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Fungal Growth and Development Based on Functional Genomics and Microbiomics
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Fungal Growth and Development Based on Functional Genomics and Microbiomics

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: 30 August 2025 | Viewed by 2458

Special Issue Editor

Prof. Dr. Caihong Dong

E-Mail Website1 Website2
Guest Editor
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
Interests: growth and development; cordyceps; mushroom; gene editing; mycoparasite

Special Issue Information

Dear Colleagues,

The Special Issue, titled "Fungal Growth and Development Based on Functional Genomics and Microbiomics", aims to explore the intricate mechanisms governing fungal growth and development, as well as their interactions with microbial communities, through cutting-edge genomic and microbiomic technologies. This Issue seeks to gather innovative research that elucidates the genetic mechanisms underpinning fungal development, growth patterns, and interactions within diverse microbial communities. By integrating functional genomics and microbiome analyses, we aim to uncover how environmental factors, host interactions, and microbial cohabitation influence fungal behavior and physiology. Contributions may include studies on gene expression profiling, metabolic pathways, symbiotic partnerships, and the role of environmental stresses in shaping fungal communities. The overarching goal is to advance our understanding of fungal biology and its ecological significance, providing insights that could lead to novel applications in agriculture, biotechnology, and medicine. We invite researchers from various disciplines to submit their findings and contribute to this growing field of study.

Prof. Dr. Caihong Dong
Guest Editor

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 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

  • growth and development
  • functional genomics
  • microbiomics
  • interaction
  • fungi

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

Published Papers (3 papers)

