TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes

Abstract

Microbial systematics is heavily influenced by genome-based methods and challenged by an ever increasing number of taxon names and associated sequences in public data repositories. This poses a challenge for database systems, particularly since it is obviously advantageous if such data are based on a globally recognized approach to manage names, such as the International Code of Nomenclature of Prokaryotes. The amount of data can only be handled if accurate and reliable high-throughput platforms are available that are able to both comply with this demand and to keep track of all changes in an efficient and flexible way. The List of Prokaryotic names with Standing in Nomenclature (LPSN) is an expert-curated authoritative resource for prokaryotic nomenclature and is available at https://lpsn.dsmz.de. The Type (Strain) Genome Server (TYGS) is a high-throughput platform for accurate genome-based taxonomy and is available at https://tygs.dsmz.de. We here present important updates of these two previously introduced, heavily interconnected platforms for taxonomic nomenclature and classification, including new high-level facilities providing access to bioinformatic algorithms, a considerable expansion of the database content, and new ways to easily access the data.

Figure 1.

Left, dependencies of the TYGS and LPSN platforms and relationships to the legacy GGDC platform and to the DSMZ gene phylogeny server. Right, description of the most relevant (partially shared) contents of the TYGS and LPSN databases.

Figure 2.

(A) statistics on the cumulative, non-linear growth of TYGS type-strain genome sequences per month. (B) non-cumulative number of TYGS job submissions per month since its establishment in 2019. Job submissions are grouped according to the top-level domain of the e-mail address included in each job submission. The top-level domain was matched to the country of origin wherever possible.

Figure 3.

(A) Number of new prokaryotic names included in LPSN grouped by year and taxonomic category and nomenclatural status (shades of blue, validly published under the ICNP; shades of red, not validly published). Left, all names; right, names currently regarded as correct name (3) in LPSN. (B) Number of new prokaryotic names validly published under the ICNP and number of emendations of such names included in LPSN, grouped by year and country of origin of the taxonomic study. Left, number of validly published names; right, number of emendations of such names. The country of origin of each study represents the country of origin of the author indicated as corresponding author including an e-mail address.