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 Long read sequencing on the PacBio Vega or Oxford Nanopore GridION. Genome data obtained either is exported as fastq(.gz) file(s). Afterwards, a long read genome assembly is performed under Linux using the Flye software, resulting either in a complete genome (bacterial chromosome(s) and extrachromosomal elements) or a small set of contigs. Genome Annotation (gene calling, functional assignments, etc.) is performed using the Bakta software. Final genome data finally is uploaded to the Type Strain Genome Server TYGS (tygs.dsmz.de), a platform for the genome-based taxonomy of prokaryotes. 

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

Download the service order form here.

Dr. Cathrin Spröer

Senior scientist

References

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  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.
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  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.