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Muggia L, Ametrano CG, Sterflinger K, Tesei D. An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota. Life (Basel) 2020; 10:E356. [PMID: 33348904 PMCID: PMC7765829 DOI: 10.3390/life10120356] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 12/26/2022] Open
Abstract
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.
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Affiliation(s)
- Lucia Muggia
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Claudio G. Ametrano
- Grainger Bioinformatics Center, Department of Science and Education, The Field Museum, Chicago, IL 60605, USA;
| | - Katja Sterflinger
- Academy of Fine Arts Vienna, Institute of Natual Sciences and Technology in the Arts, 1090 Vienna, Austria;
| | - Donatella Tesei
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria;
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Quan Y, Ahmed SA, Menezes da Silva N, Al-Hatmi AMS, Mayer VE, Deng S, Kang Y, Sybren de Hoog G, Shi D. Novel black yeast-like species in chaetothyriales with ant-associated life styles. Fungal Biol 2020; 125:276-284. [PMID: 33766306 DOI: 10.1016/j.funbio.2020.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/15/2020] [Accepted: 11/23/2020] [Indexed: 10/22/2022]
Abstract
Among ancestral fungi in Chaetothyriales, several groups have a life style in association with tropical ants, either in domatia or in carton-nests. In the present study, two strains collected from ant carton in Thailand and Malaysia were found to represent hitherto undescribed species. Morphological, physiological, phylogenetic data and basic genome information are provided for their classification. Because of the relatively large phylogenetic distances with known species confirmed by overall genome data, large subunit (LSU) and Internal Transcribed Spacer (ITS) ribosomal DNA sequences were sufficient for taxonomic circumscription of the species. The analyzed strains clustered with high statistical support as a clade in the family Trichomeriaceae. Morphologically they were rather similar, lacking sporulation in vitro. In conclusion, Incumbomyces delicatus and Incumbomyces lentus were described as new species based on morphological, physiological and phylogenetic analysis.
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Affiliation(s)
- Yu Quan
- Center of Expertise in Mycology of Radboud University Medical Center / Canisius Wilhelmina Hospital, Nijmegen, the Netherlands; Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education of Guizhou & Guizhou Talent Base for Microbiology and Human Health, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China; College of Food and Pharmaceutical Engineering, Guizhou Institute of Technology, Guiyang, China
| | - Sarah A Ahmed
- Center of Expertise in Mycology of Radboud University Medical Center / Canisius Wilhelmina Hospital, Nijmegen, the Netherlands; Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan
| | - Nickolas Menezes da Silva
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Parana, Curitiba, Brazil
| | - Abdullah M S Al-Hatmi
- Center of Expertise in Mycology of Radboud University Medical Center / Canisius Wilhelmina Hospital, Nijmegen, the Netherlands; Ministry of Health, Directorate General of Health Services, Ibri, Oman
| | - Veronika E Mayer
- Division of Structural and Functional Botany, Department of Botany and Biodiversity Research, University of Vienna, Wien, Austria
| | - Shuwen Deng
- Department of Medical Microbiology, People's Hospital of Suzhou National New & Hi-Tech Industrial Development Zone, Jiangsu, China
| | - Yingqian Kang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education of Guizhou & Guizhou Talent Base for Microbiology and Human Health, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - G Sybren de Hoog
- Center of Expertise in Mycology of Radboud University Medical Center / Canisius Wilhelmina Hospital, Nijmegen, the Netherlands; Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan.
| | - Dongmei Shi
- Department of Dermatology & Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Shandong, China.
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