Recognizing organized recombination in Whole Genome Sequence data: Type I Restriction Modification systems in Elizabethkingia species

Contig assembly algorithms utilizing short-read Illumina data (150-250 bp) terminate contig extension whenever two or more possible extension alternatives are found; thus sequence repeats (including multiple copies of the... [ view full abstract ]

Contig assembly algorithms utilizing short-read Illumina data (150-250 bp) terminate contig extension whenever two or more possible extension alternatives are found; thus sequence repeats (including multiple copies of the ribosomal rRNA genes) are understood to cause contig breaks.   Our team has made extensive use of optical mapping data to orient Illumina-based contigs and generate closed circular genomes for various bacterial species.    This analytic strategy uncovered a set of contigs that undergo organized recombination, with individual DNA strands containing different sequence configurations.   Pac-Bio sequencing of the strains confirmed the observation.  We surmise this variability to be due to mixed populations of cells, some of which are descended from cells that underwent a recombination event.  The contigs were determined to constitute the mobile domains of a Type I restriction modification system, which are known to undergo organized recombination and are common among bacterial species.   We will discuss how regions undergoing organized recombination can be overlooked in the genome assembly process, and will present methods for discovering them.  While many questions remain regarding the rate of organized recombination events, if they are found to occur more frequently and predictably than SNP mutations then they could be useful in outbreak investigations.   We will present data from the well-characterized Type I region in a single outbreak strain of Elizabethkingia anophelis, and discuss our findings regarding the several Type I Restriction Modification Systems present in certain strains from various Elizabethkingia species.