and diversify in the field. We also conducted bioinformatic analyses to look for patterns in the genomic evolution of begomoviruses, and discovered there is a persistent bias compared to how human genes or even other DNA viruses evolve: they show much higher rates of cytosines turning into thymines. This means that more complicated models of genomic evolution may be necessary in order to accurately trace how begomoviruses have spread and are continuing to move around the world. Finally, this project caused us to take a good, long look at the way scientists organize the begomoviruses, and how we assign a newly sequenced isolate to a begomovirus species. Because of the recombination that does frequently occur among begomovirus genomes, it may not be possible to have a method for assigning sequences to species that involves the whole genome, since different parts of the genome can have different evolutionary histories. The development of better methods to detect, anticipate and follow begomoviruses will help farmers throughout the world, but this project also helped develop the next generation of scientists here in America. At Rutgers, a graduate student, two visiting graduate students from Brazil, and four undergraduates were trained in viral evolution. One Latina undergraduate from Rutgers travelled to Brazil to collect and sequence begomovirus samples as part of a US-Brazil exchange program (International Research Experience for Undergraduates). Her experience was profiled on the NSF Division for Environmental Biology blog: http://nsfdeb.wordpress.com/2014/07/23/international-research-experience-for-undergraduates-ireu-supplements-notes-from-the-field/. Personnel exchanges such as these have strengthened the relationship between my lab and institution with our collaborator in Brazil, paving the way for other international internships for future students. As we study global disease problems, providing younger scientists with opportunities for international experience is an important part of their career preparation.
