Figure 4
Sequence analysis of four sex determination/differentiation-related genes in P. margaritifera . (A) Amino acid sequence alignment of P. margaritifera Dmrt (Pmarg-Dmrt2, Pmarg-Dmrt) with the DM domain of various DMRT proteins. The zinc module consisting of intertwined CCHC and HCCC Zn2+-binding sites is shown with blue (Site I) and orange (Site II) boxes. (B) The phylogenetic tree generated using the DM domain of the DMRT proteins. (C) Amino acid sequence alignment of P. margaritifera Sox9 (Pmarg-Sox9) with the HMG domain of various the SOX proteins. The three helices structuring the HMG domain are indicated with blue (H1), orange (H2) and green (H3) boxes. The nuclear export/localization signals (NES and NLS) are indicated in plain and dashed lines, respectively. (D) The phylogenetic tree generated using the HMG domain of SOX proteins. (E) Amino acid sequence alignment of P. margaritifera fem1-like (Pmarg-Fem1-like) with four consecutive ankyrin repeats (blue box) of various FEM proteins. (F) The phylogenetic tree generated using four consecutive ankyrin repeats of the FEM proteins. (G) Amino acid sequence alignment of P. margaritifera foxl2 (Pmarg-Foxl2) with the Forkhead domains of various FOX proteins. The putative NLS sequence is underlined. The three helices (H1, H2 and H3; blue boxes), the two wings (W1, W2) and the β-strands (orange boxes) structuring the Forkhead domain are indicated. (H) The phylogenetic tree generated using the Forkhead domain of the FOX proteins. Alignments were generated using Clustal W2. Identical amino acids and amino acids with conserved similarities are indicated by asterisks and by dots/colons, respectively. The numbers of amino acid residues at the beginning and at the end of the different domains are indicated. The phylogenetic trees were generated using MEGA v6 via the neighbor-joining method. Numbers in the branches represent the bootstrap values (as a percentage) from 100 replicates. GenBank accession numbers of the reference sequences are listed in Additional file 1: Table S1.