School of Informatics and Computing IUPUI

BHI Colloquium: Derrick C. Scott, Ph.D.

Utilizing Next Generation Sequencing to Generate Bacterial Genomic Sequences for Evolutionary Analysis

Abstract

Many important questions in the field of prokaryotic biology cannot be answered due to the low availability of sequenced and finished genomes. Recent improvements in technology and decreases in price have made the ambition of de novo bacterial genomic sequencing a reality for a wide range of researchers. However, with the advancement of sequencing technology comes the need for an evaluation to determine the most reliable bioinformatics methods in generating a complete and accurate assembly. Biases inherent in the sequencing technology and GC-rich genomes complicate genome assemblies. Here, we sequenced bacterial strains from the GC-rich Caulobacter genus and the closely related Brevundimonas genus. We found that the Pacific Biosciences RS II sequencing systems was the best sequencer to use in conjunction with the HGAP2 assembler. Using our newly acquired sequences, we found that the genus Caulobacter exhibits extensive genome rearrangements giving the appearance of “Genome Scrambling”. We found that these extensive rearrangements had no correlation to genome relatedness within the genus and that they did not disrupt the conservation of NA1000 essential genes between the species. We also found that using the 16S rRNA region to group these bacteria were as accurate as using entire conserved operons spanning thousands of base pairs.

About Derrick Scott

Derrick C. Scott joined Delaware State University in 2016 as a bioinformaticist in the department of Biological Sciences. He graduated from Virginia State University before matriculating at Virginia Tech where he earned a Master’s degree in Molecular Biology. His thesis work entailed the discovery and deactivation of a fungal gene that was necessary for pathogenicity in economically important plants. Afterwards, he earned his Ph.D. in Integrative Biology from the University of South Carolina by discovering a new strain of bacteria and determining the best methodology to sequence and assemble High-GC bacterial genomes. His current research consists of studying bacterial genomics and the evolutionary history of Caulobacters as well as using transcriptomics to understand genome instability in Chinese hamster ovary cells.

Start
Friday November 09, 2018 12:00 PM
End
Friday November 09, 2018 01:00 PM
Location
IT 252
Contact
Robyn Hart
Contact Email
robhart@iupui.edu
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