Integrated proteogenomics database

Bacteria iconP. aeruginosa MPAO1_tryptic

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 [1]. 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 [2]. 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 [3]. 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:

Hierarchy Resource Link
1 NCBI RefSeq CP027857.1; from 12/10/2018
2 Prodigal [4] Ab initio gene predictions from Prodigal (v1.12)
3 ChemGenome [5] 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. [6]

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.

References

  1. Jacobs, M. A., Alwood, A., Thaipisuttikul, I., Spencer, D., Haugen, E., Ernst, S., et al. 2003. Comprehensive transposon mutant library of Pseudomonas aeruginosa. Proc Natl Acad Sci U S A. 100(24): 14339–44.
  2. Olivas, A. D., Shogan, B. D., Valuckaite, V., Zaborin, A., Belogortseva, N., Musch, M., et al. 2012. Intestinal tissues induce an SNP mutation in Pseudomonas aeruginosa that enhances its virulence: possible role in anastomotic leak. PLoS One 7(8): e44326.
  3. Varadarajan, A. R., Raymond, N. A., Valentin, J., Castañeda Ocampo, O. E., Somerville, V., Pietsch, F., Buhmann, M. T., Skipp, P., van der Mei, C. H., Ren, Q., Schreiber, F., Webb, S. W., Ahrens, C. H. 2020. An integrated model system to study biofilm-associated adaptation to antimicrobials and resistance evolution in Pseudomonas aeruginosa MPAO1. (manuscript to be submitted Jan 2020).
  4. Hyatt, D., Chen, G.L., Locascio, P.F., Land, M.L., Larimer, F.W., and Hauser, L.J. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119.
  5. Singhal, P., Jayaram, B., Dixit, S.B., and Beveridge, D.L. 2008. Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations. Biophys J 94: 4173-4183.
  6. Omasits, U., Varadarajan, A. R., Schmid, M., Goetze, S., Melidis, D., Bourqui, M., Nikolayeva, O., Quebatte, M., Patrignani, A., Dehio, C., Frey, J. E., Robinson, M. D., Wollscheid, B., and Ahrens, C. H. 2017. An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics. Genome Research. 27: 2083-2095.
iPtgxDB Release Info
Versions

Version

1
Versions

Date

03.03.2019

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Compression icon

TAR.GZ

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Size

10.9 MB
Data icon

MD5

5406a0dce2318fff802857fb0f13aff8
Data icon

SHA1

ad0997f5c4ab726bad4fc27d6f67f2296d748cb3
Compression icon

ZIP

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Size

11.2 MB
Data icon

MD5

c7cbc71b87745380c2e7473a9fcc0e1f
Data icon

SHA1

29f86c98ac6a6df084a54d94b875edd88aa7078d