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Over recent years, genomic information has increasingly been used for prokaryotic species definition and classification. Genome sequence-based alternatives to the gold standard DNA-DNA hybridization (DDH) relatedness have been developed, notably average nucleotide identity (ANI), which is one of the most useful measurements for species delineation in the genomic era. However, the strictly intracellar lifestyle, the few measurable phenotypic properties and the low level of genetic heterogeneity made the current standard genomic criteria for bacterial species definition inapplicable to species. We evaluated a range of whole genome sequence (WGS)-based taxonomic parameters to develop guidelines for the classification of isolates at genus and species levels. By comparing the degree of similarity of 74 WGSs from 31 species and 61 WGSs from members of three closely related genera also belonging to the order (, 11 genomes; , 22 genomes; and , 28 genomes) using digital DDH (dDDh) and ANI by orthology (OrthoANI) parameters, we demonstrated that WGS-based taxonomic information, which is easy to obtain and use, can serve for reliable classification of isolates within the genus and species. To be classified as a member of the genus , a bacterial isolate should exhibit OrthoANI values with any species with a validly published name of ≥83.63 %. To be classified as a new species, an isolate should not exhibit more than any of the following degrees of genomic relatedness levels with the most closely related species: >92.30 and >99.19 % for the dDDH and OrthoANI values, respectively. When applied to four rickettsial isolates of uncertain status, the above-described thresholds enabled their classification as new species in one case. Thus, we propose WGS-based guidelines to efficiently delineate species, with OrthoANI and dDDH being the most accurate for classification at the genus and species levels, respectively.
This article was published in the following journal.
Name: International journal of systematic and evolutionary microbiology
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The type species of BETACORONAVIRUS genus causing gastroenteritis respiratory diseases in mammals. Previously separate species HUMAN CORONAVIRUS OC43; BOVINE CORONAVIRUS; Human enteric coronavirus; Equine coronavirus; and Porcine hemagglutinating encephalomyelitis virus merged into this species on the basis of similar genome nucleotide sequence and genome organization.
The type species of ALPHACORONAVIRUS genus causing gastroenteritis, peritonitis and respiratory diseases in dogs, cats and swine. Previously separate species TRANSMISSIBLE GASTROENTERITIS VIRUS; PORCINE RESPIRATORY CORONAVIRUS; CANINE CORONAVIRUS AND FELINE CORONAVIRUS merged into this species on the basis of similar genome nucleotide sequence and genome organization.
A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human GENOME.
Short tracts of DNA sequence that are used as landmarks in GENOME mapping. In most instances, 200 to 500 base pairs of sequence define a Sequence Tagged Site (STS) that is operationally unique in the human genome (i.e., can be specifically detected by the polymerase chain reaction in the presence of all other genomic sequences). The overwhelming advantage of STSs over mapping landmarks defined in other ways is that the means of testing for the presence of a particular STS can be completely described as information in a database.
Techniques to determine the entire sequence of the GENOME of an organism or individual.
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