Application of omics research in seaweeds with a focus on red seaweeds

Abstract

Targeted ‘omics’ research for seaweeds, utilizing various computational and informatics frameworks, has the potential to rapidly develop our understanding of biological processes at the molecular level and contribute to solutions for the most pressing environmental and social issues of our time. Here, a systematic review into the current status of seaweed omics research was undertaken to evaluate the biological diversity of seaweed species investigated (red, green and brown phyla), the levels to which the work was undertaken (from full genome to transcripts, proteins or metabolites) and the field of research to which it has contributed. We report that from 1994 to 2021 the majority of seaweed omics research has been performed on the red seaweeds (45% of total studies), with more than half of these studies based upon two genera Pyropia and Gracilaria. A smaller number of studies examined brown seaweed (key genera Saccharina and Sargassum) and green seaweed (primarily Ulva). Overall, seaweed omics research is most highly associated with the field of evolution (46% of total studies), followed by the fields of ecology, natural products and their biosynthesis, omics methodology and seaweed–microbe interactions. Synthesis and specific outcomes derived from omics studies in the red seaweeds are provided. Together, these studies have provided a broad-scale interrogation of seaweeds, facilitating our ability to answer fundamental queries and develop applied outcomes. Crucial to the next steps will be establishing analytical tools and databases that can be more broadly utilized by practitioners and researchers across the globe because of their shared interest in the key seaweed genera.

Identification of reproductive sex‐biased gene expression in Asparagopsis taxiformis (lineage 6) gametophytes

“…From the aquaculture perspective, either one of these free‐living stages can be utilized to produce biomass for methane reduction in cattle (Charrier et al., 2017). Despite this tremendous diversity, there are limited molecular insights on critical aspects of seaweed reproduction (particularly of factors involved in gamete formation, fusion, and meiosis), and this restricts progress toward large‐scale commercialization of new seaweed species (Patwary et al., 2021). For example, a greater understanding of Pyropia (nori) seaweed has led to a booming commercial industry around identifying and controlling the conchocelis‐phase of the life cycle (Buschmann et al., 2017).…”

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

“…Despite their importance, Rhodophyte omics have been relatively underdeveloped, particularly in regard to published whole genome and transcriptome assemblies, with relatively few published and even fewer annotated [18,19]. However, recent years have seen a sharp increase in the number of Rhodophyte assemblies published.…”

Quantification of Xylanolytic and Cellulolytic Activities of Fungal Strains Isolated from Palmaria palmata to Enhance R-Phycoerythrin Extraction of Palmaria palmata: From Seaweed to Seaweed

“…Algae may be the most diverse group of organisms alive, representing one third of the total divisions of the plant kingdom [4]. Among macroalgae, red seaweeds (Rhodophyceae) are characterized by the highest specific diversity, representing 45% of total seaweed species, followed by brown (Phaeophyceae) and green ones (Chlorophyceae) [5,6]. Red seaweeds are also the main macroalgal group in terms of commercial values [6] and in terms of secondary metabolite production [7].…”