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. Author manuscript; available in PMC: 2022 Nov 26.
Published in final edited form as: Nat Microbiol. 2022 May 26;7(6):918–927. doi: 10.1038/s41564-022-01128-6

Extended Data Fig. 5. Genomic maps of Lak, Garnet, and Amethyst phages.

Extended Data Fig. 5

A-C. TAG recoded genomes have genes with in-frame TAG codons (orange). Suppressor tRNAs (tRNA TAG, red) are predicted to suppress translation termination at TAG stop codons. Regions of the genome encoding structural and lysis genes (pink) coincide with high use of alternative code. In Lak phage (A), genes involved in DNA replication (yellow) are mostly encoded in alternative code. Origins and termini are unmarked in these genomes as we were unable to define clear replichores for Lak (A) and Garnet and Amethyst (B-C) appear to utilize unidirectional genome replication based on GC skew patterns. In some cases, unique or interesting genes have been noted with text. Clade representatives: Lak = C1--CH_A02_001D1_final, Garnet = pig_ID_3640_F65_scaffold_1252, Amethyst = pig_EL5596_F5_scaffold_275.