Bacterial phylogenomic study including whole genome sequencing (WGS)

Whole genome sequencing including the comparison of closely-related genome-sequenced type strains should be included in publications for newly described bacterial species. DSMZ offers genome assembly via SpaDES on short read genome data, which is recorded in house. Hereby, a minimum genomic coverage of 50x from the target bacterium is guaranteed. After genome assembly, contigs are annotated via Prokka and compared against our in house Type Strain Genome Server TYGS.

Required material: A living culture (agar plate or slant) is preferred. Lyophilized material might as well be sent.

Dr. Cathrin Spröer

Senior scientist

References

  1. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol. 2018 Jan;68(1):461-466. doi: 10.1099/ijsem.0.002516. PubMed PMID: 29292687.
  2. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012 May;19(5):455-77. doi: 10.1089/cmb.2012.0021. Epub 2012 Apr 16. PubMed PMID: 22506599; PubMed Central PMCID: PMC3342519.
  3. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014 Jul 15;30(14):2068-9. doi: 10.1093/bioinformatics/btu153. Epub 2014 Mar 18. PubMed PMID: 24642063.
  4. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun. 2019 May 16;10(1):2182. doi: 10.1038/s41467-019-10210-3. PubMed PMID: 31097708; PubMed Central PMCID: PMC6522516.