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.2024 Jan 8;18(1):wrae109.
doi: 10.1093/ismejo/wrae109.

SeqCode in the golden age of prokaryotic systematics

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SeqCode in the golden age of prokaryotic systematics

Diego Javier Jiménez et al. ISME J..

Abstract

The SeqCode is a new code of prokaryotic nomenclature that was developed to validate taxon names using genome sequences as the type material. The present article provides an independent view about the SeqCode, highlighting its history, current status, basic features, pros and cons, and use to date. We also discuss important topics to consider for validation of novel prokaryotic taxon names using genomes as the type material. Owing to significant advances in metagenomics and cultivation methods, hundreds of novel prokaryotic species are expected to be discovered in the coming years. This manuscript aims to stimulate and enrich the debate around the use of the SeqCode in the upcoming golden age of prokaryotic taxon discovery and systematics.

Keywords: Candidatus names; metagenomics; not-yet-cultivated prokaryotes; prokaryotic nomenclature; prokaryotic taxonomy.

© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.

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Conflict of interest statement

None declared.

Figures

Figure 1
Figure 1
Timeline of the SeqCode. Illustrating the key events and scientific publications surrounding the development of the SeqCode and its use up to march–April 2024. The SeqCode is governed by the SeqCode committee that also oversee the operation of the SeqCode registry. In the SeqCode registry, several general requirements must be followed to create and validate novel taxon names under the SeqCode, such as the use of high-quality genomes, proper formed name and etymology, accession numbers of the assemblies, and effective publication. We predict that the SeqCode will support the next golden age of prokaryotic taxon discovery. In this new era, advances in isolation techniques, top-down enrichment approaches, in situ explorations, cell-sorting methods, long-read DNA sequencing technologies, and new bioinformatic tools will boost the discovery of novel taxa. Abbreviations in the figure:Systematic and Applied Microbiology (SAM);International Journal of Systematic and Evolutionary Microbiology (IJSEM); International Code of Nomenclature of Prokaryotes (ICNP); Genome Taxonomy Database (GTDB); metagenome-assembled genomes (MAGs).BioRender.com was used to create the figure.
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