Undergraduate Research Project

Heather Grossman

(Sponsor: David Gauthier)

This project was in part funded by Departmental Undergraduate Research Funds

Mycobacterium pseudoshottsii and Mycobacterium shottsii are newly discovered, slowly growing bacteria recently discovered in striped bass of Chesapeake Bay. M. pseudoshottsii and M. shottsii likely represent intermediate evolutionary states between the pathogens M. marinum and M. ulcerans, and whole-genome comparisons among these bacteria have the potential to greatly refine our understanding of the evolution and development of pathogenesis in this group.  This project was focused on finishing the draft genome assembly for M. shottsii, with the goal of performing whole-genome comparisons with other mycobacteria.  Gaps in the draft M. shottsii assembly were amplified, and product cloned and sequenced with Sanger cycle sequencing to yield finishing reads.  Finishing reads generated during the semester were then used to augment existing assemblies.  The overall number of scaffolds (large, gapped sequences) in the end-of-semester assembly increased over the beginning of the semester, however, the overall quality of the assembly increased, as measured by largest scaffold, total contigs placed in scaffolds, N50 score, and a reduced number of surrogate sequences.  The overall assembly of M. shottsii was only marginally improved by our efforts this semester, however the difficulties we encountered with finishing primer sets revealed a number of important considerations of primer design and methodology that had been originally overlooked. Lessons learned from this work will be applied to greatly improve the efficiency of future finishing efforts on this genome.