Pseudomonas aeruginosa strain MPAO1 (Genbank #CP027857) is an opportunistic human pathogen that belongs to the notorious group of Gram-negative ESKAPE pathogens. MPAO1 is also the parental strain for the widely used transposon (Tn) mutant library from the University of Washington . In early 2019, there was only one strain at the NCBI that was annotated as MPAO1 (Genbank #GCF_000247435.1), and which had been sequenced using Illumina's short read technology and assembled into 140 contigs . To provide an optimal basis for subsequent functional genomics and evolution studies for P. aeruginosa strain MPAO1, we re-sequenced and assembled its genome purely de novo, combining long PacBio and short Illumina MiSeq reads . The complete MPAO1 genome sequence harbors several deletions and insertions compared to the PAO1-UW reference genome including numerous MPAO1-unique genes.
An iPtgxDB was created by hierarchically integrating protein coding sequences from these annotation resources:
|1||NCBI RefSeq||CP027857.1; from 12/10/2018|
|2||Prodigal ||Ab initio gene predictions from Prodigal (v1.12)|
|3||ChemGenome ||Ab initio gene predictions from ChemGenome (v2.0, http://www.scfbio-iitd.res.in/chemgenome/chemgenomenew.jsp; with parameters: method, Swissprot space; length threshold, 70 nt; initiation codons, ATG, CTG, TTG, GTG)|
|4||in silico ORFs||The in silico ORFs annotations were generated as described by Omasits and Varadarajan et al. |
Only ORFs above a selectable length threshold (here 18 aa) were considered. The iPtgxDB was created using the hierarchy RefSeq > Prodigal > Chemgenome > in silico. Files were parsed to extract the identifier, coordinates and sequences of bona fide protein-coding sequences (CDS) and pseudogene entries.
|iPtgxDB Release Info|