Additional file 2 of Genome-wide identification and spatiotemporal expression analysis of cadherin superfamily members in echinoderms
Creators: name: Chess, Macie M.
name: Douglas, William
name: Saunders, Josiah
name: Ettensohn, Charles A.
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Fig. S1. Phylogenetic analysis of amino acid sequences for echinoderm DCHS2 utilizing maximum likelihood and neighbor-joining methods. Both analyses were conducted on echinoderm, non-echinoderm deuterostome, and protostome dachsous-2 (DCHS2) proteins using MEGA11 software. The clade representing the DCHS2 orthologs is colored purple. Two EGFLAM sequences from Mus musculus and Crassostrea gigas were included as an outgroup for both analyses. Full species and protein names for each taxon and their respective GenBank accession number(s) and their amino acid sequences are listed in Additional file 1. A. A maximum likelihood analysis was performed using the WAG+F+G substitution model with 500 bootstrap replicates utilizing amino acid sites with &gt;90% coverage across all taxa. B. A neighbor-joining analysis was performed using the p-distance substitution model with 5000 bootstrap replicates with pairwise deletion of amino acid sites. Fig. S2. Phylogenetic analysis of amino acid sequences for echinoderm CSTN1 utilizing maximum likelihood and neighbor-joining methods. Both analyses were conducted on echinoderm, non-echinoderm deuterostome, and protostome calsyntenin-1 (CSTN1) proteins using MEGA11 software. The clade representing the CSTN1 orthologs is colored dark blue. Two EGFLAM sequences from Mus musculus and Crassostrea gigas were included as an outgroup for both analyses. Full species and protein names for each taxon and their respective GenBank accession number(s) and their amino acid sequences are listed in Additional file 1. A. A maximum likelihood analysis was performed using the WAG+F+G substitution model with 500 bootstrap replicates utilizing amino acid sites with &gt;90% coverage across all taxa. B. A neighbor-joining analysis was performed using the p-distance substitution model with 5000 bootstrap replicates with pairwise deletion of amino acid sites. Fig. S3. Phylogenetic analysis of amino acid sequences for echinoderm Fat4 utilizing maximum likelihood and neighbor-joining methods. Both analyses were conducted on echinoderm, non-echinoderm deuterostome, and protostome Fat4 proteins using MEGA11 software. The clade representing the fat atypical cadherin 4 (Fat4) orthologs is colored red. Two EGFLAM sequences from Mus musculus and Crassostrea gigas were included as an outgroup for both analyses. Full species and protein names for each taxon and their respective GenBank accession number(s) and their amino acid sequences are listed in Additional file 1. A. A maximum likelihood analysis was performed using the WAG+F+G substitution model with 500 bootstrap replicates utilizing amino acid sites with &gt;90% coverage across all taxa. B. A neighbor-joining analysis was performed using the p-distance substitution model with 5000 bootstrap replicates with pairwise deletion of amino acid sites.