Prophage genomics reveals patterns in phage genome organization and replication

Han Suh Kang; Katelyn McNair; Daniel A. Cuevas; Barbara A. Bailey; Anca M. Segall; Robert A. Edwards

Several prophage genome characteristics correlate with the host's characteristics (34) . For example, the prophage's and host's GC content correlated strongly (R 2 = 0.95; Fig. 4 ). As we have shown previously, the GC content of phage genomes can be accurately used to predict the phyla of the host associated with a phage (to >95% accuracy), however GC content can not be accurately used to predict the phages' host at lower taxonomic levels (35) . Even though %GC content correlates at the 7 . CC-BY 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/114819 doi: bioRxiv preprint phyla level, there are not enough degrees of freedom in %GC calculations to separate thousands of phages and their hosts. Percent GC is basically a k-mer DNA profile with k = 1. Higher k-mer DNA profiles increase the correlation between phage and host, but when k exceeds 7 nucleotides the data become sparse and over fit the predictions (35) .