Insights into the Red Seaweed Asparagopsis taxiformis Using an Integrative Multi-Omics Analysis

The red seaweed <i>Asparagopsis taxiformis</i> (Bonnemaisoniaceae, Rhodophyta) produces a bioactive natural product, bromoform, which, when fed to ruminant livestock, can eradicate methane emissions. However, to cultivate enough <i>A. taxiformis</i> to produce a yield that would have a meaningful impact on global greenhouse gas emissions, we need to advance our current understanding of the biology of this seaweed species. Here, we used both a domesticated diploid tetrasporophyte (>1.5 years in culture) and wild samples to establish a high-quality draft nuclear genome for <i>A. taxiformis</i> (lineage 6 based upon phylogenetic analyses using the <i>cox2-3</i> spacer). The constructed nuclear genome is 142 Mb in size (including 70.67% repeat regions) and was determined to encode for approximately 10,474 protein-coding genes, including those associated with secondary metabolism, photosynthesis, and defence. To obtain information regarding molecular differences between cultured and wild tetrasporophytes, we further explored differential gene expression relating to their different growth environments. Cultured tetrasporophytes, which contained a relatively higher level of bromoform compared to wild tetrasporophytes, demonstrated an enrichment of regulatory factors, such as protein kinases and transcription factors, whereas wild tetrasporophytes were enriched for the expression of defence and stress-related genes. Wild tetrasporophytes also expressed a relatively high level of novel secretory genes encoding proteins with von Willebrand factor A protein domains (named rhodophyte VWAs). Gene expression was further confirmed by proteomic investigation of cultured tetrasporophytes, resulting in the identification of over 400 proteins, including rhodophyte VWAs, and numerous enzymes and phycobiliproteins, which will facilitate future functional characterisation of this species. In summary, as the most comprehensive genomic resource for any <i>Asparagopsis</i> species, this resource for lineage 6 provides a novel avenue for seaweed researchers to interrogate genomic information, which will greatly assist in expediating production of <i>Asparagopsis</i> to meet demand by both aquaculture and agriculture, and to do so with economic and environmental sustainability.