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  1. Article ; Online: Evaluation of Different Gene Prediction Tools in

    Kirkland, Theo N / Beyhan, Sinem / Stajich, Jason E

    Journal of fungi (Basel, Switzerland)

    2023  Volume 9, Issue 11

    Abstract: Gene prediction is required to obtain optimal biologically meaningful information from genomic sequences, but automated gene prediction software is imperfect. In this study, we compare the original annotation of ... ...

    Abstract Gene prediction is required to obtain optimal biologically meaningful information from genomic sequences, but automated gene prediction software is imperfect. In this study, we compare the original annotation of the
    Language English
    Publishing date 2023-11-09
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2784229-0
    ISSN 2309-608X ; 2309-608X
    ISSN (online) 2309-608X
    ISSN 2309-608X
    DOI 10.3390/jof9111094
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  2. Article ; Online: Extremophilic and extremotolerant fungi.

    Gostinčar, Cene / Stajich, Jason E / Gunde-Cimerman, Nina

    Current biology : CB

    2023  Volume 33, Issue 14, Page(s) R752–R756

    Abstract: There are few places on Earth that are truly aseptic. Even environments that we may consider 'extreme', such as glaciers, deserts, or hypersaline bodies of water (Figure 1), can harbour life. The organisms that thrive in such environments - mostly ... ...

    Abstract There are few places on Earth that are truly aseptic. Even environments that we may consider 'extreme', such as glaciers, deserts, or hypersaline bodies of water (Figure 1), can harbour life. The organisms that thrive in such environments - mostly microbes - are often referred to as 'extremophiles'. However, what constitutes extreme is in the eye of the beholder. Extremophilic organisms are so adapted to their environment that they perceive extreme conditions as optimal for their growth and can sometimes even be stressed by what we perceive as moderate. Stress is therefore not an optimal criterion for defining what is extreme. Instead, extreme conditions can be seen as those in which the majority of species cannot grow or even survive.
    MeSH term(s) Extremophiles ; Fungi ; Adaptation, Physiological ; Water
    Chemical Substances Water (059QF0KO0R)
    Language English
    Publishing date 2023-07-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 1071731-6
    ISSN 1879-0445 ; 0960-9822
    ISSN (online) 1879-0445
    ISSN 0960-9822
    DOI 10.1016/j.cub.2023.06.011
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3208: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (2.OG)
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  3. Article ; Online: Draft genome sequence of a black yeast fungus

    Kurbessoian, Tania / Stevenson, Danielle / Haro, Renata / Ying, Samantha / Stajich, Jason E

    Microbiology resource announcements

    2024  Volume 13, Issue 2, Page(s) e0091323

    Abstract: A 30.28 Mb draft genome sequence was assembled and annotated for the melanized ascomycetous ... ...

    Abstract A 30.28 Mb draft genome sequence was assembled and annotated for the melanized ascomycetous fungus
    Language English
    Publishing date 2024-01-05
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.00913-23
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  4. Article ; Online: Morphological and phylogenetic resolution of

    Lovett, Brian / Barrett, Hana / Macias, Angie M / Stajich, Jason E / Kasson, Lindsay R / Kasson, Matt T

    Mycologia

    2024  Volume 116, Issue 2, Page(s) 267–290

    Abstract: The entomopathogenic ... ...

    Abstract The entomopathogenic fungus
    MeSH term(s) Animals ; United States ; Phylogeny ; Bayes Theorem ; Hypocreales ; Hemiptera/microbiology ; DNA-Directed RNA Polymerases/genetics ; North Carolina
    Chemical Substances DNA-Directed RNA Polymerases (EC 2.7.7.6)
    Language English
    Publishing date 2024-01-26
    Publishing country England
    Document type Journal Article
    ZDB-ID 281335-x
    ISSN 1557-2536 ; 0027-5514
    ISSN (online) 1557-2536
    ISSN 0027-5514
    DOI 10.1080/00275514.2023.2296337
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1291: Show issues Location:
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  5. Article ; Online: Fungal biodiversity and conservation mycology in light of new technology, big data, and changing attitudes.

