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Fungal '-Omics': Is the Best Yet to Come?
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Fungal '-Omics': Is the Best Yet to Come?

A special issue of Journal of Fungi (ISSN 2309-608X).

Deadline for manuscript submissions: closed (31 January 2016) | Viewed by 39880

Special Issue Editor

Prof. Dr. Luis V. Lopez-Llorca

E-Mail Website
Guest Editor
Multidisciplinary Institute for Environmental Studies/Department of Marine Sciences and Applied Biology, University of Alicante, Apdo. 99, E-03080 Alicante, Spain
Interests: biocontrol; nematophagous fungi; entomopathogenic fungi; chitosan; plant pathology; endophytes; fungal "omics"
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Fungi are amazing organisms with a unique lifestyle based on their cellular and filamentous bodies and their nutrition is based on the secretion of extracellular enzymes in their environments. They interact both with these environments and also with the organisms that live in them. This has resulted in a broad fungal diversity with an even broader framework of fungal interactions. Some of these interactions result in important plant and animal diseases, and others can be exploited to control fungal and other pathogens. In the environment, fungi are the major decomposers of biomass and play an essential role in biogeochemical cycling. For this purpose they are being developed as a source of biofuels. Fungi are also used as cell factories to produce antibiotics, enzymes, and other compounds for diverse industrial uses. Sequencing technologies and Bioinformatics have had, and will have, a deep impact on mycology. With ca. half of the 1000 Fungal Genomes Project (www.1000.fungalgenome.org) completed, Fungal-omics has come of age. Fungal-omics has implications in Fungal Evolution, Fungal Pathogenicity, and Fungal Ecology, just to give a few examples. Finally, Fungal Biotechnology will, with the help of Fungal-omics, partly turn into synthetic genomics in which fungi will have a lot to offer.

Topics including but not limited to:

-Sequencing technologies and Bioinformatics
Impact of next generation NGS on fungal-omics
Single molecule sequencing impact in mycology
Bioinformatics tools for Fungal-omics: available and required
-Fungal Evolution
Genome wide association studies (GWAS) and population genomics of fungi
Evolutionary and Comparative Fungal Genomics
-Fungal Pathogens and Pathogenicity
Molecular controls of cell death in fungi
Omics in early detection and epidemiology of fungal pathogens
Comparative and Functional Genomics of Fungal Pathogens
Genomics of fungal host-specificity and evasion of host immunity
Antifungals: Genomics and the search for new targets
Fungal metabolomics: a source for new-paradigm drugs and agrochemicals?
-Fungal Interactions and Ecology
Fungal Interactomics. Mycorrhizae and other fungal endophytes.
Fungus-invertebrate interactions
Fungal-omics and host behavior modification
Metagenomics and Fungal Ecology
-Fungal Biotechnology
Fungal Proteomics
Fungal CAZYs and Glycogenomics
Synthetic genomics. What are fungi to offer?
-Functional Fungal Genomics: Fungal Transcriptomics and beyond
-Fungal Epigenomics

Prof. Dr. Luis V. Lopez-Llorca
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

  • NGS
  • bioinformatics
  • fungal genomics
  • fungal proteomics
  • fungal metabolomics
  • functional fungal genomics
  • evolutionary fungal genomics
  • fungal synthetic biology

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Published Papers (5 papers)

