Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
8.4
4.0
Journals
JoF
Special Issues
Advances in Fungal Genomics and Biotechnology: From Codon Optimization to...
share announcement

Advances in Fungal Genomics and Biotechnology: From Codon Optimization to Protein Expression

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: 31 July 2026 | Viewed by 1300

Special Issue Editors

Dr. Mian Zhou

E-Mail Website
Guest Editor
State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
Interests: yeast; gene transcription regulation, protein translation efficiency; recombinant expression systems
Dr. Wei Wang

E-Mail Website
Guest Editor
State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
Interests: filamentous fungal engineering; industrial enzyme production; transcriptional regulation mechanisms; synthetic biology

Special Issue Information

Dear Colleagues,

Recently, many fungi have emerged as pivotal chassis organisms for protein expression. Leveraging diversified biotechnologies such as promoter editing, codon optimization, and protein engineering can effectively enhance the expression efficiency of target proteins and increase industrial output. Mechanistic investigations into protein expression regulation provide critical molecular targets for these optimization paradigms. Valuable protein products can also be produced by organic waste from households or agriculture. This Special Issue aims to address the above hot research topics to produce insights into the green biomanufacturing importance of fungi.

This Special Issue of the Journal of Fungi aims to present state-of-the-art reviews and research articles on the topic of “Advances in Fungal Genomics and Biotechnology: From Codon Optimization to Protein Expression” in order to support sustainable bioproduction.

Dr. Mian Zhou
Dr. Wei Wang
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 250 words) can be sent to the Editorial Office for assessment.

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 2600 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.

Keywords

  • fungal chassis systems
  • protein expression optimization
  • genomic biotechnology

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

24 pages, 7122 KB  
Article
Transposable Element-Driven Genomic Plasticity: Unveiling the Evolutionary Mechanisms of Lifestyle Transition and Ecological Adaptation in Endophytic Fungi
by Yunfeng Lai, Cunzhong Fan, Zhibin Zhang, Riming Yan, Du Zhu and Huilin Yang
J. Fungi 2026, 12(4), 273; https://doi.org/10.3390/jof12040273 - 9 Apr 2026
Viewed by 394
Abstract
The genomic basis underlying the remarkable ecological flexibility of endophytic fungi (EF), particularly their potential to transition between symbiotic, saprophytic, and pathogenic lifestyles, remains poorly understood. Through comparative genomics of 75 Ascomycota and a validation set of 36 Fusarium genomes, we uncovered a [...] Read more.
The genomic basis underlying the remarkable ecological flexibility of endophytic fungi (EF), particularly their potential to transition between symbiotic, saprophytic, and pathogenic lifestyles, remains poorly understood. Through comparative genomics of 75 Ascomycota and a validation set of 36 Fusarium genomes, we uncovered a distinct pattern of genome evolution in EF, contrasting with the well-known “gene loss” model in obligate symbionts. Our analysis reveals that EF genomes are significantly expanded, primarily driven by the accumulation of DNA transposable elements (TEs). Crucially, this TE-mediated genomic plasticity is coupled with the retention and significant expansion of gene families for both saprotrophy and potential pathogenesis. We propose a novel “dual-trophic potential” model: TE-driven genomic expansion and plasticity provide the genetic raw material for EF to maintain a versatile repertoire of ecological tools, facilitating adaptive shifts across the endophytic–saprophytic–pathogenic continuum. This study reframes our understanding of fungal endophytism from a static symbiotic state to a dynamic, genetically enabled ecological strategy. Full article
(This article belongs to the Special Issue Advances in Fungal Genomics and Biotechnology: From Codon Optimization to Protein Expression)
►▼ Show Figures

Figure 1

16 pages, 5106 KB  
Article
Natural Selection Drives AT-Biased Codon Usage in Mitochondrial Genomes of Early-Diverging Conidiobolus Fungi (Zoopagomycota)
by Yanan Cao, Xianli Guo, Jialin Yang, Xiyue Yan, Yanping Xu, Qiang Li and Zehou Liu
J. Fungi 2026, 12(4), 231; https://doi.org/10.3390/jof12040231 - 24 Mar 2026
Viewed by 590
Abstract
Codon usage bias (CUB) in mitochondrial genomes reflects evolutionary forces such as mutation, selection, and genetic drift, yet its dynamics in early-diverging fungal lineages like Conidiobolus (Zoopagomycota) remain unclear. This study systematically analyzed mitochondrial core protein-coding genes (PCGs) from eight Conidiobolus species to [...] Read more.
Codon usage bias (CUB) in mitochondrial genomes reflects evolutionary forces such as mutation, selection, and genetic drift, yet its dynamics in early-diverging fungal lineages like Conidiobolus (Zoopagomycota) remain unclear. This study systematically analyzed mitochondrial core protein-coding genes (PCGs) from eight Conidiobolus species to elucidate the drivers of CUB and phylogenomic patterns. Nucleotide composition revealed pronounced AT richness (73.32% ± 3.38%) and low GC3 (13.40% ± 5.11%), indicating a preference for A/T-ending codons. Neutrality and ENC-GC3s plots demonstrated that natural selection, rather than mutation pressure, predominantly shaped codon bias, supported by weak GC12-GC3 correlations (slopes: 0.037–0.335) and significant ENC deviations from mutation-driven expectations. PR2-bias analysis further highlighted a strong bias toward A over T and C over G. Correspondence analysis linked major codon usage variations to GC3s, CAI, and FOP indices. Phylogenetic reconstructions based on relative synonymous codon usage (RSCU) and concatenated mitochondrial sequences revealed discordant topologies, particularly in the placement of C. polytocus and C. polyspermus, suggesting divergent evolutionary trajectories. Optimal codon analysis identified species-specific preferences dominated by A/T termini. These findings underscore natural selection as the primary force driving AT-biased mitochondrial CUB in Conidiobolus, while phylogenomic discordance highlights complex evolutionary pressures in this ecologically diverse fungal genus. This study provides foundational insights into mitochondrial genome evolution and codon adaptation mechanisms in early-diverging fungi. Full article
(This article belongs to the Special Issue Advances in Fungal Genomics and Biotechnology: From Codon Optimization to Protein Expression)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-2
Back to TopTop