Comparative Analysis and Distribution of Omega-3 lcPUFA Biosynthesis Genes in Marine Molluscs

Abstract

Recent research has identified marine molluscs as an excellent source of omega-3 long-chain polyunsaturated fatty acids (lcPUFAs), based on their potential for endogenous synthesis of lcPUFAs. In this study we generated a representative list of fatty acyl desaturase (Fad) and elongation of very long-chain fatty acid (Elovl) genes from major orders of Phylum Mollusca, through the interrogation of transcriptome and genome sequences, and various publicly available databases. We have identified novel and uncharacterised Fad and Elovl sequences in the following species: Anadara trapezia, Nerita albicilla, Nerita melanotragus, Crassostrea gigas, Lottia gigantea, Aplysia californica, Loligo pealeii and Chlamys farreri. Based on alignments of translated protein sequences of Fad and Elovl genes, the haeme binding motif and histidine boxes of Fad proteins, and the histidine box and seventeen important amino acids in Elovl proteins, were highly conserved. Phylogenetic analysis of aligned reference sequences was used to reconstruct the evolutionary relationships for Fad and Elovl genes separately. Multiple, well resolved clades for both the Fad and Elovl sequences were observed, suggesting that repeated rounds of gene duplication best explain the distribution of Fad and Elovl proteins across the major orders of molluscs. For Elovl sequences, one clade contained the functionally characterised Elovl5 proteins, while another clade contained proteins hypothesised to have Elovl4 function. Additional well resolved clades consisted only of uncharacterised Elovl sequences. One clade from the Fad phylogeny contained only uncharacterised proteins, while the other clade contained functionally characterised delta-5 desaturase proteins. The discovery of an uncharacterised Fad clade is particularly interesting as these divergent proteins may have novel functions. Overall, this paper presents a number of novel Fad and Elovl genes suggesting that many mollusc groups possess most of the required enzymes for the synthesis of lcPUFAs.

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

“…Research investigating the Fad and Elovl gene families that desaturate and elongate LC‐PUFAs has largely been restricted to bilaterian taxa (Carmona‐Antoñanzas et al., 2011; Castro et al., 2012; Fonseca‐Madrigal et al., 2014; Kabeya et al., 2017; Li et al., 2017; Li et al., 2010; Mohd‐Yusof et al., 2010; Monroig, Guinot, et al., 2012; Monroig, Navarro, et al., 2012; Monroig, Webb, et al., 2011; Monroig et al., 2010, 2016, 2017, 2013; Morais et al., 2009; Surm et al., 2015). We have investigated the phylogenetic and molecular evolutionary histories of the Fad and Elovl gene families in phylum Cnidaria, to provide insights into evolution and the distribution of these gene families in Metazoa outside of bilaterian taxa.…”

“…Variations of Fad and Elovl gene copy number were also observed within the same species as observed in the brown ecotype of A. tenebrosa , which had one less Fad and Elovl compared with the other three ecotypes. This may be an actual case of copy number variation or also could be an artifact of low expression of this gene in this ecotype (Surm et al., 2015). …”

“…Similarly, whole genome duplication events have resulted in the diversification of elongase enzymes observed in vertebrates (Elovl2 and 5) not present in other chordates, which contain a single elongase enzyme referred to as Elovl2/5 (Castro, Tocher, & Monroig, 2016; Monroig et al., 2016). Gene duplication events of Fad and Elovl gene families have also occurred in a lineage‐specific manner across other bilaterian taxa, such as molluscs (Monroig, Navarro, et al., 2012; Surm et al., 2015). Despite these key observations, the distribution and evolution of Fad and Elovl genes remain unresolved in early diverging metazoan phyla such as Cnidaria.…”

Biosynthesis of Polyunsaturated Fatty Acids in Sea Urchins: Molecular and Functional Characterisation of Three Fatty Acyl Desaturases from Paracentrotus lividus (Lamark 1816)

“…A recent study on Fads and Elovl repertoire among several classes of molluscs including cephalopods, gastropods and bivalves [18] highlighted that lineage-specific gene duplication events accounted for the presence of one or more Fads copies among the mollusc classes under investigation. These results further evidenced that the evolutionary history of genes involved in the LC-PUFA biosynthetic pathways of invertebrates, particularly the Fads-like desaturases, might differ markedly from those of vertebrates [6,12,19].…”

Insights into the innate immunome of actiniarians using a comparative genomic approach

“…Sequences were run on a Genetic Analyser 3500 from Applied Biosystems (ThermoFisher). Sequence chromatograms were visualised in Geneious version R8.1.4 [61] and aligned to the transcript from which the primers were designed, as per [62]. To confirm the ORF for the candidate gene, sequence similarity was compared.…”