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      Genome evolution and transcriptome plasticity is associated with adaptation to monocot and dicot plants in Colletotrichum fungi

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          Abstract

          Background

          Colletotrichum fungi infect a wide diversity of monocot and dicot hosts, causing diseases on almost all economically important plants worldwide. Colletotrichum is also a suitable model for studying gene family evolution on a fine scale to uncover events in the genome associated with biological changes.

          Results

          Here we present the genome sequences of 30 Colletotrichum species covering the diversity within the genus. Evolutionary analyses revealed that the Colletotrichum ancestor diverged in the late Cretaceous in parallel with the diversification of flowering plants. We provide evidence of independent host jumps from dicots to monocots during the evolution of Colletotrichum, coinciding with a progressive shrinking of the plant cell wall degradative arsenal and expansions in lineage-specific gene families. Comparative transcriptomics of 4 species adapted to different hosts revealed similarity in gene content but high diversity in the modulation of their transcription profiles on different plant substrates. Combining genomics and transcriptomics, we identified a set of core genes such as specific transcription factors, putatively involved in plant cell wall degradation.

          Conclusions

          These results indicate that the ancestral Colletotrichum were associated with dicot plants and certain branches progressively adapted to different monocot hosts, reshaping the gene content and its regulation.

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          Most cited references106

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            Gene Ontology: tool for the unification of biology

            Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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              MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

              We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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                Author and article information

                Contributors
                Journal
                Gigascience
                Gigascience
                gigascience
                GigaScience
                Oxford University Press
                2047-217X
                2024
                28 June 2024
                28 June 2024
                : 13
                : giae036
                Affiliations
                Department of Agricultural and Food Sciences (DISTAL) , University of Bologna, Viale Fanin 40-50, 40127 Bologna, Italy
                Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE) , University of Salamanca, Calle del Duero, 37185 Villamayor, Salamanca, Spain
                Department of Food Hygiene and Technology and Institute of Food Science and Technology , University of León, Campus Vegazana, 24007 León, Spain
                Center for Health and Bioresources , Austrian Institute of Technology (AIT), Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
                Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology , Fungal Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
                Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology , Fungal Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
                Joint Genome Institute, Lawrence Berkeley National Laboratory , United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
                Joint Genome Institute, Lawrence Berkeley National Laboratory , United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
                Joint Genome Institute, Lawrence Berkeley National Laboratory , United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
                Joint Genome Institute, Lawrence Berkeley National Laboratory , United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
                Joint Genome Institute, Lawrence Berkeley National Laboratory , United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
                Joint Genome Institute, Lawrence Berkeley National Laboratory , United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
                Joint Genome Institute, Lawrence Berkeley National Laboratory , United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
                Laboratory of Biodiversity and Microbial Ecology (LUBEM) , IBSAM, ESIAB, EA 3882, University of Brest, Technopôle Brest-Iroise, Parv. Blaise Pascal, 29280 Plouzané, France
                Department of Microbiology, Faculty of Agriculture and Forestry , University of Helsinki, Siltavuorenpenger 5, 00170 Helsinki, Finland
                UMR 7257, Architecture et Fonction des Macromolécules Biologiques, The French National Centre for Scientific Research (CNRS) , University of Aix-Marseille (AMU), 163 Avenue de Luminy, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
                The French National Institute for Agricultural Research (INRA) , USC 1408 AFMB, 163 Avenue de Luminy, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
                UMR 7257, Architecture et Fonction des Macromolécules Biologiques, The French National Centre for Scientific Research (CNRS) , University of Aix-Marseille (AMU), 163 Avenue de Luminy, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
                The French National Institute for Agricultural Research (INRA) , USC 1408 AFMB, 163 Avenue de Luminy, Parc Scientifique et Technologique de Luminy, 13288 Marseille, France
                Department of Biological Sciences , King Abdulaziz University, 23453 Jeddah, Saudi Arabia
                Joint Genome Institute, Lawrence Berkeley National Laboratory , United States Department of Energy, McMillan rd, CA 94720 Berkeley, USA
                Department of Plant and Microbial Biology , University of California Berkeley, Berkeley, CA, USA
                Mycology and Nematology Genetic Diversity and Biology Laboratory , Agricultural Research Service, United States Department of Agriculture, 10300 Baltimore Ave, MD 20705, Beltsville, USA
                Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology , Fungal Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
                Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE) , University of Salamanca, Calle del Duero, 37185 Villamayor, Salamanca, Spain
                Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE) , University of Salamanca, Calle del Duero, 37185 Villamayor, Salamanca, Spain
                Author notes
                Correspondence address. Riccardo Baroncelli. E-mail: riccardo.baroncelli@ 123456unibo.it
                Correspondence address. Michael R. Thon. E-mail: mthon@ 123456usal.es
                Author information
                https://orcid.org/0000-0002-5878-1159
                https://orcid.org/0000-0002-0898-2358
                https://orcid.org/0000-0002-0165-305X
                https://orcid.org/0000-0003-1676-0242
                https://orcid.org/0000-0002-0229-0975
                https://orcid.org/0000-0001-9097-1123
                https://orcid.org/0000-0002-5838-1972
                https://orcid.org/0000-0001-7966-3496
                https://orcid.org/0000-0003-2293-9329
                https://orcid.org/0000-0002-3660-4629
                https://orcid.org/0000-0001-7413-8852
                https://orcid.org/0000-0003-0771-2329
                https://orcid.org/0000-0002-9168-5214
                https://orcid.org/0000-0002-3434-8588
                https://orcid.org/0000-0002-3136-8903
                https://orcid.org/0000-0001-6886-8090
                https://orcid.org/0000-0002-4363-1123
                https://orcid.org/0000-0003-3248-6490
                https://orcid.org/0000-0002-7225-7003
                Article
                giae036
                10.1093/gigascience/giae036
                11212070
                38940768
                5138f320-37f1-4032-ae7a-1ad8d5b71a55
                © The Author(s) 2024. Published by Oxford University Press GigaScience.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 31 August 2023
                : 05 April 2024
                : 25 May 2024
                Page count
                Pages: 18
                Categories
                Research
                AcademicSubjects/SCI00960
                AcademicSubjects/SCI02254

                fungal genomics,comparative transcriptomics,fungal evolution,anthracnose,plant cell walls

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