Next generation sequencing–driven genomic and transcriptomic profiling of Karenia spp. in Gulf and Middle Eastern environments: diversity, toxin potential, and management

Harmful Algal Blooms (HABs) of the Karenia spp. present an escalating threat to the desalination infrastructure and aquaculture sectors of the Arabian Gulf (AG) and Middle East. While conventional monitoring has documented bloom frequency, there is an urgent need to synthesize how molecular advancements can transition regional management from descriptive observation to predictive, omics-driven early warning systems. A systematic, reproducible literature search was conducted across Web of Science, Scopus, and PubMed (1990–2025). Studies were evaluated using specific inclusion criteria focusing on the intersection of Karenia spp. functional genomics and regional ecological stressors in the Middle East. Synthesis of current data reveals a strong scientific consensus that NGS-based RNA-Seq is the only viable method for resolving the gigabase-scale, histone-deficient transcriptomes of Karenia spp. Research identifies Polyketide Synthase (PKS) gene clusters and spliced leader-mediated regulation as the universal machinery for toxin biosynthesis across the genus. However, a critical comparison of global datasets highlights a significant geographical disparity; while North American and East Asian strains are well-characterized, functional genomic data for endemic Middle Eastern isolates are almost entirely absent. Current molecular probes, developed for temperate strains, do not account for the unique evolutionary adaptations, such as specialized thermotolerance and osmoregulation genes, required for survival in the AG’s hypersaline environment. The review concludes that the reliance on international genetic models represents a major regional knowledge gap. There is scientific disagreement regarding whether global genetic markers are portable to the Middle East or if regional hypersalinity triggers unique regulatory responses. To address this, we argue for an integrated strategy through establishing open-access regional reference and utilizing metatranscriptomics to identify the biotic interactions that regulate bloom collapse. This shift is critical to fulfill regional sustainability goals by providing the mechanistic insights necessary to safeguard multi-billion-dollar desalination assets and food security.