TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy

By Jan P. Meier-Kolthoff, Markus Göker. Nature Communications, 2019

2,918 citations recorded by the source corpus.

Microbial taxonomy is increasingly influenced by genome-based computational methods. Yet such analyses can be complex and require expert knowledge. Here we introduce TYGS, the Type (Strain) Genome Server, a user-friendly high-throughput web server for genome-based prokaryote taxonomy, connected to a large, continuously growing database of genomic, taxonomic and nomenclatural information. It infers genome-scale phylogenies and state-of-the-art estimates for species and subspecies boundaries from user-defined and automatically determined closest type genome sequences. TYGS also provides comprehensive access to nomenclature, synonymy and associated taxonomic literature. Clinically important examples demonstrate how TYGS can yield new insights into microbial classification, such as evidence for a species-level separation of previously proposed subspecies of Salmonella enterica. TYGS is an integrated approach for the classification of microbes that unlocks novel scientific approaches to microbiologists worldwide and is particularly helpful for the rapidly expanding field of genome-based taxonomic descriptions of new genera, species or subspecies. Information on type material is of fundamental importance in prokaryote taxonomy. Here, the authors develop TYGS, the Type (Strain) Genome Server, for genome-based prokaryote taxonomy and analysis using a comprehensive database of genomic and taxonomic data.

Subfields: Ecology, Food Science, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/255c0f6ffbe2f6eddfea007e0816ce9b4a8e9516

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Citations in the corpus

TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes (2021, positive): “The content of the TYGS and LPSN databases was introduced in previous publications (2,17) and is here only briefly recapitulated (Figure 1).”
List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ (2020, methodology): “Abbreviations: DSMZ, Leibniz- Institut DSMZ- Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH/Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH; ICNP, International Code of Nomenclature of Prokaryotes; LPSN, List of Prokaryotic names with Standing in Nomen”