Integrative genome and transcriptome mining identifies a diverse repertoire of cyclooxygenase/prostaglandin- endoperoxide synthase-like candidates in Porifera

Abstract Cyclooxygenases/prostaglandin-endoperoxide synthases (COX/PTGS) catalyse the committed step of prostanoid biosynthesis, yet their evolutionary distribution outside Bilateria and Cnidaria remains unresolved, and previous metazoan surveys recovered no convincing Porifera homologues. We integrated translated transcriptomes, annotated proteins, 213 sponge genome assemblies and 75 public RNA-seq runs to test for COX/PTGS-like genes in Porifera. Candidates were evaluated by reciprocal curated-database annotation, exact amino-acid deduplication, domain architecture, P05979-equivalent residues, genomic structure, splice-aware RNA reconstruction and phylogenetic placement. Genome mining recovered 67 broad models; reconciliation of 65 RNA-evaluable models yielded 47 non-overlapping loci in 22 species, and 15 stringent assembly-level candidates showed complete predicted-intron reconstruction and exact transcript-derived ORF confirmation. In 18 non-redundant focal candidates, all seven monitored peroxidase/haem residues and the Tyr385-centred radical/positioning core were retained, while channel-associated substitutions separated canonical-compatible from product-positioning, channel-constriction and divergent substrate-entry profiles. A domain-restricted maximum-likelihood analysis separated all 54 primary Porifera candidates plus 12 experimentally characterised COX proteins from 33 strict non-COX animal haem-peroxidase comparators with maximal SH-aLRT/UFBoot support; the family partition persisted under an LG+C60 posterior-mean-site-frequency sensitivity analysis. These results revise the apparent absence of COX/PTGS-like homologues from Porifera and support a diverse, taxonomically structured candidate repertoire. By extending the minimum supported phylogenetic depth of the COX/PTGS-like lineage beyond the cnidarian–bilaterian node, these findings are consistent, under a vertical-inheritance interpretation, with the presence of a COX/PTGS-like homologue in the last common ancestor shared by Porifera, Cnidaria and Bilateria. Catalytic activity, product specificity and duplication history remain to be established experimentally.