Table 2 Mutations fixed during long-term adaptation of ID8 and NC28 lineages
GenotypeProtein functionProtein nameAa positionEmbedded ImageNuc. positionEmbedded ImageFirst passage obs.
ID8wt1CoatF77I → T2792T → C10
DNA pilotH79S → F4762C → T20
DNA packagingC65I → V1912A → G30
DNA bindingJ15A → V2483C → T40
CoatF312Silent3498C → T70
DNA pilotH135G → D4930G → A70
ID8wt2ScaffoldingD45A → S2108G → T20
SpikeG65T → A4175A → G20
DNA pilotH88T → I4789C → T30
DNA pilotH173G → E5044G → A40
DNA packagingC53A → G1877A → G70
ID8evol1DNA pilotH91C → G4797G → T10
CoatF12L → P2597C → T30
DNA pilotH53Q → K4683A → C70
ID8evol2SpikeG2F → L3986T → C40
DNA pilotH79S → A4761T → G80
DNA pilotH336S → F5533C → T80
NC28wt1DNA pilotH4A → D5098C → A10
Scaffolding (lysis)D/E181 (59)A → V (silent)2871C → T30
DNA pilotH230T → A5775A → G30
NC28wt2DNA pilotH3G → D5095G → A10
CoatF151N → S3537A → G40
CoatF240H → R3804A → G40
DNA pilotH265G → A5881G → C50
NC28evol1Noncoding389G → T10
DNA pilotH230T → A5775A → G10
DNA pilotH7G → D5107G → A30
SpikeG176A → V4933C → T60
NC28evol2DNA pilotH6V → L5103G → T20
DNA pilotH230T → A5775A → G30
DNA replicationA115A → T1101G → A60
  • A list of the mutations that fixed during the adaptation of the ID8 and NC28 wild-type and evol lineages, under selection on growth rate and capsid stability. Certain regions of the bacteriophage genome have overlapping genes, indicated with the second affected gene in parentheses. The final column lists the first passage in which the mutation was observed in whole-population Sanger sequencing performed every 10 passages. Aa, amino acid; Nuc., nucleotide; obs., observed.