Do you really know your model organism? New insights on Pseudoalteromonas haloplanktis TAC125 genome organization by next and third generation sequencing technologies. re-sequence Pseudoalteromonas haloplanktis TAC125 genome using Illumina, PacBio and ONT technologies

In this study we re-sequenced P. haloplanktis TAC125 genome using NGS (Illumina) and the two third generation sequencing methods (ONT and PacBio). The re-sequencing efforts not only identified one miss assembled tandem repeat of 1.2 Kb in the reference chromosome NC_007481.1, but also revealed the presence of a large plasmid that was unnoticed in the first genome sequence (Médigue et al., 2005). Besides the annotation and analysis of the newly identified plasmid (pMEGA), we further characterized pMtBL identifying a plasmid segregation system. The available reference genome sequences and high coverage long read data also allowed us to generate accurate and realistic measures of advantages and limitations of these newer sequencing technologies for de novo genome sequencing application, and how they were affected by sequencing depth. The findings can be informative for all researchers who are planning de novo genome sequencing projects using these newer technologies.