Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes

Jongsik Chun; Aharon Oren; Antonio Ventosa; Henrik Christensen; David Ruiz Arahal; Milton S da Costa; Alejandro P Rooney; Hana Yi; Xue-Wei Xu; Sofie De Meyer; Martha E Trujillo

doi:10.1099/ijsem.0.002516

Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes

Int J Syst Evol Microbiol. 2018 Jan;68(1):461-466. doi: 10.1099/ijsem.0.002516.

Authors

Affiliations

¹ Department of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea.
² The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel.
³ Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain.
⁴ Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
⁵ Departamento de Microbiología y Ecología, and Colección Española de Cultivos Tipo (CECT), Universitat de València, València, Spain.
⁶ Center for Neurosciences and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal.
⁷ U.S. Department of Agriculture, Agricultural Research Service, Crop Bioprotection Research Unit, Peoria, IL 61604, USA.
⁸ Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea.
⁹ Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China.
¹⁰ Centre for Rhizobium Studies, Murdoch University, Murdoch, WA, Australia.
¹¹ Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain.

PMID: 29292687
DOI: 10.1099/ijsem.0.002516

Abstract

Advancement of DNA sequencing technology allows the routine use of genome sequences in the various fields of microbiology. The information held in genome sequences proved to provide objective and reliable means in the taxonomy of prokaryotes. Here, we describe the minimal standards for the quality of genome sequences and how they can be applied for taxonomic purposes.

Keywords: average nucleotide identity; genome sequence; minimal standards; phylogenomics; prokaryotic taxonomy.

MeSH terms

Genomics / standards*
Phylogeny*
Prokaryotic Cells / classification*
Sequence Analysis, DNA / standards*
Terminology as Topic