YerA41, a Yersinia ruckeri bacteriophage: determination of non-sequencable bacteriophage genome and investigation of bacterial response to infection.

YerA41 is a myoviridae bacteriophage that was originally isolated due its ability to infect Yersinia ruckeri bacteria, the causative agent of enteric redmouth disease of salmonid fish. Several attempts to determine its genomic DNA sequence using traditional and next generation sequencing technologies failed, indicating that the phage genome is modified such way that it is an unsuitable template for PCR amplification and sequencing. To determine the YerA41 genome sequence we isolated RNA from phage-infected Y. ruckeri cells at different time points post-infection, and sequenced it. The host-genome specific reads were substracted and de novo assembly was performed on the unaligned reads. Total RNA from phage-infected Y. ruckeri cells was isolated at different time points post-infection and sequenced. The host-genome specific reads were substracted and de novo assembly was performed on the unaligned reads.