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Research

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4492 KiB  
Article
Proteomic Analysis of Pathogenic Fungi Reveals Highly Expressed Conserved Cell Wall Proteins
by Jackson Champer, James I. Ito, Karl V. Clemons, David A. Stevens and Markus Kalkum
J. Fungi 2016, 2(1), 6; https://doi.org/10.3390/jof2010006 - 12 Jan 2016
Cited by 42 | Viewed by 9757
Abstract
We are presenting a quantitative proteomics tally of the most commonly expressed conserved fungal proteins of the cytosol, the cell wall, and the secretome. It was our goal to identify fungi-typical proteins that do not share significant homology with human proteins. Such fungal [...] Read more.
We are presenting a quantitative proteomics tally of the most commonly expressed conserved fungal proteins of the cytosol, the cell wall, and the secretome. It was our goal to identify fungi-typical proteins that do not share significant homology with human proteins. Such fungal proteins are of interest to the development of vaccines or drug targets. Protein samples were derived from 13 fungal species, cultured in rich or in minimal media; these included clinical isolates of Aspergillus, Candida, Mucor, Cryptococcus, and Coccidioides species. Proteomes were analyzed by quantitative MSE (Mass Spectrometry—Elevated Collision Energy). Several thousand proteins were identified and quantified in total across all fractions and culture conditions. The 42 most abundant proteins identified in fungal cell walls or supernatants shared no to very little homology with human proteins. In contrast, all but five of the 50 most abundant cytosolic proteins had human homologs with sequence identity averaging 59%. Proteomic comparisons of the secreted or surface localized fungal proteins highlighted conserved homologs of the Aspergillus fumigatus proteins 1,3-β-glucanosyltransferases (Bgt1, Gel1-4), Crf1, Ecm33, EglC, and others. The fact that Crf1 and Gel1 were previously shown to be promising vaccine candidates, underlines the value of the proteomics data presented here. Full article
(This article belongs to the Special Issue Fungal '-Omics': Is the Best Yet to Come?)
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1122 KiB  
Article
The Biological Diversity and Production of Volatile Organic Compounds by Stem-Inhabiting Endophytic Fungi of Ecuador
by Susan M. Rundell, Daniel J. Spakowicz, Alexandra Narváez-Trujillo and Scott A. Strobel
J. Fungi 2015, 1(3), 384-396; https://doi.org/10.3390/jof1030384 - 2 Dec 2015
Cited by 7 | Viewed by 6757
Abstract
Fungal endophytes colonize every major lineage of land plants without causing apparent harm to their hosts. Despite their production of interesting and potentially novel compounds, endophytes—particularly those inhabiting stem tissues—are still a vastly underexplored component of microbial diversity. In this study, we explored [...] Read more.
Fungal endophytes colonize every major lineage of land plants without causing apparent harm to their hosts. Despite their production of interesting and potentially novel compounds, endophytes—particularly those inhabiting stem tissues—are still a vastly underexplored component of microbial diversity. In this study, we explored the diversity of over 1500 fungal endophyte isolates collected from three Ecuadorian ecosystems: lowland tropical forest, cloud forest, and coastal dry forest. We sought to determine whether Ecuador’s fungal endophytes are hyperdiverse, and whether that biological diversity is reflected in the endophytes’ chemical diversity. To assess this chemical diversity, we analyzed a subset of isolates for their production of volatile organic compounds (VOCs), a representative class of natural products. This study yielded a total of 1526 fungal ITS sequences comprising some 315 operational taxonomic units (OTUs), resulting in a non-asymptotic OTU accumulation curve and characterized by a Fisher’s α of 120 and a Shannon Diversity score of 7.56. These figures suggest that the Ecuadorian endophytes are hyperdiverse. Furthermore, the 113 isolates screened for VOCs produced more than 140 unique compounds. These results present a mere snapshot of the remarkable biological and chemical diversity of stem-inhabiting endophytic fungi from a single neotropical country. Full article
(This article belongs to the Special Issue Fungal '-Omics': Is the Best Yet to Come?)
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Review

