Trojan family genes in avian and non-avian species.

<p>Gene names combine the respective homologue: Mystran (MYS), Trojan (TRO), Thracian (THR), Protein phosphatase (PP) or Transmembrane protein (TP) and the species abbreviation. Avian species: <i>A</i>. <i>platyrhynchos</i> (ANAPL), <i>C</i>. <i>brachyrhynchos</i> (CORBR), <i>C</i>. <i>canorus</i> (CUCCA), <i>F</i>. <i>peregrinus</i> (FALPE), <i>F</i>. <i>albicollis</i> (FICAL), <i>G</i>. <i>fortis</i> (GEOFO), <i>M</i>. <i>gallopavo</i> (MELGA), <i>M</i>. <i>undulatus</i> (MELUN), <i>O</i>. <i>hoazin</i> (OPPHO), <i>T</i>. <i>guttata</i> (TAEGU); Non-avian species: <i>A</i>. <i>carolinensis</i> (ANOCA), <i>C</i>. <i>mydas</i> (CHEMY), <i>C</i>. <i>picta</i> (CHRPI), <i>L</i>. <i>chalumnae</i> (LATCH). An arrow indicates a gene found on more than one scaffold and the direction the scaffolds were combined.</p><p>Trojan family genes in avian and non-avian species.</p

The Trojan family in chicken.

<p>A) <i>Mystran</i>, <i>Trojan</i> and <i>Thracian</i> on chicken chromosome Z. Genes are represented as hollow boxes showing their direction. Exons are shown as filled fragments within the gene boxes; B) The overall topology organization of the Trojan family proteins. Complement control protein (CCP) domains, fibronectin type III domains (FN3) and protein tyrosine phosphatase domains (PTP) are labeled. Signal peptides (SP), domains, transmembrane regions (TM), N-glycosylation (N-glyc) sites and intrinsically disordered (ID) binding sites are indicated. The Mystran CCP domain is shown in gray scale, as it was predicted slightly below threshold, but had the expected position. C) The cytoplasmic tails of Mystran, Trojan and Thracian are shown in a “snake” amino acids view. Short functional motifs are indicated: MAPK docking motif (DOC_MAPK), Grb association motif (LIG_SH_GRB), 14-3-3 docking motif (LIG_14-3-3), PKA phosphorylation motif (MOD_PKA), ITAM (LIG_TYR_ITAM) and TRAF2 interacting motif (LIG_TRAF2). For Thracian, the positions of cytoplasmic sites identified to be under positive evolutionary selection with probability higher than 90% and 95% (*) are indicated.</p

Positively selected sites in the Trojan gene family.

<p>Amino acids from chicken Mystran, Trojan and Thracian with Bayesian posterior probabilities to belong to site-class under positive selection are listed. Probability: >90%, >95% (*) or >99%(**), as inferred by Bayes-Empirical-Bayes (BEB).</p><p>Positively selected sites in the Trojan gene family.</p

Gene conversion analyzes for the Trojan family in avian species.

<p>The gene converted fragments between sequence pairs (Sequence I and Sequence II) are given with respect to their unaligned offsets and lengths within each sequence. “BC KA P-values”: Bonferroni-corrected KA (BLAST-like P-values). Names combine Mystran (MYS), Trojan (TRO) or Thracian (THR) and the corresponding species abbreviation. Species: <i>A</i>. <i>platyrhynchos</i> (ANAPL), <i>C</i>. <i>brachyrhynchos</i> (CORBR), <i>C</i>. <i>canorus</i> (CUCCA), <i>G</i>. <i>gallus</i> (GALGA), <i>G</i>. <i>fortis</i> (GEOFO), <i>O</i>. <i>hoazin</i> (OPPHO).</p><p>Gene conversion analyzes for the Trojan family in avian species.</p

Co-evolutionary analyzes of Trojan family members.

<p>A) Intermolecular co-evolution between Trojan, Mystran and Thracian. Positions of co-evolving amino acids are mapped onto proteins topology from chicken. Correlation coefficients are indicated between each pair of residues. Coordinates on the polypeptide chain are indicated for each domain and transmembrane regions. Domain types and other topology properties are shown in the legend. B) Intramolecular co-evolution from chicken Mystran, Trojan and Thracian. Numerical values indicate the protein region to which the majority of network residues are confined.</p

Expression of chicken Mystran, Trojan and Thracian.

<p>The relative expression levels of <i>Mystran</i>, <i>Trojan</i> and <i>Thracian</i> genes are presented as RNASeq reads from different organs, tissues, or cell types. Data from Ensembl 75.</p

Evolutionary selection of the Trojan family members in chicken.

<p>Amino acid postmean ω values are mapped onto the protein topologies. Non selected sites are shown in blue, selected sites with probability below 90% are shown in light blue and selected sites with probability greater than 90% are shown in orange. Sites with probability greater than 95% and 99% are indicated by one or two red dots, respectively. Domain types and other topology properties are shown in the legend. The Mystran CCP domain is shown in gray scale, as it was predicted slightly below threshold, but had the expected position.</p

Trojan family proteins in other avian and non-avian species.

<p>Domain types, other topology properties and short functional motifs are shown in the legend. Domains presented in gray were predicted below threshold, but had the expected type, position and relative size. A) Avian species. B) Non-avian species.</p

ML tree of the Trojan family members from all species.

<p>Mystrans are shown in blue, Trojans are shown in green and Thracians are shown in red. Major groups of homologues are enclosed within gray boxes. The tree is rooted to <i>L</i>. <i>chalumnae</i> and bootstrap values are indicated at nodes. Gene names combine the respective orthologue: Mystran (MYS), Trojan (TRO), Thracian (THR), Protein phosphatase (PP) or Transmembrane protein (TP) and species abbreviations. Avian species: <i>A</i>. <i>platyrhynchos</i> (ANAPL), <i>C</i>. <i>brachyrhynchos</i> (CORBR), <i>C</i>. <i>canorus</i> (CUCCA), <i>F</i>. <i>peregrinus</i> (FALPE), <i>F</i>. <i>albicollis</i> (FICAL), <i>G</i>. <i>fortis</i> (GEOFO), <i>M</i>. <i>gallopavo</i> (MELGA), <i>M</i>. <i>undulatus</i> (MELUN), <i>O</i>. <i>hoazin</i> (OPPHO), <i>T</i>. <i>guttata</i> (TAEGU); Non-avian species: <i>A</i>. <i>carolinensis</i> (ANOCA), <i>C</i>. <i>mydas</i> (CHEMY), <i>C</i>. <i>picta</i> (CHRPI), <i>L</i>. <i>chalumnae</i> (LATCH).</p