OMICS and Other Advanced Technologies in Mycological Applications

• Published in: Journal of fungi (Basel) 2023-06, Vol.9 (6), p.688
• Main Authors: Wijayawardene, Nalin N, Boonyuen, Nattawut, Ranaweera, Chathuranga B, de Zoysa, Heethaka K S, Padmathilake, Rasanie E, Nifla, Faarah, Dai, Dong-Qin, Liu, Yanxia, Suwannarach, Nakarin, Kumla, Jaturong, Bamunuarachchige, Thushara C, Chen, Huan-Huan
• Format: Article
• Language: English
• Subjects: Bar codes; Bioinformatics; Biology; Book publishing; dark taxa; DNA sequencing; Drug development; Drug resistance; Ecosystems; Evolution; fungal metabolites; fungal taxonomy; Fungi; Genes; Genomes; high-throughput sequencing; Ions; Metabolites; Metabolomics; Metagenomics; Morphology; multiomics approaches; Next-generation sequencing; Nucleotide sequencing; phylogenetic analysis; Phylogenetics; Phylogeny; Physical characteristics; Plant metabolites; Polymerase chain reaction; Proteins; Proteomics; Review; RNA polymerase; Secondary metabolites; Taxonomy; Technology application; Therapeutic applications; Transcriptomics
• ISSN: 2309-608X; 2309-608X
• DOI: 10.3390/jof9060688

Fungi play many roles in different ecosystems. The precise identification of fungi is important in different aspects. Historically, they were identified based on morphological characteristics, but technological advancements such as polymerase chain reaction (PCR) and DNA sequencing now enable more accurate identification and taxonomy, and higher-level classifications. However, some species, referred to as "dark taxa", lack distinct physical features that makes their identification challenging. High-throughput sequencing and metagenomics of environmental samples provide a solution to identifying new lineages of fungi. This paper discusses different approaches to taxonomy, including PCR amplification and sequencing of rDNA, multi-loci phylogenetic analyses, and the importance of various omics (large-scale molecular) techniques for understanding fungal applications. The use of proteomics, transcriptomics, metatranscriptomics, metabolomics, and interactomics provides a comprehensive understanding of fungi. These advanced technologies are critical for expanding the knowledge of the Kingdom of Fungi, including its impact on food safety and security, edible mushrooms foodomics, fungal secondary metabolites, mycotoxin-producing fungi, and biomedical and therapeutic applications, including antifungal drugs and drug resistance, and fungal omics data for novel drug development. The paper also highlights the importance of exploring fungi from extreme environments and understudied areas to identify novel lineages in the fungal dark taxa.