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Stop codon reassignments in the wild

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Science  23 May 2014:
Vol. 344, Issue 6186, pp. 909-913
DOI: 10.1126/science.1250691

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  1. Fig. 1 Recoded DNA sequences identified worldwide.

    (A) Workflow used to identify contigs that contain stop codon reassignment. (B) Map showing the locations of 82 environmental samples around the globe together with nine sample sites (derived from 212 samples) of the human body for which recoded sequences have been identified.

  2. Fig. 2 Stop codon reassignment by taxonomy and habitat.

    Relative abundance of amber, ochre, and opal stop codon reassignments among bacteria, eukaryotes, and viruses in metagenomes of different habitats. For the sake of clarity, contig sets with less than 1 Mb total length for each combination of domain, stop codon, and habitat were excluded; see fig. S5, A and B (15).

  3. Fig. 3 A maximum likelihood phylogenetic tree of bacterial stop codon reassigned sequences, based on concatenated alignments of protein-coding marker genes

    The arrow at the root of the tree points to the outgroup (Terrabacteria). The tree shows the recoded taxonomic groups Mycoplasmatales and Entomoplasmatales (opal to Trp), SR1 (opal to Gly), and Gracilibacteria (opal to Gly) along with non-recoded reference phyla. The highly reduced alpha-proteobacterial Candidatus Hodgkinia cicadicola genome was not included. The red circles denote two reassignment events. PVC, Planctomycetes, Verrucomicrobia, and Chlamydiae; FCB, Fibrobacteres, Chlorobi, and Bacteroidetes. Sequences published in (4, 5, 14).

  4. Fig. 4 Phage infections across genetic code boundaries.

    (A) Genome of phage 2. The phage genome is broadly divided into two domains with strong bias in codon utilization as well as strand preference. (B) Model of infection of opal-recoded hosts by amber>Gln-recoded phages.

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