TY - JOUR
T1 - SeqCode
T2 - a nomenclatural code for prokaryotes described from sequence data
AU - Hedlund, Brian P.
AU - Chuvochina, Maria
AU - Hugenholtz, Philip
AU - Konstantinidis, Konstantinos T.
AU - Murray, Alison E.
AU - Palmer, Marike
AU - Parks, Donovan H.
AU - Probst, Alexander J.
AU - Reysenbach, Anna Louise
AU - Rodriguez-R, Luis M.
AU - Rossello-Mora, Ramon
AU - Sutcliffe, Iain C.
AU - Venter, Stephanus N.
AU - Whitman, William B.
N1 - Funding Information: Funding was provided by the US National Science Foundation (DEB 1841658, DEB 1557042 and EAR 1516680) to B.H., A.-L.R. and A.M.; the US National Institute of General Medical Sciences (GM103440) from the National Institutes of Health to B.H.; the Spanish Ministry of Science, Innovation and Universities (PGC2018-096956-B-C41 and PID2021-126114NB-C42) to R.R.; the Australian Research Council (FL150100038) to P.H.; the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation, SFB 1439/1 2021—426547801) and European Regional Development Funds (FEDER) to A.P.; and the International Society for Microbial Ecology (ISME) to all authors.
PY - 2022/10/1
Y1 - 2022/10/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85136723266&partnerID=8YFLogxK
U2 - 10.1038/s41564-022-01214-9
DO - 10.1038/s41564-022-01214-9
M3 - Article
C2 - 36123442
AN - SCOPUS:85136723266
SN - 2058-5276
VL - 7
SP - 1702
EP - 1708
JO - Nature Microbiology
JF - Nature Microbiology
IS - 10
ER -