Exploring Tomato Virus Diversity in China using Deep Small RNA Sequencing
Tomatoes are one of the most important vegetable crops in the world for their nutrients and their prominence in the global vegetable economy. Viruses, however, threaten the wellbeing of the tomato plant in many regions of the world. Maintaining an updated virus information database is a prerequisite for effective viral management. Virus-derived small interfering RNA(vsiRNA) is generated through antiviral defense systems in plants and can be used for virus characterization with or without prior information. Using the small RNA data from 189 tomato samples in 20 regions in China, we explored the viral community in the tomato plants to understand the diversity and distribution of tomato viruses in China for the development of effective control strategies. Our analyses confirmed that the vsiRNAs are within 21-24 nucleotides (nt) in length with the predominate length being 21 nt. A total of 28 viruses from these samples were identified. The most common viruses within the 20 regions were the Tomato yellow leaf curl virus (TYLCV) and the Tomato mosaic virus (TMV). We were also able to discover a new virus, whose genome sequence showed homology to those of other plant viruses including the Alfalfa dwarf virus, the Persimmon virus, and the Lettuce necrotic yellows virus.
Although I am a Bioinformatics major at my college, I was uncertain if I wanted to pursue a career path involving research. Having only finished my sophomore year at Ramapo College, I did not have many opportunities to explore advanced topics in bioinformatics. By coming to BTI for the summer, I learned many fundamental bio informatics skills through my mentor, Xuepeng Sun. He taught me many valuable research techniques including how to
troubleshoot problems and how to work with large datasets using UNIX and Perl script. The many PGRP seminars and bioinformatics courses hosted by BTI also provided me with more platforms to grow as an aspiring researcher. Thank you to all who made my experience at BTI possible! This program has confirmed my passion for the blending of computer science and biology and I will continue to do bioinformatics research in the years to come.