Single Nucleotide Polymorphism annotation
SNPs significantly contributing to the PCoA separation between each family cross were identified, translated to nucleotide sequences by searching and aligning sequences to the Acropora digitiferagenome (v. OIST_v1.1) using custom scripts. All nucleotide matches were downloaded and re-formatted into a searchable BLAST database using the “blastdbcmd” command. Nucleotide matches were blasted to annotated proteins (OIST v.0.9, see reference for full instructions on annotations). Predicted proteins were filtered for only protein matches with E-values <1e-4 were retained (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=
blastx&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome).