27.peroxidases.md

Phylogenetic analysis of haem peroxidases

We identified haem peroxidases from within Acropora digitifera as all proteins annotated with Interproscan domain IPR019791. These were then used as a query set to identify haem peroxidases in other coral species using BLASTP as follows;

# Example for Acropora millepora (amil)
blastp -db other_species/amil_1.1.maker_006.proteins.fasta -query pxproteins.fasta -max_target_seqs 5 -outfmt 6 -evalue 1e-10 | awk '{print $2}' | sort -u | xargs -I{} samtools faidx other_species/amil_1.1.maker_006.proteins.fasta {} > amil.fasta

In this case “other species” included Acropora millepora, Acropora tenuis, Pachyseris speciosa and Porites lutea. All were chosen because they have high quality assembled genomes and corresponding gene model sets.

This produced a total of 105 sequences (including Acropora digitifera proteins) that we aligned using MAFFT. We then masked positions with less than 50% aligned bases to produce a final alignment with length 679.

IQ-Tree was then used to perform model finding and tree inference as follows;

iqtree -s px_align.fasta -B 1000