Additional file 6 of Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes

Chromosomal locations: Chromosomal locations of arrestin genes. Table of chromosomal locations of arrestin genes in species with genomes assembled on chromosome-level. The columns â SAG(a)â contain the location of SAG for non-duplicated species (SAGb does not exist) or of SAGa for teleosts. This applies to all columns. Note that ARR3 is located on the sex chromosome X in all mammals. SDP ARR0: SDPs distinguishing ARR0.1 from sea urchin ARR0.2 and other ARR0. The classification is based on unsupervised multi-correspondence analysis of all ARR0 with S3det. SDPs are listed that were predicted by at least two out of the four following methods: Xdet, S3det, SH and multi-RELIEF. Additionally, the functional annotations of homologous positions in bovine ARRB1 are listed. SDP SAG: SDPs distinguishing SAGa and SAGb in teleosts. The classification is based on unsupervised MCA of all filtered teleost SAG with S3det. During filtering, SAGb from pufferfish and stickleback were excluded due to sequence coverage < 70%. SDPs are listed that were predicted by at least two out of the four following methods: Xdet, S3det, SH and multi-RELIEF. Additionally, the functional annotations of homologous positions in bovine SAG are listed. SDP ARRB2: SDPs distinguishing ARRB2a and ARRB2b in teleosts. The classification was given in supervised MCA of all filtered teleost ARRB2. Due to redundancy > 98%, ARRB2a of platyfish (Xiphophorus maculatus), pufferfish and medaka were excluded from the analysis. SDPs are listed that were predicted by at least two out of the four following methods: Xdet, S3det, SH and multi-RELIEF. Additionally, the functional annotations of homologous positions in bovine ARRB2 are listed. SDP ARR3: SDPs distinguishing ARR3a and ARR3b in teleosts. The classification is based on unsupervised MCA of all teleost ARR3 with S3det. SDPs are listed that were predicted by at least two out of the four following methods: Xdet, S3det, SH and multi-RELIEF. Additionally, the functional annotations of homologous positions in bovine ARR3 are listed. Codeml: Analysis of positive selection after arrestin duplication. Specific branches within the arrestin gene tree were tested for positive selection using the branch-site model of codeml, part of the PAML program. The null-hypothesis assumes purifying or neutral selection on the foreground and background branches, while the alternative model allows for positive selection on the foreground branch. Fractions of sites are given, that are predicted to belong to the respective classes (p) together with their dN/dS ratios (w). If the null hypothesis was rejected, sites that were under positive selection under BEB were mapped onto the respective bovine ortholog. (XLSX 44.5 kb)