Insights into the phylogenetic and molecular evolutionary histories of Fad and Elovl gene families in Actiniaria

Abstract

The biosynthesis of long‐chain polyunsaturated fatty acids (LC‐PUFAs, ≥ C20) is reliant on the action of desaturase and elongase enzymes, which are encoded by the fatty acyl desaturase (Fad) and elongation of very long‐chain fatty acid (Elovl) gene families, respectively. In Metazoa, research investigating the distribution and evolution of these gene families has been restricted largely to Bilateria. Here, we provide insights into the phylogenetic and molecular evolutionary histories of the Fad and Elovl gene families in Cnidaria, the sister phylum to Bilateria. Four model cnidarian genomes and six actiniarian transcriptomes were interrogated. Analysis of the fatty acid composition of a candidate cnidarian species, Actinia tenebrosa, was performed to determine the baseline profile of this species. Phylogenetic analysis revealed lineage‐specific gene duplication in actiniarians for both the Fad and Elovl gene families. Two distinct cnidarian Fad clades clustered with functionally characterized Δ5 and Δ6 proteins from fungal and plant species, respectively. Alternatively, only a single cnidarian Elovl clade clustered with functionally characterized Elovl proteins (Elovl4), while two additional clades were identified, one actiniarian‐specific (Novel ElovlA) and the another cnidarian‐specific (Novel ElovlB). In actiniarians, selection analyses revealed pervasive purifying selection acting on both gene families. However, codons in the Elovl gene family show patterns of nucleotide variation consistent with the action of episodic diversifying selection following gene duplication events. Significantly, these codons may encode amino acid residues that are functionally important for Elovl proteins to target and elongate different precursor fatty acids. In A. tenebrosa, the fatty acid analysis revealed an absence of LC‐PUFAs > C20 molecules and implies that the Elovl enzymes are not actively contributing to the elongation of these LC‐PUFAs. Overall, this study has revealed that actiniarians possess Fad and Elovl genes required for the biosynthesis of some LC‐PUFAs, and that these genes appear to be distinct from bilaterians.

A process of convergent amplification and tissue‐specific expression dominates the evolution of toxin and toxin‐like genes in sea anemones

“…Evidence of genome‐wide expansions was also explored that could potentially bias the TTL copy numbers reported. Variations in the copy number of nontoxin genes, in similar data sets to those investigated here, have been previously reported (Smith, Pavasovic, Surm, Phillips, & Prentis, ; Surm, Toledo, Prentis, & Pavasovic, ), but the expansions in these gene families are not consistent with the expansions we observe in TTL gene families. Results from copy number analysis of the GFP gene family also showed copy variation different from that observed in TTL gene families (Supporting Information Table .2).…”

Desaturases and elongases involved in polyunsaturated fatty acid biosynthesis in aquatic invertebrates: a comprehensive review

“…Unfortunately, this interesting study did not provide functional data and thus it remains unknown whether the cnidarian Fad retrieved in silico are indeed front-end desaturases with similar functions as their plant or fungal sister sequences. More clearly though, Fad genes hypothesised to play roles in PUFA biosynthesis in cnidarians cannot be regarded as orthologues of vertebrate front-end desaturases (i.e., Fads), since the latter formed a separate clade from the two Cnidaria clades described above (Surm et al 2018). These results emphasise the diversity of desaturase enzymes with putative roles in PUFA biosynthesis in animals.…”

“…The copy number of Fad-like genes varied among species, with species like H. vulgaris and N. vectensis having one gene, while three copies exist in E. pallida. The Cnidaria Fad genes formed two distinct clades, one including functionally characterised Δ6 desaturases from the green plant Borago officinalis and another clade including the Δ5 desaturase from the fungus Mortierella alpina (Surm et al 2018). Unfortunately, this interesting study did not provide functional data and thus it remains unknown whether the cnidarian Fad retrieved in silico are indeed front-end desaturases with similar functions as their plant or fungal sister sequences.…”

“…Surm et al (2018) recently examined the repertoire of front-end desaturases (termed "Fad") and Elovl genes in the phylum Cnidaria, in which genomes from representatives of a range of cnidarian taxa (H. vulgaris, Acropora digitifera, Nematostella vectensis and Exaiptasia pallida) have been interrogated. Moreover, the expression of cnidarian Fad (and Elovl) genes was further confirmed through extensive searches against transcriptome assemblies within six actiniarian species (Surm et al 2018). The copy number of Fad-like genes varied among species, with species like H. vulgaris and N. vectensis having one gene, while three copies exist in E. pallida.…”

Fatty acid bioconversion in harpacticoid copepods in a changing environment: a transcriptomic approach

“…While we are aware that a de novo assembly may artificially introduce an 309 inflated number of contigs (60), the sequences were sufficiently distinct to confidently state that they belong to 310 different genes. It is indeed known that gene duplication is an important driver of the diversity of desaturase and 311 elongase genes (61,62). We would therefore like to advance the hypothesis that an elevated front-end desaturase 312 and elongase gene duplication frequency in harpacticoid copepods could be the key element for their high LC-313 PUFA bioconversion capacity.…”