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Cross-Disciplinary Genomics Approaches to Studying Emerging Fungal Infections

An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
Grainger Bioinformatics Center, Department of Science and Education, The Field Museum, Chicago, IL 60605, USA
Academy of Fine Arts Vienna, Institute of Natual Sciences and Technology in the Arts, 1090 Vienna, Austria
Department of Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
Author to whom correspondence should be addressed.
Life 2020, 10(12), 356;
Received: 12 November 2020 / Revised: 10 December 2020 / Accepted: 12 December 2020 / Published: 17 December 2020
(This article belongs to the Special Issue Advances in Fungal -Omics)
Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi. View Full-Text
Keywords: extremophiles; fungi; human opportunistic; lichens; plant pathogens extremophiles; fungi; human opportunistic; lichens; plant pathogens
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MDPI and ACS Style

Muggia, L.; Ametrano, C.G.; Sterflinger, K.; Tesei, D. An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota. Life 2020, 10, 356.

AMA Style

Muggia L, Ametrano CG, Sterflinger K, Tesei D. An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota. Life. 2020; 10(12):356.

Chicago/Turabian Style

Muggia, Lucia, Claudio G. Ametrano, Katja Sterflinger, and Donatella Tesei. 2020. "An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota" Life 10, no. 12: 356.

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