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Research

19 pages, 7233 KiB  
Article
Whole-Genome Sequencing of Flammulina filiformis and Multi-Omics Analysis in Response to Low Temperature
by Xinmin Liang, Jing Han, Yuqin Cui, Xueqin Shu, Mengting Lei, Bo Wang, Dinghong Jia, Weihong Peng, Xiaolan He and Xun Liu
J. Fungi 2025, 11(3), 229; https://doi.org/10.3390/jof11030229 - 17 Mar 2025
Viewed by 583
Abstract
The growth of Flammulina filiformis is strongly dependent on low-temperature cues for the initiation of primordia formation. To obtain a comprehensive understanding of the molecular mechanisms that govern the mycelial response to cold stress, de novo genome sequencing of the F. filiformis monokaryon [...] Read more.
The growth of Flammulina filiformis is strongly dependent on low-temperature cues for the initiation of primordia formation. To obtain a comprehensive understanding of the molecular mechanisms that govern the mycelial response to cold stress, de novo genome sequencing of the F. filiformis monokaryon and multi-omics data (transcriptome and metabolome) analyses of the mycelia, primordia, and fruiting bodies were conducted in the present study. Genome sequencing based on PacBio HiFi and Hi-C resulted in a 36.3 Mb genome sequence that mapped to 12 chromosomes, comprising 11,886 protein-coding genes. A total of 25 cold-responsive (COR) genes and 520 cold-adapted enzymes were identified in the genome. Multi-omics analyses showed that the pathways related to carbohydrate metabolism in the mycelia under low temperature (10 °C) were significantly enriched. Further examination of the expression profiles of carbohydrate-active enzymes (CAZymes) involved in carbohydrate metabolism revealed that out of 515 CAZyme genes in F. filiformis, 58 were specifically upregulated in mycelia under low-temperature conditions. By contrast, the expression levels of these genes in primordia and fruiting bodies reverted to those prior to low-temperature exposure. These indicate that CAZyme genes are important for the low-temperature adaptation of F. filiformis. This research contributes to the targeted breeding of F. filiformis. Full article
(This article belongs to the Special Issue Fungal Growth and Development Based on Functional Genomics and Microbiomics)
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17 pages, 7327 KiB  
Article
SsNEP2 Plays a Role in the Interaction Between Sclerotinia sclerotiorum and Coniothyrium minitans
by Huizhang Zhao, Zihang Zhu, Yueli Xu, Haixuan Wang, Jiatao Xie, Jiasen Cheng, Daohong Jiang and Yanping Fu
J. Fungi 2025, 11(2), 151; https://doi.org/10.3390/jof11020151 - 16 Feb 2025
Viewed by 671
Abstract
Sclerotinia sclerotiorum, a fungal pathogen that is spread worldwide and causes serious diseases on crops, can be parasitized specifically by the mycoparasite Coniothyrium minitans. SsNEP2, encoding a necrosis-inducing protein in S. sclerotiorum, was previously inferred to play a role in the [...] Read more.
Sclerotinia sclerotiorum, a fungal pathogen that is spread worldwide and causes serious diseases on crops, can be parasitized specifically by the mycoparasite Coniothyrium minitans. SsNEP2, encoding a necrosis-inducing protein in S. sclerotiorum, was previously inferred to play a role in the virulence to host plants. In this study, silencing of SsNEP2 in S. sclerotiorum had no significant (p < 0.01) influence on mycelial morphology, while overexpression led to lower mycelial growth and more branches. When amended with the fermentation broth of the SsNEP2 silencing mutants, conidial germination of C. minitans was promoted, while conidial production decreased. When parasitized by C. minitans, enhanced resistance of the SsNEP2 silencing mutants and weaker resistance of the overexpressed transformants were observed compared to the wild-type S. sclerotiorum strain 1980. In addition, the expression of SsNEP2 in C. minitans enhanced mycelial parasitism on S. sclerotiorum and restored the effect of silencing SsNEP2 in S. sclerotiorum on mycoparasitism. Thus, we highlight the role of SsNEP2 as a PAMP-like protein in the mycoparasitism between C. minitans and its host fungus S. sclerotiorum. SsNEP2 can be used to promote the biological potential of C. minitans. Full article
(This article belongs to the Special Issue Fungal Growth and Development Based on Functional Genomics and Microbiomics)
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17 pages, 7903 KiB  
Article
Characterization of Endofungal Bacteria and Their Role in the Ectomycorrhizal Fungus Helvella bachu
by Caihong Wei, Mengqian Liu, Guoliang Meng, Miao Wang, Xin Zhou, Jianping Xu, Jianwei Hu, Lili Zhang and Caihong Dong
J. Fungi 2024, 10(12), 889; https://doi.org/10.3390/jof10120889 - 23 Dec 2024
Cited by 1 | Viewed by 915
Abstract
Helvella bachu, an ectomycorrhizal fungus, forms a symbiotic relationship with Populus euphratica, a rare and endangered species crucial to desert riparian ecosystems. In this study, endofungal bacteria (EFBs) within the fruiting bodies of H. bachu were confirmed by a polyphasic approach, [...] Read more.
Helvella bachu, an ectomycorrhizal fungus, forms a symbiotic relationship with Populus euphratica, a rare and endangered species crucial to desert riparian ecosystems. In this study, endofungal bacteria (EFBs) within the fruiting bodies of H. bachu were confirmed by a polyphasic approach, including genomic sequencing, real-time quantitative PCR targeting the 16S rRNA gene, full-length and next-generation sequencing (NGS) of the 16S rRNA gene, and culture methods. The genera Stenotrophomonas, Variovorax, Acidovorax, and Pedobacter were abundant in the EFBs of fruiting bodies associated with three Populus hosts and were consistently present across different developmental stages. Notably, S. maltophilia and V. paradoxus were detected in high abundance, as revealed by full-length 16S rRNA sequencing, with S. maltophilia also isolated by culture methods. KO-pathway analysis indicated that pathways related to primary, secondary, and energy metabolism were predominantly enriched, suggesting these bacteria may promote H. bachu growth by producing essential compounds, including sugars, proteins, and vitamins, and secondary metabolites. This study confirmed the presence of EFBs in H. bachu and provided the first comprehensive overview of their structure, functional potential, and dynamic changes throughout fruiting body maturation, offering valuable insights for advancing the artificial domestication of this species. Full article
(This article belongs to the Special Issue Fungal Growth and Development Based on Functional Genomics and Microbiomics)
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