lysozyme g coding sequences

Full-length and near full-length lysozyme g coding sequences used in this analysis are presented in fasta format with shortened species names. Ns are added to the beginning of some sequences to generate correct reading frames

Phylogeny of <i>Mlxip</i> and <i>Mlxipl</i> coding sequences.

<p>Phylogeny inferred by the Bayesian method, implemented in MrBayes version 3.2.2, is shown, using the coding sequence alignment from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0149682#pone.0149682.s002" target="_blank">S2 Fig</a> based on the alignment presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0149682#pone.0149682.s012" target="_blank">S12 Fig</a>. The phylogeny is rooted between the sequences for <i>Mlxip</i> (shown in the upper portion) and <i>Mlxipl</i> (lower portion). Branch lengths are proportional to the number of inferred nucleotide substitutions. Numbers at the node represent posterior probabilities after 2,000,000 generations. Similar phylogenies were generated when Maximum likelihood or neighbor-joining methods were used.</p

Variability in MondoA and ChREBP protein sequences.

<p>JS Divergence scores across the alignment of MondoA and ChREBP protein sequences. Plots of JS Scores for MondoA, ChREBP and combined MondoA and ChREBP protein sequences are shown. JS Scores for each position are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0149682#pone.0149682.s017" target="_blank">S5 Table</a>. A schematic organization of the domains in MondoA and ChREBP is shown below the plot. Alignment of sequences and locations of domains are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0149682#pone.0149682.s007" target="_blank">S7 Fig</a>.</p

Consensus sequences for MCR1-6, bHLH-Zip and DCD domains in mammalian MondoA and ChREBP protein sequences.

<p>Consensus sequences from 10 mammalian ChREBP and MondoA protein sequences of Mondo Conserved Regions (MCR1-6), basic helix-loop helix leucine-zipper (bHLH-Zip) and the dimerization and cytoplasmic localization (DCD) domains are displayed by WebLogos. Numbers below residues indicate position in alignments of the 10 mammalian ChREBP or MondoA sequences. Heights of letters indicate abundance of that residue in the 10 sequences. Color of residues indicate chemical properties, with green being polar amino acids (G, S, T, Y, C, Q, and N), blue are basic (K, R, and H), red are acidic (D and E) and black are hydrophobic (A, V, L, I, P, W, F, and M).</p

Comparison of the average JS Divergence scores for domains in MondoA and ChREBP protein sequences.

<p>Comparison of the average JS Divergence scores for domains in MondoA and ChREBP protein sequences.</p

Introns in <i>Mlxip</i> and <i>Mlxipl</i> genes are at homologous locations.

<p>Alignment of human and mouse ChREBP, MondoA, and Mlx (encoded by <i>MLXIPL</i>, <i>MLXIP</i>, and <i>MLX</i>, respectively) protein sequences and <i>Drosophila melanogaster</i> Mondo (encoded by <i>Mio</i>) protein sequence with locations of introns, and phases indicated. Protein sequences were aligned with Clustal Omega. Locations of introns are indicated by ^ with the number referring to the phase of the codon interrupted by the intron. Introns at near identical locations, and of the same phase are boxed, with solid boxes indicated very similar locations, while dotted boxes are similar.</p

Alignment of Retn and Retnl protein sequences.

<p>Alignment of predicted resistin and resistin-like protein sequences from human, mouse, opossum, Anole lizard, and coelacanth (lobe-finned fish). The human Retn sequence is shown at the top in single letter code. Dots in the alignments represent identity to the human Retn sequence, with differences indicated in single letter code. Asterisks below the alignment identify residues that are perfectly conserved among all of the selected sequences.</p

Evolution of the Vertebrate Resistin Gene Family

<div><p>Resistin (encoded by <i>Retn</i>) was previously identified in rodents as a hormone associated with diabetes; however human resistin is instead linked to inflammation. Resistin is a member of a small gene family that includes the resistin-like peptides (encoded by <i>Retnl</i> genes) in mammals. Genomic searches of available genome sequences of diverse vertebrates and phylogenetic analyses were conducted to determine the size and origin of the resistin-like gene family. Genes encoding peptides similar to resistin were found in Mammalia, Sauria, Amphibia, and Actinistia (coelacanth, a lobe-finned fish), but not in Aves or fish from Actinopterygii, Chondrichthyes, or Agnatha. <i>Retnl</i> originated by duplication and transposition from <i>Retn</i> on the early mammalian lineage after divergence of the platypus, but before the placental and marsupial mammal divergence. The resistin-like gene family illustrates an instance where the locus of origin of duplicated genes can be identified, with <i>Retn</i> continuing to reside at this location. Mammalian species typically have a single copy <i>Retn</i> gene, but are much more variable in their numbers of <i>Retnl</i> genes, ranging from 0 to 9. Since <i>Retn</i> is located at the locus of origin, thus likely retained the ancestral expression pattern, largely maintained its copy number, and did not display accelerated evolution, we suggest that it is more likely to have maintained an ancestral function, while <i>Retnl</i>, which transposed to a new location, displays accelerated evolution, and shows greater variability in gene number, including gene loss, likely evolved new, but potentially lineage-specific, functions.</p></div

Phylogeny of <i>Retn</i> and <i>Retnl</i> genes.

<p>Phylogeny inferred by the Bayesian method for 136 <i>Retn</i> and <i>Retnl</i> sequences from diverse vertebrates. The phylogeny was rooted with the Coelacanth <i>Retn</i> sequence. Similar phylogenies were obtained if sequences from Sauria (coelacanth sequence not used) were used as the outgroup or if other methods were used (e.g., see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130188#pone.0130188.s006" target="_blank">S6 Fig</a>). Numbers at the nodes indicate posterior probabilities, with those for the nodes in early mammalian evolution shown in bold. Branch lengths are proportional to the inferred amount of change, with the scale bar at the bottom. Diamonds indicate inferred gene duplication events. <i>Retnl</i> genes are shown in the upper part of the tree while <i>Retn</i> genes are below.</p

Genomic organization of genes near <i>Retnl</i> genes of representative vertebrate species.

<p><i>Retnl</i> genes are labeled in red. Genes that share genomic location with human genes are labeled in black, while genes labeled in green are either lineage-specific genes or are found at a different genomic location in the human genome (genes without names do not have a human ortholog). Chromosome, genomic scaffold, or sequence accession numbers, with approximate coordinates and size, of the displayed fragment is shown. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130188#pone.0130188.s009" target="_blank">S1 Table</a> for details on genomic locations of <i>Retnl</i> genes. Gene sizes and distances between genes are not to scale. Arrowheads indicate direction of transcription. Gene symbols are: <i>Retnl</i>, resistin-like; <i>Morc1</i>, MORC family CW-type zinc finger 1; <i>Guca1c</i>, Guanylate cyclase activator 1C; <i>Trat1</i>, T cell receptor associated transmembrane adaptor 1; <i>Dzip3</i>, DAZ interacting zinc finger protein 3; <i>Kiaa1524</i>, KIAA1524; <i>Myh15</i>, Myosin, heavy chain 15; <i>Hhla2</i>, HERV-H LTR-associating 2; <i>Hjurp</i>, Holliday junction recognition protein; <i>Sh2d1b</i>, SH2 domain containing 1B; <i>Ift57</i>, Intraflagellar transport 57; and <i>Mrps23</i>, Mitochondrial ribosomal protein S23.</p