A Genomics Resource for 12 Edible Seaweeds to Predict Seaweed-Secreted Peptides with Potential Anti-Cancer Function

SIMPLE SUMMARY: Edible seaweed, also known as sea vegetables, are macroalgae that can be eaten and used in cooking. They contain enriched bioactive compounds such as polysaccharides, which have a variety of functions such as antioxidants, anti-aging, and immune regulation. This study was a voyage of biological discovery that sought to thoroughly examine all of the DNA (known as a genome) of 12 edible seaweeds. The collected genomic sequence data are publicly accessible as a critical functional reference for the discovery of bioactive products and genome-assisted breeding for edible seaweeds. Secreted proteins frequently circulate throughout the body and, thus, have access to the majority of organs and tissues in animals. We investigate the potential secreted short peptides in seaweed using a comparative analysis of protein families that interact with human cancer genes. Some of the secreted proteins may be therapeutic agents interacting with surface receptors in human cells due to their circulating function. In summary, our data integration predicted the first shortlist of secreted peptides of edible seaweeds, which may provide novel information about anti-tumour mechanisms, thus accelerating the study of seaweed biology and improving seaweed nutraceutical practice. ABSTRACT: Seaweeds are multicellular marine macroalgae with natural compounds that have potential anticancer activity. To date, the identification of those compounds has relied on purification and assay, yet few have been documented. Additionally, the genomes and associated proteomes of edible seaweeds that have been identified thus far are scattered among different resources and with no systematic summary available, which hinders the development of a large-scale omics analysis. To enable this, we constructed a comprehensive genomics resource for the edible seaweeds. These data could be used for systematic metabolomics and a proteome search for anti-cancer compound and peptides. In brief, we integrated and annotated 12 publicly available edible seaweed genomes (8 species and 268,071 proteins). In addition, we integrate the new seaweed genomic resources with established cancer bioinformatics pipelines to help identify potential seaweed proteins that could help mitigate the development of cancer. We present 7892 protein domains that were predicted to be associated with cancer proteins based on a protein domain–domain interaction. The most enriched protein families were associated with protein phosphorylation and insulin signalling, both of which are recognised to be crucial molecular components for patient survival in various cancers. In addition, we found 6692 seaweed proteins that could interact with over 100 tumour suppressor proteins, of which 147 are predicted to be secreted proteins. In conclusion, our genomics resource not only may be helpful in exploring the genomics features of these edible seaweed but also may provide a new avenue to explore the molecular mechanisms for seaweed-associated inhibition of human cancer development.