Matthew Crum

Matthew Crum
Year: 2013

Genome assembly and analysis of wild tomato for markers associated with Tomato Yellow Leaf Curl Virus

The tomato is one of the most important fruit crops and humans have been domesticating them for hundreds of years in order to maximize the crop’s yield. Through the use of selective breeding, tomatoes have been able to produce much greater yields, but this process has also reduced the genetic diversity of domesticated tomatoes and limited their ability to adapt and fight diseases. Scientists and breeders have been trying to battle this problem through introgression of new and diverse genes and alleles from wild tomatoes species which still maintain their genetic diversity into the domestic tomato. By taking advantage of the disease resistance of wild-type tomatoes, scientists have been able to transfer resistances to certain diseases into domestic tomatoes. In order to identify which genes or alleles the domestic tomato needs in order to resist a disease, first the genetic basis for the wild tomatoes resistance must be identified. Using Next-Generation-Sequencing combined with bioinformatics analysis tools, it has become possible to sequence genomes and compare them much more efficiently. Using Bowtie2 (a tool which aligns Next-Gen-Sequence reads to a reference genome), samtools (a set of tools used to manipulate Next-Gen-Sequence reads), and Gbrowse (a genome visualization tool) we have been able to map and analyze multiple wild tomato accessions, including both resistant and susceptible inbreds, and compare their genomes in order to find loci which may contribute to resistance of Tomato Yellow Leaf Curl Virus.

My Experience

This experience has helped me grow in areas which span the purely scientific and academic to the development of inter-personal skills necessary to work in team settings. I have been more thoroughly introduced to using the Linux environment, improved my perl scripting skills, and been taught to use various bioinformatics tools such as Bowtie2 and samtools. This internship gave me a chance to observe firsthand the strength of applied bioinformatics in resolving biological problems that would have required far more resources otherwise. Perhaps most importantly, my experience with my mentor, Naama Menda, has taught me the skills necessary to work in a research setting. The freedom I was allowed in working out the kinks in my project helped me develop self-reliance while Naama’s assistance when I became stuck demonstrated the value, and often necessity, of asking for help and collaborating with others to accomplish a common goal.