Reconstructing genomes of hydrocarbon degrading microbes

We are now roughly halfway through our research projects here at UTMSI and things are coming together quite well.  Over the past few weeks I have been attempting to isolate near complete genomes of organisms from microbial communities that are involved in the degradation of various hydrocarbons (i.e. n-hexadecane, naphthalene, phenanthrene) found in oil-contaminated sea surface waters in the Gulf of Mexico.  We acquired ~114 giga bases of raw sequencing data from our samples enriched with these hydrocarbons and quality-trimmed the sequences prior to assembly.  Metagenomic assembly of these trimmed sequences was completed this previous week and I began to manually bin the assembled sequences, along with numerous reference genomes, using a tetranucleotide-based emergent self-organizing map (ESOM).  The overall quality of the bins were assessed for completeness and quality.  9 out of the 24 bins contained genomes that were roughly >50% complete; however, 4 of these bins came back with greater than 10% contamination.  These 4 bins are now currently in the process of being manually refined in hopes of  lowering contamination.  Our assembled sequences were also submitted for gene and functional annotation.

For the remainder of the project we will continue to refine the bins and use the genomic data we gather to make comparative analyses in regards to phylogenetic relationship and metabolic pathways.

map

tetranucleotide-based ESOM displaying first attempt at our genomic bins. Each dot represents a DNA fragment from the community. Bold colored areas are bins that ran >50% complete with less than 10% contamination

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