Genomic Data in Pathogenic Fungi

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

Deadline for manuscript submissions: closed (30 November 2017) | Viewed by 34808

Special Issue Editor


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Guest Editor
Departments of Pathology and Medicine, University of California, San Diego, School of Medicine, San Diego, CA 92161, USA
Interests: coccidioidomycosis; valley fever; fungal genomics; vaccine development
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Special Issue Information

Dear Colleagues,

We are soliciting articles describing genomes, transcriptomes, regulation of transcription and proteomic data relating to the pathogenicity of primary pathogenic fungi and opportunistic fungi. Studies of phylogeny of pathogenic fungi will also fall within the scope of this Special Issue. Data about genes or networks that are associated with pathogenesis and/or dimorphism are of particular interest. Both original data and reviews of published data are appropriate. Human pathogens will be given preference, although fungi that cause disease in other organisms will be considered.

Prof. Dr. Theo N. Kirkland
Guest editor

Manuscript Submission Information

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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

  • Fungi
  • Pathogenesis
  • Dimorphism
  • Genomics
  • Gene expression
  • Phylogeny

Published Papers (5 papers)

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Editorial

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2 pages, 139 KiB  
Editorial
Special Issue: Genomic Data in Pathogenic Fungi
by Theo N. Kirkland
J. Fungi 2018, 4(1), 40; https://doi.org/10.3390/jof4010040 - 20 Mar 2018
Viewed by 2911
(This article belongs to the Special Issue Genomic Data in Pathogenic Fungi)

Research

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13 pages, 3148 KiB  
Article
Analysis of Transposable Elements in Coccidioides Species
by Theo N. Kirkland, Anna Muszewska and Jason E. Stajich
J. Fungi 2018, 4(1), 13; https://doi.org/10.3390/jof4010013 - 19 Jan 2018
Cited by 15 | Viewed by 5130
Abstract
Coccidioides immitis and C. posadasii are primary pathogenic fungi that cause disease in immunologically-normal animals and people. The organism is found exclusively in arid regions of the Southwestern United States, Mexico, and South America, but not in other parts of the world. This [...] Read more.
Coccidioides immitis and C. posadasii are primary pathogenic fungi that cause disease in immunologically-normal animals and people. The organism is found exclusively in arid regions of the Southwestern United States, Mexico, and South America, but not in other parts of the world. This study is a detailed analysis of the transposable elements (TE) in Coccidioides spp. As is common in most fungi, Class I and Class II transposons were identified and the LTR Gypsy superfamily is the most common. The minority of Coccidioides Gypsy transposons contained regions highly homologous to polyprotein domains. Phylogenetic analysis of the integrase and reverse transcriptase sequences revealed that many, but not all, of the Gypsy reverse transcriptase and integrase domains clustered by species suggesting extensive transposition after speciation of the two Coccidiodies spp. The TEs were clustered and the distribution is enriched for the ends on contigs. Analysis of gene expression data from C. immitis found that protein-coding genes within 1 kB of hAT or Gypsy TEs were poorly expressed. The expression of C. posadasii genes within 1 kB of Gypsy TEs was also significantly lower compared to all genes but the difference in expression was smaller than C. immitis. C. posadasii orthologs of C. immitis Gyspsy-associated genes were also likely to be TE-associated. In both C. immitis and C. posadasii the TEs were preferentially associated with genes annotated with protein kinase gene ontology terms. These observations suggest that TE may play a role in influencing gene expression in Coccidioides spp. Our hope is that these bioinformatic studies of the potential TE influence on expression and evolution of Coccidioides will prompt the development of testable hypotheses to better understand the role of TEs in the biology and gene regulation of Coccidioides spp. Full article
(This article belongs to the Special Issue Genomic Data in Pathogenic Fungi)
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18 pages, 1710 KiB  
Article
Candidate Genes for Aggressiveness in a Natural Fusarium culmorum Population Greatly Differ between Wheat and Rye Head Blight
by Valheria Castiblanco, Hilda Elena Castillo and Thomas Miedaner
J. Fungi 2018, 4(1), 14; https://doi.org/10.3390/jof4010014 - 16 Jan 2018
Cited by 15 | Viewed by 4982
Abstract
Fusarium culmorum is one of the species causing Fusarium head blight (FHB) in cereals in Europe. We aimed to investigate the association between the nucleotide diversity of ten F. culmorum candidate genes and field ratings of aggressiveness in winter rye. A total of [...] Read more.
Fusarium culmorum is one of the species causing Fusarium head blight (FHB) in cereals in Europe. We aimed to investigate the association between the nucleotide diversity of ten F. culmorum candidate genes and field ratings of aggressiveness in winter rye. A total of 100 F. culmorum isolates collected from natural infections were phenotyped for FHB at two locations and two years. Variance components for aggressiveness showed significant isolate and isolate-by-environment variance, as expected for quantitative host-pathogen interactions. Further analysis of the isolate-by-environment interaction revealed the dominant role of the isolate-by-year over isolate-by-location interaction. One single-nucleotide polymorphism (SNP) in the cutinase (CUT) gene was found to be significantly (p < 0.001) associated with aggressiveness and explained 16.05% of the genotypic variance of this trait in rye. The SNP was located 60 base pairs before the start codon, which suggests a role in transcriptional regulation. Compared to a previous study in winter wheat with the same nucleotide sequences, a larger variation of pathogen aggressiveness on rye was found and a different candidate gene was associated with pathogen aggressiveness. This is the first report on the association of field aggressiveness and a host-specific candidate gene codifying for a protein that belongs to the secretome in F. culmorum. Full article
(This article belongs to the Special Issue Genomic Data in Pathogenic Fungi)
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2938 KiB  
Article
Diversity of Cell Wall Related Proteins in Human Pathogenic Fungi
by Anna Muszewska, Sebastian Piłsyk, Urszula Perlińska-Lenart and Joanna S. Kruszewska
J. Fungi 2018, 4(1), 6; https://doi.org/10.3390/jof4010006 - 29 Dec 2017
Cited by 23 | Viewed by 6203
Abstract
The cell wall is one of the major keys to fungal identity. Fungi use their cell wall to sense the environment, and localize nutrients and competing microorganism. Pathogenic species additionally modify their cell walls to hide from a host’s immune system. With the [...] Read more.
The cell wall is one of the major keys to fungal identity. Fungi use their cell wall to sense the environment, and localize nutrients and competing microorganism. Pathogenic species additionally modify their cell walls to hide from a host’s immune system. With the growing number of fungal infections and alarming shortage of available drugs, we are in need of new approaches to fight pathogens. The cell wall seems to be a natural target, since animal host cells are devoid of it. The current knowledge about fungal cell wall components is often limited, and there is huge diversity both in structure and composition between species. In order to compare the distribution of diverse proteins involved in cell wall biosynthesis and maintenance, we performed sequence homology searches against 24 fungal proteomes from distinct taxonomic groups, all reported as human pathogens. This approach led to identification of 4014 cell wall proteins (CWPs), and enabled us to speculate about cell wall composition in recently sequenced pathogenic fungi with limited experimental information. We found large expansions of several CWP families, in particular taxa, and a number of new CWPs possibly involved in evading host immune recognition. Here, we present a comprehensive evolutionary history of fungal CWP families in the context of the fungal tree of life. Full article
(This article belongs to the Special Issue Genomic Data in Pathogenic Fungi)
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Other

