SeqCode Publications


The SeqCode and the SeqCode Registry are described in the publications below, currently under review

SeqCode, a nomenclatural code for prokaryotes described from sequence data

Brian P. Hedlund, Maria Chuvochina, Philip Hugenholtz, Konstantinos T. Konstantinidis, Alison E. Murray, Marike Palmer, Donovan H. Parks, Alexander J. Probst, Anna-Louise Reysenbach, Luis M. Rodriguez-R, Ramon Rossello-Mora, Iain C. Sutcliffe, Stephanus N. Venter, and William B. Whitman. Nature Microbiology (2022). https://doi.org/10.1038/s41564-022-01214-9


Most prokaryotes cannot easily be grown in the laboratory and distributed as pure cultures. Thus, these organisms could not be officially named. A code of nomenclature — the SeqCode — provides paths to name such organisms on the basis of genomic data, aiming to unify field and laboratory studies in microbiology.


Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type

William B Whitman, Maria Chuvochina, Brian P Hedlund, Philip Hugenholtz, Kostas T Konstantinidis, Alison Murray, Marike Palmer, Donovan H Parks, Alexander J Probst, Anna-Louise Reysenbach, Luis M Rodriguez-R, Ramon Rossello-Mora, Iain Sutcliffe, and Stephanus N Venter Systematic and Applied Microbiology (2022). https://doi.org/10.1016/j.syapm.2022.126305


Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.


The International Code of Nomenclature of Prokaryotes Described from Sequence Data

Edited by William B Whitman, Maria Chuvochina, Brian P Hedlund, Philip Hugenholtz, Kostas T Konstantinidis, Alison Murray, Marike Palmer, Donovan H Parks, Alexander J Probst, Anna-Louise Reysenbach, Luis M Rodriguez-R, Ramon Rossello-Mora, Iain Sutcliffe, and Stephanus N Venter


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