Integration and excision of Yucahu. (A) For the 60 cm sample, elevated coverage and paired reads indicate that Yucahu-i is integrated into the genome, excised from some genomes (blue lines), and coexists in circularized form (yellow lines). The red box indicates elevated coverage from a related gene from another genome. (B) For the 165 cm sample, low coverage over the MGE and read sequence discrepancies indicate that most cells in this sample lack the MGE. (C) For the 70 cm sample, coverage and paired read information indicate that Yucahu-i is integrated into essentially all cells. The circularized Yucahu-i is present but rare. Paired reads pointing out internal to the MGE indicate that a 2644 bp element has integrated into the plasmid and coexists in circularized form.
