Filling the Gaps: Genomic Sequencing of Arhodomonas sp. Seminole

Abstract

  Bacteria Arhodomonas sp. Seminole, found in Seminole, Oklahoma, is an aerobic, halophilic bacterium. Arhodomonas was then found to be a salt-loving bacterium, and could metabolize harsh chemicals such as benzene and toluene. Its cells were ruptured to expose and purify the DNA by itself in order to begin examining the makeup of amino acid. After obtaining the DNA, the shotgun effect was used in order to break apart the DNA. This would allow the reconstruction of the pieces in a more manageable structure. As group 23, Dr. Canaan presented us with two segments of DNA, an upstream and downstream contig, which was thought to be adjacent. We then used Blastx, a website to align the two contigs with the related protein sequence. We proceeded to align the fused contig with the protein sequence and found a significantly close match was found. This led to the creation of DNA primers that would allow us to create numerous copies of the joined contig by polymerase chain reaction, or PCR. After formulating the primers, we continued to test whether or not these new DNA segments were the missing bases in our original contigs by agarose gel electrophoresis. Our PCR product did not provide distinct banding indicating inconclusive results. This does not disprove the idea that these contigs could be joined. The alignment blasts done before the gel electrophoresis demonstrates otherwise. Further experimenting is necessary to verify or disprove our hypothesis.