Christopher Neely
Year: 2018
Faculty Advisor: Zhangjun Fei
Mentor: Lei Gao

“Pan-genomic analysis of Solanum habrochaites, a wild tomato plant”


Project Summary:

Solanum habrochaites is a diploid, wild tomato species that grows on the slopes of the Andes Mountains. Its unique phenotype includes glandular trichomes on the fruit, and these trichomes have been shown to be related to sesquiterpenes and other chemicals that repel insects. Because of these and other specificities, it has been commonly used as an important source of novel genes for tomato breeding. Therefore, we are interested in better understanding the genomic differences between S. habrochaites and the cultivated tomato, S. lycopersicum. To accomplish this, we constructed a pan-genome based on recent sequencing data from seven available S. habrochaites accessions. For each accession, we de novo assembled quality-filtered reads, aligned the assembled contigs to the reference genome from S. lycopersicum, and then extracted unaligned sequences. A total of 354.4 Mbp of non-reference sequences were obtained and annotated, yielding 4,002 protein-coding genes, of which 3,736 were functionally annotated. Enrichment analysis showed that Gene Ontology (GO) terms related to protein binding, ligase activity, and DNA helicase activity were significantly overrepresented in the non-reference portion of the pan-genome. The presence/absence variation (PAV) analysis showed that the core genome is comprised of over 27,000 genes, and that most genes are shared by all the accessions, with few genes specific to 5 or fewer accessions. Further analysis of genes specific in S. habrochaites will facilitate interpretation of its specificities and provide instructive information for future breeding practices in tomatoes.

My Experience:

Working at the Boyce Thompson Institute in the Fei Bioinformatics Laboratory has given me a wonderful glimpse of the life of a researcher. Completing this project required a lot of studying and planning. I learned that the answer for how to do something often comes from the community of researchers seeking to complete similar tasks or to answer similar questions. I became a lot more comfortable with finding information on my own and with relying on my mentor for larger picture issues. I also learned the importance of effective communication with my mentor during the project. Working at BTI has strengthened my resolve to be a professional researcher, and I know that I want to continue my career in in the field of biology. Once I return to the West Coast, I plan to continue to expand my skill set in analyzing big data.