OMICS and Other Advanced Technologies in Mycological Applications

Abstract

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.

Gut Mycobiome and Asthma

“…Expanding the research to include a wider range of ethnic and geographical populations is also important, as the gut mycobiome shows significant variability across populations, even within the same regions of the world [ 85 ]. Additionally, integrating multi-omics approaches, including proteomics, metabolomics, and transcriptomics from gut fungi, provides a more nuanced view of how alterations in the gut mycobiome may exacerbate airway inflammation [ 86 ]. Expanding this approach to include bacterial and fungal microbiome data from various body sites, particularly the lungs and upper airways, can enhance our understanding of the complex interactions and implications of microbiome changes on respiratory health [ 87 ].…”

Current Advances in the Functional Genes of Edible and Medicinal Fungi: Research Techniques, Functional Analysis, and Prospects

“…Despite the many benefits, there are still certain limitations to genomics technologies. For example, genomics can only provide information about metabolic potential, metabolomics and proteomics show poor reproducibility, there are limitations in multi-omics technology in annotating and interpreting the functions of individual genes and molecules, and omics technologies are relatively homogenously applied [35]. Most of the genomes of edible and medicinal fungi that have been sequenced thus far are single genomes, which do not cover a wide range of genetic diversity and are difficult to study.…”

Comparative genomic analyses provide insight into the pathogenicity of three Pseudomonas syringae pv. actinidiae strains from Anhui Province, China

“…Recently, whole genome sequencing (WGS) strategies towards phytopathogens have provided high-quality sequences to characterize virulence-associated genes [ 13 ] and uncovered pathogenic mechanisms for attacking plants [ 14 ]. With decreased sequencing costs and rapid development of sequencing techniques, the genomes of diverse bacterial strains have been sequenced.…”