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2130 KiB  
Review
Omics for Investigating Chitosan as an Antifungal and Gene Modulator
by Federico Lopez-Moya and Luis V. Lopez-Llorca
J. Fungi 2016, 2(1), 11; https://doi.org/10.3390/jof2010011 - 3 Mar 2016
Cited by 28 | Viewed by 5685
Abstract
Chitosan is a biopolymer with a wide range of applications. The use of chitosan in clinical medicine to control infections by fungal pathogens such as Candida spp. is one of its most promising applications in view of the reduced number of antifungals available. [...] Read more.
Chitosan is a biopolymer with a wide range of applications. The use of chitosan in clinical medicine to control infections by fungal pathogens such as Candida spp. is one of its most promising applications in view of the reduced number of antifungals available. Chitosan increases intracellular oxidative stress, then permeabilizes the plasma membrane of sensitive filamentous fungus Neurospora crassa and yeast. Transcriptomics reveals plasma membrane homeostasis and oxidative metabolism genes as key players in the response of fungi to chitosan. A lipase and a monosaccharide transporter, both inner plasma membrane proteins, and a glutathione transferase are main chitosan targets in N. crassa. Biocontrol fungi such as Pochonia chlamydosporia have a low content of polyunsaturated free fatty acids in their plasma membranes and are resistant to chitosan. Genome sequencing of P. chlamydosporia reveals a wide gene machinery to degrade and assimilate chitosan. Chitosan increases P. chlamydosporia sporulation and enhances parasitism of plant parasitic nematodes by the fungus. Omics studies allow understanding the mode of action of chitosan and help its development as an antifungal and gene modulator. Full article
(This article belongs to the Special Issue Fungal '-Omics': Is the Best Yet to Come?)
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1430 KiB  
Review
Genome Studies on Nematophagous and Entomogenous Fungi in China
by Weiwei Zhang, Xiaoli Cheng, Xingzhong Liu and Meichun Xiang
J. Fungi 2016, 2(1), 9; https://doi.org/10.3390/jof2010009 - 5 Feb 2016
Cited by 10 | Viewed by 6625
Abstract
The nematophagous and entomogenous fungi are natural enemies of nematodes and insects and have been utilized by humans to control agricultural and forestry pests. Some of these fungi have been or are being developed as biological control agents in China and worldwide. Several [...] Read more.
The nematophagous and entomogenous fungi are natural enemies of nematodes and insects and have been utilized by humans to control agricultural and forestry pests. Some of these fungi have been or are being developed as biological control agents in China and worldwide. Several important nematophagous and entomogenous fungi, including nematode-trapping fungi (Arthrobotrys oligospora and Drechslerella stenobrocha), nematode endoparasite (Hirsutella minnesotensis), insect pathogens (Beauveria bassiana and Metarhizium spp.) and Chinese medicinal fungi (Ophiocordyceps sinensis and Cordyceps militaris), have been genome sequenced and extensively analyzed in China. The biology, evolution, and pharmaceutical application of these fungi and their interacting with host nematodes and insects revealed by genomes, comparing genomes coupled with transcriptomes are summarized and reviewed in this paper. Full article
(This article belongs to the Special Issue Fungal '-Omics': Is the Best Yet to Come?)
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1676 KiB  
Review
Transcriptomic Crosstalk between Fungal Invasive Pathogens and Their Host Cells: Opportunities and Challenges for Next-Generation Sequencing Methods
by Francisco J. Enguita, Marina C. Costa, Ana Marisa Fusco-Almeida, Maria José Mendes-Giannini and Ana Lúcia Leitão
J. Fungi 2016, 2(1), 7; https://doi.org/10.3390/jof2010007 - 14 Jan 2016
Cited by 17 | Viewed by 10055
Abstract
Fungal invasive infections are an increasing health problem. The intrinsic complexity of pathogenic fungi and the unmet clinical need for new and more effective treatments requires a detailed knowledge of the infection process. During infection, fungal pathogens are able to trigger a specific [...] Read more.
Fungal invasive infections are an increasing health problem. The intrinsic complexity of pathogenic fungi and the unmet clinical need for new and more effective treatments requires a detailed knowledge of the infection process. During infection, fungal pathogens are able to trigger a specific transcriptional program in their host cells. The detailed knowledge of this transcriptional program will allow for a better understanding of the infection process and consequently will help in the future design of more efficient therapeutic strategies. Simultaneous transcriptomic studies of pathogen and host by high-throughput sequencing (dual RNA-seq) is an unbiased protocol to understand the intricate regulatory networks underlying the infectious process. This protocol is starting to be applied to the study of the interactions between fungal pathogens and their hosts. To date, our knowledge of the molecular basis of infection for fungal pathogens is still very limited, and the putative role of regulatory players such as non-coding RNAs or epigenetic factors remains elusive. The wider application of high-throughput transcriptomics in the near future will help to understand the fungal mechanisms for colonization and survival, as well as to characterize the molecular responses of the host cell against a fungal infection. Full article
(This article belongs to the Special Issue Fungal '-Omics': Is the Best Yet to Come?)
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