Ideonella sakaiensis Genome Assembly (renamed Piscinibacter sakaiensis)
This hybrid genome sequencing study combined Oxford Nanopore long-read sequencing with Illumina short-read sequencing to resolve the genome structure of polyethylene terephthalate (PET)-catabolizing bacterium Ideonella sakaiensis (now called Piscinibacter sakaiensis). Previously, the genome was fragmented into 227 contigs. Using a hybrid approach, we were able to identify a 2.1 MB chromosome and a 128 kb megaplasmid. The latter structure could additionally be confirmed with pulse-field gel electrophoresis. A 20 kb contig, upon which the causative hydrolase for PET depolymerization is located, could not be definitively placed in the main chromosome using various assemblers. However, manual searching of the contents of the contig indicate that it is duplicated upstream of the terephthalic acid (TPA) catabolism genes, which are responsible for assimilating TPA, one of the monomers of PET, into central carbon metabolism. Given the high density of transposons in this genomic region, mobile genetic elements may therefore play a role in the acquisition of the PET depolymerization phenotype of I. sakaiensis. Further investigation of this curious genetic element is invited to better understand the genomic and evolutionary factors responsible for this microorganism's metabolism of PET plastic.