SeqCode: A Nomenclatural Code for Prokaryotes Described From Sequence Data

Authors

Brian P. Hedlund, University of Nevada, Las Vegas
Maria Chuvochina, The University of Queensland, Australia
Philip Hugenholtz, The University of Queensland, Australia
Konstantinos T. Konstantinidis, Heart of Georgia Technical College
Alison E. Murray, Desert Research Institute
Marike Palmer, University of Nevada, Las Vegas
Donovan H. Parks, The University of Queensland, Australia
Alexander J. Probst, University of Duisburg-Essen
Anna-Louise Reysenbach, Portland State University
Luis M. Rodriguez-R, University of Innsbruck
Ramon Rossello-Mora, Mediterranean Institute of Advanced Studies
Iain C. Sutcliffe, Northumbria University
Stephanus N. Venter, University of Pretoria
William B. Whitman, University of Georgia

Document Type

Article

Publication Date

9-19-2022

Publication Title

Nature Microbiology

Volume

7

First page number:

1702

Last page number:

1708

Abstract

Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry (https://seqco.de/), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, including Candidatus names, and provide examples for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.

Controlled Subject

Microbial biology; Microorganisms; Life sciences

Disciplines

Cell Biology | Integrative Biology | Molecular Biology | Structural Biology

File Format

PDF

File Size

1300 KB

Language

English

Rights

IN COPYRIGHT. For more information about this rights statement, please visit http://rightsstatements.org/vocab/InC/1.0/

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 License.

Repository Citation

Hedlund, B. P., Chuvochina, M., Hugenholtz, P., Konstantinidis, K. T., Murray, A. E., Palmer, M., Parks, D. H., Probst, A. J., Reysenbach, A., Rodriguez-R, L. M., Rossello-Mora, R., Sutcliffe, I. C., Venter, S. N., Whitman, W. B. (2022). SeqCode: A Nomenclatural Code for Prokaryotes Described From Sequence Data. Nature Microbiology, 7 1702-1708.
http://dx.doi.org/10.1038/s41564-022-01214-9