Fig. 1. Identification of phage genes involved in retron evasion.

a Genomic comparison of T5 and T5-like phage SP15. The tRNA-rich region (TRR; genomic region of ~8 kb) in T5j and SP15, was missing in T5n and SP15m. Visualized using Clinker⁴¹, the TRR is marked in green, and the highlighted TRR in SP15 is outlined with a brown box. This boxed line indicates the specific area chosen for further experiments. b Heatmap depicting the change in the efficiency of plating (EOP) of the phage assay on the bacteria carrying the defense system from Gao et al.³. Bacteria carrying pLG001, labeled as Empty vector, served as the negative control. EOP was calculated by dividing the number of phage plaques on bacteria carrying the defense system by the number of phage plaques on bacteria carrying the empty vector. The names of retrons, specifically Ec67 (Eco2), Ec78 (Eco7), and Ec86 (Eco1), were updated based on the retron classification and nomenclature introduced by Mestre et al.⁵. The photograph of the spot assay and the phage count graph are provided in Supplementary Fig. 2a, b. c Fragmentation of TRR from SP15. A TRR map, comprising the open reading frame (ORF) indicated in dark green and the tRNA in dark blue, is presented. The numerical annotations above the map correspond to the genomic positions in SP15 (accession number: AP019559). Synthetic fragments of TRR were produced through PCR, assembled into plasmid under pBAD inducible promoter, and subsequently introduced into bacteria that harbor retrons. d Genetic organization of the TRR fragment 6 (F6) and 8 (F8). Heatmap illustrating the EOP of phages on bacteria carrying retron-Eco7 (e) or Eco2 (f) and various TRR fragments; the photograph of the spot assay and the phage count graph are provided in Supplementary Fig. 3a–d. g Heatmap illustrating the EOP of phages on bacteria carrying retron-Eco2 and fragmented F8; the photograph of the spot assay and the phage count graph are provided in Supplementary Fig. 4a, b. h Heatmap illustrating the EOP of phages on bacteria carrying retron-Eco7 and fragmented F8 and F6. The photograph of the spot assay and the phage count graph are presented in Supplementary Fig. 4c–f. The phage assay used to calculate the EOP presented in this figure was performed in triplicate. Source data are provided as a Source Data File.