A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights

Abstract

Genomic information has already been applied to prokaryotic species definition and classification. However, the contribution of the genome sequence to prokaryotic genus delimitation has been less studied. To gain insights into genus definition for the prokaryotes, we attempted to reveal the genus-level genomic differences in the current prokaryotic classification system and to delineate the boundary of a genus on the basis of genomic information. The average nucleotide sequence identity between two genomes can be used for prokaryotic species delineation, but it is not suitable for genus demarcation. We used the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance. A comprehensive genomic survey indicated that the POCP can serve as a robust genomic index for establishing the genus boundary for prokaryotic groups. Basically, two species belonging to the same genus would share at least half of their proteins. In a specific lineage, the genus and family/order ranks showed slight or no overlap in terms of POCP values. A prokaryotic genus can be defined as a group of species with all pairwise POCP values higher than 50%. Integration of whole-genome data into the current taxonomy system can provide comprehensive information for prokaryotic genus definition and delimitation.

Oceanivirga salmonicida gen. nov., sp. nov., a member of the Leptotrichiaceae isolated from Atlantic salmon (Salmo salar)

“…POCP calculations for strain NCIMB 703044 T versus C. abscessus CCUG 39713 T , S. sanguinegens CCUG 41628 T Palmer et al (1994). and S. moniliformis DSM 12112 T were 46.25, 41.03 and 32.87, respectively, thereby confirming the proposed intergenera POCP boundary of below 50 % for prokaryotic lineages (Qin et al, 2014).…”

“…Strain NCIMB 703044 T constantly displayed DDH estimate levels of 19.2±2.29 to 26.2±2.42 to all type species of the Leptotrichiaceae genera using formula 2 [identities/high-scoring pair (HSP) length], thereby clearly falling below the cut-off for species boundary of 70 % DNA heterogeneity (Johnson, 1984) (data not shown). However, since ANI was found to be not suitable for genus delimitation (Qin et al, 2014), the percentage of conserved proteins (POCP) was assessed to support the designation of a novel genus. POCP calculations for strain NCIMB 703044 T versus C. abscessus CCUG 39713 T , S. sanguinegens CCUG 41628 T Palmer et al (1994).…”

Dethiosulfatarculus sandiegensis gen. nov., sp. nov., isolated from a methanogenic paraffin-degrading enrichment culture and emended description of the family Desulfarculaceae

“…Levels of hybridization between SPR T and these strains were 12.7-18.1, 15.5-21.3, 12.5-26 and 13-17.6 %, respectively, depending on the distance formula utilized. Genome sequences were also compared via pairwise BLASTP of all predicted protein sequences as outlined by Qin et al (2014). Based on this analysis, SPR shared 27.0, 46.2, 26.9 and 46.9 % of predicted proteins with Desulfatiglans anilini DSM 4660 T , Desulfarculus baarsii DSM 2075 T , Desulfococcus multivorans DSM 2059 T and Desulfocarbo indianensis SCBM T , respectively.…”

Sphingobacterium populi sp. nov., isolated from bark of Populus × euramericana

“…The POCP value between the strain 7Y-4 T and S. spiritivorum ATCC 33861 T (>50 %) indicted that strain 7Y-4 T belonged to genus Sphingobacterium (Qin et al, 2014).…”

“…The percentage of conserved proteins (POCP) analysis was performed as described by Qin et al (2014). In brief, the conserved proteins between a pair of genomes were determined by aligning all of the protein sequences of one genome (query genome) with all of the protein sequences of another genome using the BLASTP program.…”