Proteogenomics for Non-model Ocean-Derived Fungi

Most biological and biomedical experiments are designed and studied using the most common model organisms (MOs) like humans, mice, Escherichia coli, Saccharomyces cerevisiae, Neurospora crassa, worms, fruit flies, zebrafish, and Arabidopsis thaliana. These model organisms have been extensively studied and have a well-established set of genetic, physiological, and other tools available for research. In contrast, non-model organisms (NMOs) are those that are not traditionally used in scientific research and do not have a well-established set of genetic or other biological tools available for their study. The majority of MOs are associated with land habitats but rarely with ocean environments. The ocean forms the largest portion of our planet, yet ocean-derived organisms are the least explored, and these organisms are primarily NMOs. However, these are thrilling living entities, such as ocean-derived fungi (ODF). These ODFs are a diverse group of fungi that live in different ocean sectors, including the ocean, estuaries, and coastal ecosystems. These fungi are found to colonize and adapt to different substrates. They are important decomposers in marine ecosystems, breaking down dead organic matter and recycling nutrients. ODFs have adapted to survive in the unique and challenging conditions of the ocean environment, including high salt concentrations, low nutrient availability, and exposure to waves and currents. ODFs are potent producers of natural compounds with pharmaceutical and industrial applications, such as antibiotics, anticancer agents, antivirals, and enzymes for industrial processes. ODFs are an exciting group of fungi; however, these are the least studied because of the nonavailability of MOs from this group. Hence, there is a massive scope of expanding our current knowledge about ODFs, their genetic traits, potential future drug-producing capabilities, and lifestyle traits.With the advent of next-generation DNA sequencing, there is huge potential for the characterization of the genetic material of ODF as NMOs. Parallel proteomic methods also pose huge potential. A marriage of NGS and proteomic methods generates a new avenue called proteogenomics, which focuses on better annotation of existing genomic data. Both methods are getting cheaper and accessible to the research community for studying the proteogenomics of NMOs. Herein, the proteogenomic protocol development and data analyses are illustrated for the ocean-derived fungus Scopulariopsis brevicaulis.