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28 pages, 13313 KiB  
Tutorial
FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes
by Evelina Y. Basenko, Jane A. Pulman, Achchuthan Shanmugasundram, Omar S. Harb, Kathryn Crouch, David Starns, Susanne Warrenfeltz, Cristina Aurrecoechea, Christian J. Stoeckert, Jr., Jessica C. Kissinger, David S. Roos and Christiane Hertz-Fowler
J. Fungi 2018, 4(1), 39; https://doi.org/10.3390/jof4010039 - 20 Mar 2018
Cited by 211 | Viewed by 14647
Abstract
FungiDB (fungidb.org) is a free online resource for data mining and functional genomics analysis for fungal and oomycete species. FungiDB is part of the Eukaryotic Pathogen Genomics Database Resource (EuPathDB, eupathdb.org) platform that integrates genomic, transcriptomic, proteomic, and phenotypic datasets, and other types [...] Read more.
FungiDB (fungidb.org) is a free online resource for data mining and functional genomics analysis for fungal and oomycete species. FungiDB is part of the Eukaryotic Pathogen Genomics Database Resource (EuPathDB, eupathdb.org) platform that integrates genomic, transcriptomic, proteomic, and phenotypic datasets, and other types of data for pathogenic and nonpathogenic, free-living and parasitic organisms. FungiDB is one of the largest EuPathDB databases containing nearly 100 genomes obtained from GenBank, Aspergillus Genome Database (AspGD), The Broad Institute, Joint Genome Institute (JGI), Ensembl, and other sources. FungiDB offers a user-friendly web interface with embedded bioinformatics tools that support custom in silico experiments that leverage FungiDB-integrated data. In addition, a Galaxy-based workspace enables users to generate custom pipelines for large-scale data analysis (e.g., RNA-Seq, variant calling, etc.). This review provides an introduction to the FungiDB resources and focuses on available features, tools, and queries and how they can be used to mine data across a diverse range of integrated FungiDB datasets and records. Full article
(This article belongs to the Special Issue Genomic Data in Pathogenic Fungi)
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