    Lofgren, Lotus A / Stajich, Jason E

    Current biology : CB

    2021  Volume 31, Issue 19, Page(s) R1312–R1325

    Abstract: Fungi have successfully established themselves across seemingly every possible niche, substrate, and biome. They are fundamental to biogeochemical cycling, interspecies interactions, food production, and drug bioprocessing, as well as playing less heroic ...

    Abstract Fungi have successfully established themselves across seemingly every possible niche, substrate, and biome. They are fundamental to biogeochemical cycling, interspecies interactions, food production, and drug bioprocessing, as well as playing less heroic roles as difficult to treat human infections and devastating plant pathogens. Despite community efforts to estimate and catalog fungal diversity, we have only named and described a minute fraction of the fungal world. The identification, characterization, and conservation of fungal diversity is paramount to preserving fungal bioresources, and to understanding and predicting ecosystem cycling and the evolution and epidemiology of fungal disease. Although species and ecosystem conservation are necessarily the foundation of preserving this diversity, there is value in expanding our definition of conservation to include the protection of biological collections, ecological metadata, genetic and genomic data, and the methods and code used for our analyses. These definitions of conservation are interdependent. For example, we need metadata on host specificity and biogeography to understand rarity and set priorities for conservation. To aid in these efforts, we need to draw expertise from diverse fields to tie traditional taxonomic knowledge to data obtained from modern -omics-based approaches, and support the advancement of diverse research perspectives. We also need new tools, including an updated framework for describing and tracking species known only from DNA, and the continued integration of functional predictions to link genetic diversity to functional and ecological diversity. Here, we review the state of fungal diversity research as shaped by recent technological advancements, and how changing viewpoints in taxonomy, -omics, and systematics can be integrated to advance mycological research and preserve fungal biodiversity.
    MeSH term(s) Attitude ; Big Data ; Biodiversity ; Ecosystem ; Fungi/genetics ; Humans ; Mycology ; Technology
    Language English
    Publishing date 2021-10-12
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 1071731-6
    ISSN 1879-0445 ; 0960-9822
    ISSN (online) 1879-0445
    ISSN 0960-9822
    DOI 10.1016/j.cub.2021.06.083
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3208: Show issues Location:
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  6. Article ; Online: Fungi are key players in extreme ecosystems.

    Coleine, Claudia / Stajich, Jason E / Selbmann, Laura

    Trends in ecology & evolution

    2022  Volume 37, Issue 6, Page(s) 517–528

    Abstract: Extreme environments on Earth are typically devoid of macro life forms and are inhabited predominantly by highly adapted and specialized microorganisms. The discovery and persistence of these extremophiles provides tools to model how life arose on Earth ... ...

    Abstract Extreme environments on Earth are typically devoid of macro life forms and are inhabited predominantly by highly adapted and specialized microorganisms. The discovery and persistence of these extremophiles provides tools to model how life arose on Earth and inform us on the limits of life. Fungi, in particular, are among the most extreme-tolerant organisms with highly versatile lifestyles and stunning ecological and morphological plasticity. Here, we overview the most notable examples of extremophilic and stress-tolerant fungi, highlighting their key roles in the functionality and balance of extreme ecosystems. The remarkable ability of fungi to tolerate and even thrive in the most extreme environments, which preclude most organisms, have reshaped current concepts regarding the limits of life on Earth.
    MeSH term(s) Earth, Planet ; Ecosystem ; Extreme Environments ; Extremophiles ; Fungi
    Language English
    Publishing date 2022-03-01
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 284965-3
    ISSN 1872-8383 ; 0169-5347
    ISSN (online) 1872-8383
    ISSN 0169-5347
    DOI 10.1016/j.tree.2022.02.002
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    In stock of ZB MED Bonn / Germany

    Zs Bio TEE: Show issues
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  7. Article ; Online: Fungal Genomes and Insights into the Evolution of the Kingdom.

    Stajich, Jason E

    Microbiology spectrum

    2017  Volume 5, Issue 4

    Abstract: The kingdom Fungi comprises species that inhabit nearly all ecosystems. Fungi exist as both free-living and symbiotic unicellular and multicellular organisms with diverse morphologies. The genomes of fungi encode genes that enable them to thrive in ... ...

