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

Derrick C. Scott
Assistant Professor of Bioinformatics, Biological Sciences, Delaware State University

Thursday, May 3, 2018 15:00 - 16:00
Building 227, Room A202
Gaithersburg

Thursday, May 3, 2018 13:00 - 14:00
Room 1-4072
Boulder

Slides: PDF

Host: Tony Kearsley

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.

Bio: Derrick C. Scott is an Assistant Professor of Bioinformatics in the Biological Sciences department at Delaware State University. Hailing from Varnville, SC, he studied Biology at Virginia State University. He then matriculated 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 included studies on bacterial genomics and the evolutionary history of Caulobacters as well as attempting to find a way to stabilize Chinese Hamster Ovary genomes to decrease the costs of medicines. He has authored and co-authored numerous publications and is well versed in fungal, bacterial, viral, and plant genomics.

Note: Visitors from outside NIST must contact Cathy Graham; (301) 975-3800; at least 24 hours in advance.

Created April 23, 2018, Updated November 15, 2019