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. 2018 Oct 13;10(11):3058–3075. doi: 10.1093/gbe/evy228

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© The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Fig. 1. — —LAOdcs are ancient in Firmicutes. (A) Unrooted maximum likelihood phylogeny of LAOdc Cluster I (PhyML, LG+I+G4, 504 sequences, 295 amino-acid positions), displayed as a cladogram. The corresponding phylogram is available at the newick format as supplementary material, Supplementary Material online. Leaf colors correspond to taxonomic groups (Firmicutes: Red, pink, blue, light blue, fade green, and brown, Cyanobacteria: Green, Actinobacteria: Yellow, other: Grey). External colored rings correspond to copy A (blue) and B (red). LAOdc sequences discussed in the text or for which functional information is available are indicated with gray arrows. Red dots correspond to bootstrap values (BV), ranging from 0% (smallest circles) to 100% (largest circles). Sequences that are displayed in their genomic context are mapped with asterisks. (B) Taxonomic distribution of AAT-fold LAOdc mapped on a ribosomal protein tree of Firmicutes (PhyML, LG+I+G4, 38 sequences, 6,133 amino-acid positions). For clarity the tree is displayed as a cladogram. The corresponding phylogram is available at the newick format as supplementary material, Supplementary Material online. Red dots correspond to bootstrap values (BV), ranging from 0% (smallest circles) to 100% (largest circles). Taxa that are represented in (C) are mapped with asterisks. The blue diamonds pinpoint the emergence of copy A and copy B. Rectangles at leaves indicate that at least one genome of the considered taxon encodes one or more AAT-fold LAOdc. A green rectangle indicates that the ancestor of the taxon likely contains one (or more) AAT-fold LAOdc gene, whereas a red rectangle indicates that some members of the taxon acquired secondarily their AAT-fold LAOdc by HGT. (C) Genomic context of LAOdc A and B in a sample of Firmicutes. LAOdc A presents a well-conserved association with thymidylate kinase and DNA polymerase III subunit delta coding genes, while the genomic context of LAOdc B is not conserved. Black arrows: LAOdc coding genes, colored arrows: Conserved neighbor genes.