Samantha Klasfeld
Samantha Klasfeld
Year: 2012
Faculty Advisor: Zhangjun Fei

Virus Identification in Sweet Potato Samples Collected from Mozambique and Ghana Through AnalyzingDeep siRNA Sequences

Sweet potato, Ipomoea batatas (L.) Lam. (Family Convolvulaceae), is among the most important food crops in the world and an extremely important food crop for subsistence farmers in sub-Saharan Africa (SSA). In SSA, the sweet potato production is very low and viruses are regarded as a major limiting factor of the production of this crop. Recently, deep sequencing of virus siRNAs has proven to be an efficient approach for de novo assembly of known and novel virus identification in plants. The major aim of my summer intern project was to analyze siRNA sequences generated from 35 and 38 sweet potato samples collected from Mozambique and Ghana, respectively, to identify known and novel sweet potato viruses. First the siRNA sequences were aligned to the virus sequence database to identify known viruses. Then the siRNA sequences were de novo assembled and the resulting contig sequences were compared to known virus sequence database at the amino acid level using blast, to identify novel virus sequences.

My Experience

The BTI bioinformatics program has given me the opportunity to experience a new species of lab.  Escaping the pipettes and glass-wear for the summer, I was thrilled when I realized how much quicker experiments on the computer move than those done in wet labs. Though we only had ten weeks, I felt I could be more creative while simultaneously maintaining a time line and obtaining significant amounts of data. I built a better foundation in programming by practicing Linux, Perl, etc., and Professor Fei was always willing to answer all my questions. Being particularly interested in the field of genetics and genomics, I was especially interested in relating the programming I studied in class to the study of biology. This internship excelled in giving me that exposure and the confidence to build on what I learned.