Assembly and Automated Annotation of the <i>Clostridium scatologenes</i> Genome

<p><em>Clostridium scatologenes</em> is an anaerobic bacterium that demonstrates some unusual metabolic traits such as the production of 3-methyl indole. The availability of genome level sequencing has lent itself to the exploration and elucidation of unique metabolic pathways in other organisms such as <em>Clostridium botulinum</em>. The <em>Clostridium scatologenes</em> genome, with an estimated length 4.2 million bp, was sequenced by the Applied Biosystems Solid method and the Roche 454 pyrosequencing method. The resulting DNA sequences were combined and assembled into 8267 contigs with an average length of 1250 bp with the Newbler Assembler program. Comparision of published subunits of csd gene and assembled contigs identified that one contig contained all three subunits. In addition a gene with similarity to clostridium carboxidivorans butyrate kinase was found lined next to <em>csd</em> gene. An alignment of the contig and <em>csd</em>gene sequences identified three deletions in the contig within the 4066 bases of the alignment. This implies that there is about 0.07% error rate in the sequencing itself requiring more finishing.</p> <p>Even without finishing the genome assembly into single contig, contigs were annotated in RAST pipeline predicting 2521 protein encoding genes (PEGs). The PEGs were classified by their metabolic function and compared to classified PEGs found in the closely related clostridium species, <em>Clostridium carboxidivorans</em> and <em>Clostridium. ljungdahlii</em>, which have similarly sized genomes. According to the RAST analysis, <em>Clostridium scatologenes</em> had 35% subsystem coverage of all known metabolic processes with its 2521 PEGs. This compares to 41% for <em>Clostridium carboxidivorans</em> with 4174 PEGs (29) and 42% for <em>Clostridium ljungdahlii</em> with 4184 PEGs (30), indicating that <em>Clostridium scatologenes</em>may still have more genes to be identified. Comparison of the percent genes found in the metabolic subsystems was similar except in motility and chemotaxis.</p> <p>The contigs, on which the <em>csd</em> gene and tryptophan metabolizing genes lay, were examined to see if additional genes might support these metabolic pathways. Butyrate kinase was associated with the <em>csd</em> genes but no other associations were found for the two tryptophan metabolizing genes. The tryptophan biosynthesis operon genes were all found on one contig (contig 6771) and were syntenic with other bacterial species.</p>

Name thesis:degree_name

Master of Science

Discipline thesis:degree_discipline

Department of Biology

Year

2012

Author dc:creator

• Tiwari, Jitesh

Contributors dc:contributor

• Dr. Claire Rinehart (Director), Dr. Sigrid Jacobshagen, Dr. Jonathan Quiton

• genome annotation
• bacterial genomes
• Genetics and Genomics
• Genomics

Repository record dc:identifier

https://digitalcommons.wku.edu/theses/1175

OAI identifier oai:identifier

oai:digitalcommons.wku.edu:theses-2178