Developing Functional Genomics Platforms for Fungi

Huberman, Lori B.

doi:10.1128/msystems.00730-21

Cited by 4 publications

(1 citation statement)

References 23 publications

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“…For instance, these omics techniques can be used in mycological synthetic biology and fungal biotechnology applications such as fungal gene function [ 60 ], fungal survival under temperature stress [ 61 ], Candida albicans biofilm formation and drug resistance [ 62 ], and fungal communities in forest soils [ 63 ]. The integration of cutting-edge sequencing technologies and bioinformatics techniques in mycological research has led to a marked advancement in the field.…”

Section: Approaches In Taxonomy and Classificationmentioning

confidence: 99%

OMICS and Other Advanced Technologies in Mycological Applications

Wijayawardene,

Boonyuen,

Ranaweera

et al. 2023

JoF

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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.

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Section: Approaches In Taxonomy and Classificationmentioning

confidence: 99%

OMICS and Other Advanced Technologies in Mycological Applications

Wijayawardene,

Boonyuen,

Ranaweera

et al. 2023

JoF

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Impact of Fungi on the World Economy and Its Sustainability: Current Status and Potentials

Singh¹,

Thakur²

2023

Fungal Resources for Sustainable Economy

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Current trends, limitations and future research in the fungi?

Hyde,

Baldrian,

Chen

et al. 2024

Fungal Diversity

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The field of mycology has grown from an underappreciated subset of botany, to a valuable, modern scientific discipline. As this field of study has grown, there have been significant contributions to science, technology, and industry, highlighting the value of fungi in the modern era. This paper looks at the current research, along with the existing limitations, and suggests future areas where scientists can focus their efforts, in the field mycology. We show how fungi have become important emerging diseases in medical mycology. We discuss current trends and the potential of fungi in drug and novel compound discovery. We explore the current trends in phylogenomics, its potential, and outcomes and address the question of how phylogenomics can be applied in fungal ecology. In addition, the trends in functional genomics studies of fungi are discussed with their importance in unravelling the intricate mechanisms underlying fungal behaviour, interactions, and adaptations, paving the way for a comprehensive understanding of fungal biology. We look at the current research in building materials, how they can be used as carbon sinks, and how fungi can be used in biocircular economies. The numbers of fungi have always been of great interest and have often been written about and estimates have varied greatly. Thus, we discuss current trends and future research needs in order to obtain more reliable estimates. We address the aspects of machine learning (AI) and how it can be used in mycological research. Plant pathogens are affecting food production systems on a global scale, and as such, we look at the current trends and future research needed in this area, particularly in disease detection. We look at the latest data from High Throughput Sequencing studies and question if we are still gaining new knowledge at the same rate as before. A review of current trends in nanotechnology is provided and its future potential is addressed. The importance of Arbuscular Mycorrhizal Fungi is addressed and future trends are acknowledged. Fungal databases are becoming more and more important, and we therefore provide a review of the current major databases. Edible and medicinal fungi have a huge potential as food and medicines, especially in Asia and their prospects are discussed. Lifestyle changes in fungi (e.g., from endophytes, to pathogens, and/or saprobes) are also extremely important and a current research trend and are therefore addressed in this special issue of Fungal Diversity.

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Developing Functional Genomics Platforms for Fungi

Abstract: Fungi are responsible for diseases that result in the deaths of over a million individuals each year and devastating crop infestations that threaten global food supplies. However, outside of a select few model organisms, the majority of fungal genes are uncharacterized.

Cited by 4 publications

References 23 publications

OMICS and Other Advanced Technologies in Mycological Applications

OMICS and Other Advanced Technologies in Mycological Applications

Impact of Fungi on the World Economy and Its Sustainability: Current Status and Potentials

Current trends, limitations and future research in the fungi?

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