Identification of Incomplete Annotations of Biosynthesis Pathways in Rhodophytes Using a Multi-Omics Approach

Rhodophytes (red algae) are an important source of natural products, and thus their metabolic pathways are a major research focus. Rhodophyte omics has benefitted from a recent uptick in publications of genome and transcriptome assemblies. This study aimed to use these assemblies to create a multi-omics resource in order to perform a comparative in silico exploration of Rhodophyte metabolic pathways. Genome and transcriptome assemblies of 72 Rhodophytes were functionally annotated, and analysed using metabolic reconstruction, phylogenetic analysis, orthology prediction, and gene duplication analysis. We then performed two main investigations: the identification of bioactive sterol biosynthesis pathways and the evolutionary analysis of gene duplications for known enzymes. We report that sterol pathways, including campesterol, β-sitosterol, ergocalciferol and cholesterol biosynthesis pathways, all showed incomplete annotated pathways across all Rhodophytes despite prior in vivo studies showing otherwise. Gene duplication analysis revealed high rates of duplication of halideassociated haem peroxidases in Florideophyte algae, which are involved in the biosynthesis of drug-related halogenated secondary metabolites. In summary, this research explored trends in Rhodophyte metabolic pathways, and supports prior claims that Rhodophytes utilize a different sterol biosynthesis pathway to terrestrial organisms, and shows the high duplication of haem peroxidases across more Rhodophyte organisms. This evidence will support further research into the biosynthesis of bioactive compounds in Rhodophytes, which has relevance to both pharmaceutical and nutraceutical applications.