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Enteric redmouth disease caused by the pathogen  Yersinia ruckeri  is a significant problem for fish farming around the world. Despite its importance, only a few virulence factors of  Y. ruckeri  have been identified and studied in detail. Here, we report and analyze the complete DNA sequence of pYR4, a plasmid from a highly pathogenic Norwegian  Y. ruckeri  isolate, sequenced using PacBio SMRT technology. Like the well-known pYV plasmid of human pathogenic  Yersiniae , pYR4 is a member of the IncFII family. Thirty-one percent of the pYR4 sequence is unique compared to other  Y. ruckeri  plasmids. The unique regions contain, among others genes, a large number of mobile genetic elements and two partitioning systems. The G+C content of pYR4 is higher than that of the  Y. ruckeri  NVH_3758 genome, indicating its relatively recent horizontal acquisition. pYR4, as well as the related plasmid pYR3, comprises operons that encode for type IV pili and for a conjugation system ( tra ). In contrast to other  Yersinia  plasmids, pYR4 cannot be cured at elevated temperatures. Our study highlights the power of PacBio sequencing technology for identifying mis-assembled segments of genomic sequences. Comparative analysis of pYR4 and other  Y. ruckeri  plasmids and genomes, which were sequenced by second and the third generation sequencing technologies, showed errors in second generation sequencing assemblies. Specifically, in the  Y. ruckeri  150 and  Y. ruckeri  ATCC29473 genome assemblies, we mapped the entire pYR3 plasmid sequence. Placing plasmid sequences on the chromosome can result in erroneous biological conclusions. Thus, PacBio sequencing or similar long-read methods should always be preferred for  de novo  genome sequencing. As the  tra  operons of pYR3, although misplaced on the chromosome during the genome assembly process, were demonstrated to have an effect on virulence, and type IV pili are virulence factors in many bacteria, we suggest that pYR4 directly contributes to  Y. ruckeri  virulence.

pYR4 From a Norwegian Isolate of Yersinia ruckeri Is a Putative Virulence Plasmid Encoding Both a Type IV Pilus and a Type IV Secretion System