    Abstract The kingdom Fungi comprises species that inhabit nearly all ecosystems. Fungi exist as both free-living and symbiotic unicellular and multicellular organisms with diverse morphologies. The genomes of fungi encode genes that enable them to thrive in diverse environments, invade plant and animal cells, and participate in nutrient cycling in terrestrial and aquatic ecosystems. The continuously expanding databases of fungal genome sequences have been generated by individual and large-scale efforts such as Génolevures, Broad Institute's Fungal Genome Initiative, and the 1000 Fungal Genomes Project (http://1000.fungalgenomes.org). These efforts have produced a catalog of fungal genes and genomic organization. The genomic datasets can be utilized to better understand how fungi have adapted to their lifestyles and ecological niches. Large datasets of fungal genomic and transcriptomic data have enabled the use of novel methodologies and improved the study of fungal evolution from a molecular sequence perspective. Combined with microscopes, petri dishes, and woodland forays, genome sequencing supports bioinformatics and comparative genomics approaches as important tools in the study of the biology and evolution of fungi.
    MeSH term(s) Evolution, Molecular ; Fungi/genetics ; Genes, Fungal/genetics ; Genome, Fungal/genetics
    Language English
    Publishing date 2017
    Publishing country United States
    Document type Journal Article
    ISSN 2165-0497
    ISSN (online) 2165-0497
    DOI 10.1128/microbiolspec.FUNK-0055-2016
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  8. Article ; Online: Fungal Evolution: Mucor and Phycomyces See Double.

    Stajich, Jason E

    Current biology : CB

    2016  Volume 26, Issue 16, Page(s) R775–7

    Abstract: Newly available genome sequences of two Mucoralean fungi, Phycomyces blakesleeanus and Mucor circinelloides, provide evidence for an ancient whole-genome duplication that contributed to the generation of expanded gene families. These fungi have robust ... ...

    Abstract Newly available genome sequences of two Mucoralean fungi, Phycomyces blakesleeanus and Mucor circinelloides, provide evidence for an ancient whole-genome duplication that contributed to the generation of expanded gene families. These fungi have robust responses to light that can be correlated with the expansion of gene networks involved in light sensing and signaling.
    Language English
    Publishing date 2016-08-22
    Publishing country England
    Document type Journal Article
    ZDB-ID 1071731-6
    ISSN 1879-0445 ; 0960-9822
    ISSN (online) 1879-0445
    ISSN 0960-9822
    DOI 10.1016/j.cub.2016.06.049
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3208: Show issues Location:
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  9. Article ; Online: Metagenome-Assembled Genomes of Bacterial Symbionts Associated with Insecticide-Resistant and -Susceptible Individuals of the Glassy-Winged Sharpshooter (Homalodisca vitripennis).

    Ettinger, Cassandra L / Byrne, Frank J / Redak, Richard A / Stajich, Jason E

    Microbiology resource announcements

    2022  Volume 11, Issue 7, Page(s) e0050622

    Abstract: The role of microbes in insecticide resistance is an emerging question. Here, we describe six metagenome-assembled genomes (MAGs) associated with the glassy-winged sharpshooter (Homalodisca vitripennis [Germar, 1821]) (Hemiptera, Cicadellidae). MAGs ... ...

    Abstract The role of microbes in insecticide resistance is an emerging question. Here, we describe six metagenome-assembled genomes (MAGs) associated with the glassy-winged sharpshooter (Homalodisca vitripennis [Germar, 1821]) (Hemiptera, Cicadellidae). MAGs representing the obligate symbionts
    Language English
    Publishing date 2022-06-16
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.00506-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Metagenome-Assembled Genomes of Bacteria Associated with Massospora cicadina Fungal Plugs from Infected Brood VIII Periodical Cicadas.

    Ettinger, Cassandra L / Lovett, Brian / Kasson, Matt T / Stajich, Jason E

    Microbiology resource announcements

    2022  Volume 11, Issue 10, Page(s) e0041322

    Abstract: We report six metagenome-assembled genomes (MAGs) associated with Massospora cicadina strain MCPNR19 (ARSEF 14555), an obligate entomopathogenic fungus of periodical cicadas. The MAGs include representatives ... ...

    Abstract We report six metagenome-assembled genomes (MAGs) associated with Massospora cicadina strain MCPNR19 (ARSEF 14555), an obligate entomopathogenic fungus of periodical cicadas. The MAGs include representatives of
    Language English
    Publishing date 2022-08-29
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.00413-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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