Special Issue "Genome Editing Tools in Fungi"

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungal Genomics, Genetics and Molecular Biology".

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 1505

Special Issue Editors

Agriculture & Agri-Food Canada, Ontario, Canada
Interests: mycology; metabolomics; integrated ‘omics’; synthetic biology; bioproducts discovery; natural product chemistry
Agriculture & Agri-Food Canada, Ontario, Canada
Interests: plant–pathogen interactions; effector biology; regulation of secondary metabolism; chemical genetics
Special Issues, Collections and Topics in MDPI journals
Empresa Brasileira de Pesquisa Agropecuária-EMBRAPA Genetic Resources and Biotechnology, Brasilia, Brazil
Interests: microbiology; integrated metabolomics and genomics; synthetic biology; natural polymers; biomaterials

Special Issue Information

Dear Colleagues,

Breakthrough technologies in gene editing and advances in computational biology are enabling scientists from across disciplines, such as biology, bioinformatics, and engineering, to tweak biological systems to reach desired goals. Innovations in CRISPR-Cas9 technology are rapidly advancing our knowledge of gene function at a significant speed and precision. Gene editing by the CRISPR-Cas9 system has been established in more than 40 different species of filamentous fungi (including Aspergillus, Fusarium, and Sclerotinia) and oomycetes. In addition to disrupting genes, this system has also been adapted for gene replacement and for precision editing (nucleotide changes) in fungi.

This Special Issue will focus on several key aspects and advancements in the field of gene editing in fungi. How gene editing is advancing our knowledge in inter- and intra-species interations, microbiome, microbial evolution, metabolism, and bioproduct discovery, etc., is within the scope of this Special Issue. The use of gene editing in various synthetic biology platforms will also be considered. In addition to primary research articles, we are also seeking articles that offer new perspectives in the use of this technology to further our knowledge in basic sciences and its use in synthetic biology platforms, gene and meiotic drives, etc.

Dr. David P. Overy
Dr. Rajagopal Subramaniam
Dr. Daniela Matias de Carvalho Bittencourt
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Journal of Fungi is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


  • gene editing
  • functional genetics
  • synthetic biology
  • integrated ‘omics’

Published Papers (1 paper)

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Advances and Challenges in CRISPR/Cas-Based Fungal Genome Engineering for Secondary Metabolite Production: A Review
J. Fungi 2023, 9(3), 362; https://doi.org/10.3390/jof9030362 - 15 Mar 2023
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Fungi represent an important source of bioactive secondary metabolites (SMs), which have wide applications in many fields, including medicine, agriculture, human health, and many other industries. The genes involved in SM biosynthesis are usually clustered adjacent to each other into a region known [...] Read more.
Fungi represent an important source of bioactive secondary metabolites (SMs), which have wide applications in many fields, including medicine, agriculture, human health, and many other industries. The genes involved in SM biosynthesis are usually clustered adjacent to each other into a region known as a biosynthetic gene cluster (BGC). The recent advent of a diversity of genetic and genomic technologies has facilitated the identification of many cryptic or uncharacterized BGCs and their associated SMs. However, there are still many challenges that hamper the broader exploration of industrially important secondary metabolites. The recent advanced CRISPR/Cas system has revolutionized fungal genetic engineering and enabled the discovery of novel bioactive compounds. In this review, we firstly introduce fungal BGCs and their relationships with associated SMs, followed by a brief summary of the conventional strategies for fungal genetic engineering. Next, we introduce a range of state-of-the-art CRISPR/Cas-based tools that have been developed and review recent applications of these methods in fungi for research on the biosynthesis of SMs. Finally, the challenges and limitations of these CRISPR/Cas-based systems are discussed and directions for future research are proposed in order to expand their applications and improve efficiency for fungal genetic engineering. Full article
(This article belongs to the Special Issue Genome Editing Tools in Fungi)
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