Student Presenter(s): Melody Lin
Faculty Mentor: Leonidas Salichos
School/College: Arts and Sciences, Old Westbury

While normally associated with eukaryotes, circadian rhythms exist in the microbial world. The first prokaryotes to be found containing a circadian clock were cyanobacteria, dictated by three main genes designated as kaiA, kaiB, and kaiC respectively. The Joint Genome Institute’s Integrated Microbial Genomes & Microbiomes (IMG/M) available datasets were used in order to generate lists of genomes that could be assumed to have kaiC. The first lists were generated by downloading the IMG/M’s available genome lists organized by environment and the kaiC Pfam list (PF06745), which were then parsed through using custom Perl scripts to find matching IMG genome ID numbers. These initial lists of kaiC were then run through BLAST via the JGI’s website, individually for kaiC 1 and kaiC 2 protein domains using the Synechococcus elongatus (strain PCC 7942) amino acid sequences. Then we further filtered the results to increase confidence in the list of genomes containing kaiC, and to differentiate between those containing kaiC 1 or kaiC 2 domain, or both. The results indicate that both domains of kaiC tend to be present, although those with only one domain usually have kaiC 1 rather than kaiC 2. In this study, we are exploring the prevalence and genetic variance among prokaryotes with genes such as the Kai genes.