Published February 22, 2022 | Version 1.0.0
Dataset Open

Supplemental material of the Streptococcus pyogenes whole genome MLST schema deposited in Chewie-NS

Authors/Creators

  • 1. Instituto de Microbiologia, Instituto de Microbiologia Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal

Description

This supplemental material includes the lists of accession numbers for the Blackwell et al. and NCBI RefSeq assemblies used to populate the whole genome MLST schema for Streptococcus pyogenes, the UniProt identifiers of the reference proteomes used for schema annotation and the set of complete genomes, and associated metadata, used for schema creation.

The wgMLST schema was created with chewBBACA and is publicly available at chewie-NS, where a more detailed description of schema creation, annotation and curation can be found.

Notes

RM was supported by Fundação para a Ciência e Tecnologia (grant 2020.08493.BD). Partial support was received from ONEIDA project (LISBOA-01-0145-FEDER-016417) co-funded by FEEI – Fundos Europeus Estruturais e de Investimento from Programa Operacional Regional Lisboa 2020 and by national funds from FCT–Fundação para a Ciência e a Tecnologia, and by the LISBOA-01-0145-FEDER-007391 project, cofunded by FEDER through POR Lisboa 2020 –Programa Operacional Regional de Lisboa, PORTUGAL 2020, and Fundação para a Ciência e a Tecnologia.

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Blackwell_accession_ids.txt

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Additional details

References

  • Blackwell GA, Hunt M, Malone KM, Lima L, Horesh G, Alako BTF, Thomson NR, Iqbal Z. 2021. Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences. PLoS Biol 19:e3001421.
  • O'Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, Rajput B, Robbertse B, Smith-White B, Ako-Adjei D, Astashyn A, Badretdin A, Bao Y, Blinkova O, Brover V, Chetvernin V, Choi J, Cox E, Ermolaeva O, Farrell CM, Goldfarb T, Gupta T, Haft D, Hatcher E, Hlavina W, Joardar VS, Kodali VK, Li W, Maglott D, Masterson P, McGarvey KM, Murphy MR, O'Neill K, Pujar S, Rangwala SH, Rausch D, Riddick LD, Schoch C, Shkeda A, Storz SS, Sun H, Thibaud-Nissen F, Tolstoy I, Tully RE, Vatsan AR, Wallin C, Webb D, Wu W, Landrum MJ, Kimchi A, Tatusova T, DiCuccio M, Kitts P, Murphy TD, Pruitt KD. 2016. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res 44:D733-745.
  • The UniProt Consortium. 2021. UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res 49:D480–D489.
  • Silva M, Machado MP, Silva DN, Rossi M, Moran-Gilad J, Santos S, Ramirez M, Carriço JA. 2018. chewBBACA: A complete suite for gene-by-gene schema creation and strain identification. Microb Genom 4:e000166.
  • Mamede R, Vila-Cerqueira P, Silva M, Carriço JA, Ramirez M. 2021. Chewie Nomenclature Server (chewie-NS): a deployable nomenclature server for easy sharing of core and whole genome MLST schemas. Nucleic Acids Res 49:D660–D666.