ena-STUDY-COPENHAGEN UNIVERSITY-02-03-2018-11:44:29:613-2166
Comment to the taxonomy of Sk1virus
DNA-DNA hybridization (DDH) has been used for prokaryote and phage classification at species level over decades. However, with an increasing amount of genomic information appeared, DDH may soon be an outdated taxonomic method. It may be replaced by the average nucleotide identity (ANIb). So far, there is a suggestion that classify the prokaryotes shared >95% ANIb as belonging to the same species. To evaluate if similar a suggestion is useful for phages, we collected 60 fully sequenced phages genomes (11 from GenBank and 49 newly sequenced) from the lactococcal Sk1virus genus (former known as the 936 phage group or 936 phage species), and analyzed the effect of using >95% ANIb for species differentiation based on whole genome sequence and based on core genome sequence. The results showed that, if a simple <95 % ANIb was used, a 35 new species of SK1virus would be generated. Most of core genes from SK1virus phages were located in the conserved late-expressed region and a small part were located in the early- and middle- expressed regions. Using a <95% ANI for the core genes for designation of new species also resulted in 35 new species. So both methods generated on average a new species almost for every second new sequence. The highest correlation was between where the phage was isolated. This will mean using the proposed subdivision ANIb will generate useless taxonomy below genus level, and we therefore suggest that no species should be assigned to the SK1virus genus based on whole genome or whole core genome using <95 % ANIb. But we also ask ICTV to evaluate their proposal with other high number phage sequence collections
DNA-DNA hybridization (DDH) has been used for prokaryote and phage classification at species level over decades. However, with an increasing amount of genomic information appeared, DDH may soon be an outdated taxonomic method. It may be replaced by the average nucleotide identity (ANIb). So far, there is a suggestion that classify the prokaryotes shared >95% ANIb as belonging to the same species. To evaluate if similar a suggestion is useful for phages, we collected 60 fully sequenced phages genomes (11 from GenBank and 49 newly sequenced) from the lactococcal Sk1virus genus (former known as the 936 phage group or 936 phage species), and analyzed the effect of using >95% ANIb for species differentiation based on whole genome sequence and based on core genome sequence. The results showed that, if a simple <95 % ANIb was used, a 35 new species of SK1virus would be generated. Most of core genes from SK1virus phages were located in the conserved late-expressed region and a small part were located in the early- and middle- expressed regions. Using a <95% ANI for the core genes for designation of new species also resulted in 35 new species. So both methods generated on average a new species almost for every second new sequence. The highest correlation was between where the phage was isolated. This will mean using the proposed subdivision ANIb will generate useless taxonomy below genus level, and we therefore suggest that no species should be assigned to the SK1virus genus based on whole genome or whole core genome using <95 % ANIb. But we also ask ICTV to evaluate their proposal with other high number phage sequence collections