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Figure 3 | BMC Evolutionary Biology

Figure 3

From: Compensatory evolution for a gene deletion is not limited to its immediate functional network

Figure 3

Genome network of phages T3 and T7. Genes (ovals) are identified with partial names or numbers; the only gene shown that is not found in both phages is 1.05, found only in T3. Light blue genes are those that evolved compensatory changes for ligase deletion in either T7 or T3; dark blue genes evolved compensatory changes in both T7 and at least one line of T3. Solid lines indicate direct contacts known from biochemistry, contacts inferred from yeast-2-hybrid data, or contacts inferred from known associations. For example, the three core proteins are found inside the phage head, and it is not known which of them contact each other and which contact other head proteins. Dashed lines indicate known functional interactions for two discrete phenotypes (DNA metabolism, lysis). The phage RNAP obviously interacts functionally with most of these genes through its expression of them, and those interactions are not shown. Many non-essential genes are omitted; the few listed with no connections are non-essential under lab growth conditions but evolved compensatory changes. This network represents the state of knowledge for T7 (and thus T3), but the T7 network has not been extensively explored, so this network should be acknowledged as incomplete. Furthermore, there is yet no structure of the T3 or T7 virion that reveals the locations of gp6.7, gp7.3, or gp13 nor of the relative locations of tail A to tail B, so many of the connections shown here for those proteins have been assigned by relatively weak inference. Sources include [5, 814]. Gene numbers and functions are given in Additional file 1. Abbreviations (gene name, number): Lys (lysozyme, 3.5), Holin (17.5), RNAP (RNA polymerase, 1), DNAP (DNA polymerase, 5), Tnase (terminase, 19), Scaffold (9), Capsid (major/minor capsid, 10A, 10B), T Fiber (tail fiber, 17), Tail A (11), Tail B (12), Endo (endonuclease, 3), Exo (exonuclease, 6), H/P (helicase/primase, 4A, 4B), ssB (ss DNA binding protein, 2.5).

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