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An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota
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Shed Light in the DaRk LineagES of the Fungal Tree of Life—STRES

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Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy
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Section of Mycology, Italian National Antarctic Museum (MNA), 16121 Genoa, Italy
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Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
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Center of Expertise in Mycology of Radboud University Medical Center, Canisius Wilhelmina Hospital, 6532 Nijmegen, The Netherlands
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Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy
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The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
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Genome Center, University of California, Davis, CA 95616, USA
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Microbiology & Plant Pathology, University of California Riverside, Riverside, CA 92521, USA
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Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
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Department of Materials and Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), 10115 Berlin, Germany
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Department of Earth Sciences & Department of Biology, Chemistry, Pharmacy, Freie Universität, Berlin 10115 Berlin, Germany
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Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
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Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
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Institute of Biology, University of Graz, Graz A-8010, Austria
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Department Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
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Department of Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
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Department of Genetics and Applied Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
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Department of Biochemistry and Molecular Biology, Faculty of Medicine University of Debrecen, 4032 Debrecen, Hungary
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Department of Life Sciences, University of Trieste, 34121 Trieste, Italy
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Mycotheca Universitatis Taurinensis, University of Torino, 10125 Torino, Italy
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Department of Microbiology, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Baja California 22980, Mexico
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Department CIBIO, University of Trento, 38123 Trento, Italy
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Centre for Enzyme Innovation, University of Portsmouth, Portsmouth PO1 2UP, UK
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Institute of Natural Sciences and Technology in the Arts, Academy of Fine Arts Vienna, Vienna 22180, Austria
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Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna 22180, Austria
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Department of Biosystems Engineering and BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
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School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2006, Australia
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Department of Biochemistry, Federal University of Paraná, Paraná E3100, Brazil
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Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada
*
Authors to whom correspondence should be addressed.
Life 2020, 10(12), 362; https://doi.org/10.3390/life10120362
Received: 5 December 2020 / Revised: 16 December 2020 / Accepted: 17 December 2020 / Published: 19 December 2020
(This article belongs to the Special Issue Advances in Fungal -Omics)
The polyphyletic group of black fungi within the Ascomycota (Arthoniomycetes, Dothideomycetes, and Eurotiomycetes) is ubiquitous in natural and anthropogenic habitats. Partly because of their dark, melanin-based pigmentation, black fungi are resistant to stresses including UV- and ionizing-radiation, heat and desiccation, toxic metals, and organic pollutants. Consequently, they are amongst the most stunning extremophiles and poly-extreme-tolerant organisms on Earth. Even though ca. 60 black fungal genomes have been sequenced to date, [mostly in the family Herpotrichiellaceae (Eurotiomycetes)], the class Dothideomycetes that hosts the largest majority of extremophiles has only been sparsely sampled. By sequencing up to 92 species that will become reference genomes, the “Shed light in The daRk lineagES of the fungal tree of life” (STRES) project will cover a broad collection of black fungal diversity spread throughout the Fungal Tree of Life. Interestingly, the STRES project will focus on mostly unsampled genera that display different ecologies and life-styles (e.g., ant- and lichen-associated fungi, rock-inhabiting fungi, etc.). With a resequencing strategy of 10- to 15-fold depth coverage of up to ~550 strains, numerous new reference genomes will be established. To identify metabolites and functional processes, these new genomic resources will be enriched with metabolomics analyses coupled with transcriptomics experiments on selected species under various stress conditions (salinity, dryness, UV radiation, oligotrophy). The data acquired will serve as a reference and foundation for establishing an encyclopedic database for fungal metagenomics as well as the biology, evolution, and ecology of the fungi in extreme environments. View Full-Text
Keywords: adaptation; black fungi; Dothideomycetes; Eurotiomycetes; extremophiles; genomics; metabolomics; secondary metabolites; stress conditions; transcriptomics adaptation; black fungi; Dothideomycetes; Eurotiomycetes; extremophiles; genomics; metabolomics; secondary metabolites; stress conditions; transcriptomics
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MDPI and ACS Style

Selbmann, L.; Benkő, Z.; Coleine, C.; de Hoog, S.; Donati, C.; Druzhinina, I.; Emri, T.; Ettinger, C.L.; Gladfelter, A.S.; Gorbushina, A.A.; Grigoriev, I.V.; Grube, M.; Gunde-Cimerman, N.; Karányi, Z.Á.; Kocsis, B.; Kubressoian, T.; Miklós, I.; Miskei, M.; Muggia, L.; Northen, T.; Novak-Babič, M.; Pennacchio, C.; Pfliegler, W.P.; Pòcsi, I.; Prigione, V.; Riquelme, M.; Segata, N.; Schumacher, J.; Shelest, E.; Sterflinger, K.; Tesei, D.; U’Ren, J.M.; Varese, G.C.; Vázquez-Campos, X.; Vicente, V.A.; Souza, E.M.; Zalar, P.; Walker, A.K.; Stajich, J.E. Shed Light in the DaRk LineagES of the Fungal Tree of Life—STRES. Life 2020, 10, 362. https://doi.org/10.3390/life10120362

AMA Style

Selbmann L, Benkő Z, Coleine C, de Hoog S, Donati C, Druzhinina I, Emri T, Ettinger CL, Gladfelter AS, Gorbushina AA, Grigoriev IV, Grube M, Gunde-Cimerman N, Karányi ZÁ, Kocsis B, Kubressoian T, Miklós I, Miskei M, Muggia L, Northen T, Novak-Babič M, Pennacchio C, Pfliegler WP, Pòcsi I, Prigione V, Riquelme M, Segata N, Schumacher J, Shelest E, Sterflinger K, Tesei D, U’Ren JM, Varese GC, Vázquez-Campos X, Vicente VA, Souza EM, Zalar P, Walker AK, Stajich JE. Shed Light in the DaRk LineagES of the Fungal Tree of Life—STRES. Life. 2020; 10(12):362. https://doi.org/10.3390/life10120362

Chicago/Turabian Style

Selbmann, Laura, Zsigmond Benkő, Claudia Coleine, Sybren de Hoog, Claudio Donati, Irina Druzhinina, Tamás Emri, Cassie L. Ettinger, Amy S. Gladfelter, Anna A. Gorbushina, Igor V. Grigoriev, Martin Grube, Nina Gunde-Cimerman, Zsolt Á. Karányi, Beatrix Kocsis, Tania Kubressoian, Ida Miklós, Márton Miskei, Lucia Muggia, Trent Northen, Monika Novak-Babič, Christa Pennacchio, Walter P. Pfliegler, Istvàn Pòcsi, Valeria Prigione, Meritxell Riquelme, Nicola Segata, Julia Schumacher, Ekaterina Shelest, Katja Sterflinger, Donatella Tesei, Jana M. U’Ren, Giovanna C. Varese, Xabier Vázquez-Campos, Vania A. Vicente, Emanuel M. Souza, Polona Zalar, Allison K. Walker, and Jason E. Stajich. 2020. "Shed Light in the DaRk LineagES of the Fungal Tree of Life—STRES" Life 10, no. 12: 362. https://doi.org/10.3390/life10120362

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