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      Fungal evolution: major ecological adaptations and evolutionary transitions

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          Fungi are a highly diverse group of heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of a chitinous cell wall. While unicellular fungi are far from rare, part of the evolutionary success of the group resides in their ability to grow indefinitely as a cylindrical multinucleated cell (hypha). Armed with these morphological traits and with an extremely high metabolical diversity, fungi have conquered numerous ecological niches and have shaped a whole world of interactions with other living organisms. Herein we survey the main evolutionary and ecological processes that have guided fungal diversity. We will first review the ecology and evolution of the zoosporic lineages and the process of terrestrialization, as one of the major evolutionary transitions in this kingdom. Several plausible scenarios have been proposed for fungal terrestralization and we here propose a new scenario, which considers icy environments as a transitory niche between water and emerged land. We then focus on exploring the main ecological relationships of Fungi with other organisms (other fungi, protozoans, animals and plants), as well as the origin of adaptations to certain specialized ecological niches within the group (lichens, black fungi and yeasts). Throughout this review we use an evolutionary and comparative‐genomics perspective to understand fungal ecological diversity. Finally, we highlight the importance of genome‐enabled inferences to envision plausible narratives and scenarios for important transitions.

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          Fungal endophytes: diversity and functional roles.

          All plants in natural ecosystems appear to be symbiotic with fungal endophytes. This highly diverse group of fungi can have profound impacts on plant communities through increasing fitness by conferring abiotic and biotic stress tolerance, increasing biomass and decreasing water consumption, or decreasing fitness by altering resource allocation. Despite more than 100 yr of research resulting in thousands of journal articles, the ecological significance of these fungi remains poorly characterized. Historically, two endophytic groups (clavicipitaceous (C) and nonclavicipitaceous (NC)) have been discriminated based on phylogeny and life history traits. Here, we show that NC-endophytes represent three distinct functional groups based on host colonization and transmission, in planta biodiversity and fitness benefits conferred to hosts. Using this framework, we contrast the life histories, interactions with hosts and potential roles in plant ecophysiology of C- and NC-endophytes, and highlight several key questions for future work in endophyte biology.
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            Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis.

            Ustilago maydis is a ubiquitous pathogen of maize and a well-established model organism for the study of plant-microbe interactions. This basidiomycete fungus does not use aggressive virulence strategies to kill its host. U. maydis belongs to the group of biotrophic parasites (the smuts) that depend on living tissue for proliferation and development. Here we report the genome sequence for a member of this economically important group of biotrophic fungi. The 20.5-million-base U. maydis genome assembly contains 6,902 predicted protein-encoding genes and lacks pathogenicity signatures found in the genomes of aggressive pathogenic fungi, for example a battery of cell-wall-degrading enzymes. However, we detected unexpected genomic features responsible for the pathogenicity of this organism. Specifically, we found 12 clusters of genes encoding small secreted proteins with unknown function. A significant fraction of these genes exists in small gene families. Expression analysis showed that most of the genes contained in these clusters are regulated together and induced in infected tissue. Deletion of individual clusters altered the virulence of U. maydis in five cases, ranging from a complete lack of symptoms to hypervirulence. Despite years of research into the mechanism of pathogenicity in U. maydis, no 'true' virulence factors had been previously identified. Thus, the discovery of the secreted protein gene clusters and the functional demonstration of their decisive role in the infection process illuminate previously unknown mechanisms of pathogenicity operating in biotrophic fungi. Genomic analysis is, similarly, likely to open up new avenues for the discovery of virulence determinants in other pathogens.
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              Batrachochytrium Dendrobatidis gen. et sp. nov., a Chytrid Pathogenic to Amphibians


                Author and article information

                Biol Rev Camb Philos Soc
                Biol Rev Camb Philos Soc
                Biological Reviews of the Cambridge Philosophical Society
                Blackwell Publishing Ltd (Oxford, UK )
                25 April 2019
                August 2019
                : 94
                : 4 ( doiID: 10.1111/brv.2019.94.issue-4 )
                : 1443-1476
                [ 1 ] Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG) The Barcelona Institute of Science and Technology Dr. Aiguader 88, Barcelona 08003 Spain
                [ 2 ] Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF) 08003 Barcelona Spain
                [ 3 ] ICREA, Pg. Lluís Companys 23 08010 Barcelona Spain
                Author notes
                [* ]Address for correspondence (Tel: +34 616 953 333; E‐mail: tgabaldon@ 123456icrea.cat ).
                © 2019 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

                Page count
                Figures: 4, Tables: 0, Pages: 34, Words: 32068
                Funded by: Spanish Ministry of Economy, Industry, and Competitiveness (MEIC)
                Award ID: SEV‐2012‐0208
                Award ID: BFU2015‐67107
                Funded by: European Regional Development Fund (ERDF) , open-funder-registry 10.13039/501100008530;
                Funded by: Catalan Research Agency (AGAUR) , open-funder-registry 10.13039/501100003030;
                Award ID: SGR857
                Funded by: European Union's Horizon 2020 research and innovation programme , open-funder-registry 10.13039/100010663;
                Award ID: ERC‐2016‐724173
                Funded by: Marie Sklodowska‐Curie , open-funder-registry 10.13039/100010665;
                Award ID: H2020‐MSCA‐ITN‐2014‐642095
                Original Article
                Original Articles
                Custom metadata
                August 2019
                Converter:WILEY_ML3GV2_TO_JATSPMC version:5.7.1 mode:remove_FC converted:12.11.2019


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