Abstract
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.
Highlights
The genus Yersinia consists of 17 different species (Reuter et al, 2014; Savin et al, 2014)
In order to define the relationship between the plasmid sequenced in this study and those described in literature, we performed a comparative analysis of pYR4 with plasmid sequences generated previously by Illumina and PacBio sequencing technologies
By aligning other unplaced scaffolds of the Y. ruckeri 150 assembly, we found that four more scaffolds (23, 31, 32, 34) could be placed within pYR3 (Figure 3 and Supplementary Figures 5, 6). (An unplaced scaffold is a sequence found in an assembly that is not associated with any chromosome)
Summary
The genus Yersinia consists of 17 different species (Reuter et al, 2014; Savin et al, 2014). The human pathogens within the genus are closely related to each other, they cause diverse diseases. Y. pestis, the causative agent of bubonic and pneumonic plague, is one of the most virulent organisms known (Chauhan et al, 2016). This genus includes Y. enterocolitica and Y. pseudotuberculosis, well-known human enteropathogens. Y. pestis spreads through fleabites or aerosols, whereas Y. enterocolitica and Y. pseudotuberculosis are transmitted via ingestion of contaminated food or water (Bottone, 1997; Perry and Fetherston, 1997; Jalava et al, 2006). Y. enterocolitica and Y. pseudotuberculosis are responsible for a broad range of diseases ranging from mild gastroenteritis to life-threatening septicemia (Bottone, 1997)
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