Frequent genetic exchanges revealed by a pan-mitogenome graph of a fungal plant pathogen.

Autor: van Westerhoven AC; Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands.; Laboratory of Phytopathology, Wageningen University and Research, Wageningen, Netherlands., Dijkstra J; Laboratory of Phytopathology, Wageningen University and Research, Wageningen, Netherlands., Aznar Palop JL; Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands., Wissink K; Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands., Bell J; Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands., Kema GHJ; Laboratory of Phytopathology, Wageningen University and Research, Wageningen, Netherlands., Seidl MF; Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands.

Publikováno v: MBio [mBio] 2024 Nov 13, pp. e0275824. Date of Electronic Publication: 2024 Nov 13.

Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew.

Autor: Skiadas P; Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.; Translational Plant Biology, Utrecht University, Utrecht, The Netherlands., Riera Vidal S; Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands., Dommisse J; Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands., Mendel MN; Translational Plant Biology, Utrecht University, Utrecht, The Netherlands.; Plant-Microbe Interactions, Utrecht University, Utrecht, The Netherlands., Elberse J; Translational Plant Biology, Utrecht University, Utrecht, The Netherlands., Van den Ackerveken G; Translational Plant Biology, Utrecht University, Utrecht, The Netherlands., de Jonge R; Plant-Microbe Interactions, Utrecht University, Utrecht, The Netherlands.; AI Technology for Life, Department of Information and Computing Sciences, Department of Biology, Utrecht University, Utrecht, The Netherlands., Seidl MF; Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.

Publikováno v: PLoS genetics [PLoS Genet] 2024 Oct 25; Vol. 20 (10), pp. e1011452. Date of Electronic Publication: 2024 Oct 25 (Print Publication: 2024).

Phyllosticta paracitricarpa is synonymous with the EU quarantine fungus P. citricarpa based on phylogenomic analyses.

Autor: van Ingen-Buijs VA; Evolutionary Phytopathology group, Westerdijk Fungal Biodiversity Institute, Utrecht 3584 CT, the Netherlands; Department of Plant Sciences, Laboratory of Phytopathology, Wageningen University and Research, Wageningen 6708 PB, the Netherlands; Netherlands Institute for Vectors, Invasive plants and Plant Health (NIVIP), National Plant Protection Organization (NPPO), Netherlands Food and Consumer Product Safety Authority (NVWA), Geertjesweg 15, 6706 EA, Wageningen, the Netherlands., van Westerhoven AC; Department of Plant Sciences, Laboratory of Phytopathology, Wageningen University and Research, Wageningen 6708 PB, the Netherlands; Theoretical Biology & Bioinformatics, Utrecht University, Utrecht 3584 CH, the Netherlands., Skiadas P; Theoretical Biology & Bioinformatics, Utrecht University, Utrecht 3584 CH, the Netherlands., Zuijdgeest XCL; Centre for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany., Haridas S; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Daum C; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Duffy K; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Guo J; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Hundley H; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., LaButti K; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Lipzen A; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Pangilinan J; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Riley R; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Wang J; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Yan M; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Martin F; Department of Biology, Institut National de la Recherche Agronomique, UMR INRA-Université de Lorraine 'Interaction Arbres/Microorganismes', Champenoux F-54280, France., Barry K; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Grigoriev IV; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, CA 94720, USA., Groenewald JZ; Evolutionary Phytopathology group, Westerdijk Fungal Biodiversity Institute, Utrecht 3584 CT, the Netherlands., Crous PW; Evolutionary Phytopathology group, Westerdijk Fungal Biodiversity Institute, Utrecht 3584 CT, the Netherlands; Department of Plant Sciences, Laboratory of Phytopathology, Wageningen University and Research, Wageningen 6708 PB, the Netherlands., Seidl MF; Theoretical Biology & Bioinformatics, Utrecht University, Utrecht 3584 CH, the Netherlands. Electronic address: m.f.seidl@uu.nl.

Publikováno v: Fungal genetics and biology : FG & B [Fungal Genet Biol] 2024 Sep 05; Vol. 175, pp. 103925. Date of Electronic Publication: 2024 Sep 05.

Receptor-like cytoplasmic kinases of different subfamilies differentially regulate SOBIR1/BAK1-mediated immune responses in Nicotiana benthamiana.

Autor: Huang WRH; Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands. Wen.Huang@tsl.ac.uk.; The Sainsbury Laboratory, University of East Anglia, Norwich, United Kingdom. Wen.Huang@tsl.ac.uk., Braam C; Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands., Kretschmer C; Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, 06120, Halle, Germany., Villanueva SL; Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands., Liu H; Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands., Ferik F; Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, 06120, Halle, Germany., van der Burgh AM; Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.; Teaching and Learning Centre, Wageningen University & Research, Droevendaalsesteeg 4, 6708 PB, Wageningen, The Netherlands., Boeren S; Laboratory of Biochemistry, Wageningen University and Research, Wageningen, the Netherlands., Wu J; Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.; Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China., Zhang L; Department of Plant Biochemistry, Centre for Plant Molecular Biology (ZMBP), Eberhard Karls University Tübingen, Auf der Morgenstelle 32, D-72076, Tübingen, Germany., Nürnberger T; Department of Plant Biochemistry, Centre for Plant Molecular Biology (ZMBP), Eberhard Karls University Tübingen, Auf der Morgenstelle 32, D-72076, Tübingen, Germany., Wang Y; Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China., Seidl MF; Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, 3584 CH, Utrecht, the Netherlands., Evangelisti E; Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.; Université Côte d'Azur, INRAE UMR 1355, CNRS UMR 7254, Institut Sophia Agrobiotech (ISA), 06903, Sophia Antipolis, France., Stuttmann J; Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, 06120, Halle, Germany.; Aix Marseille University, CEA, CNRS, BIAM, UMR7265, LEMiRE (Microbial Ecology of the Rhizosphere), 13115, Saint‑Paul lez Durance, France., Joosten MHAJ; Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands. matthieu.joosten@wur.nl.

Publikováno v: Nature communications [Nat Commun] 2024 May 21; Vol. 15 (1), pp. 4339. Date of Electronic Publication: 2024 May 21.

Segmental duplications drive the evolution of accessory regions in a major crop pathogen.

Autor: van Westerhoven AC; Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands.; Department of Biology, Theoretical Biology & Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands., Aguilera-Galvez C; Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands., Nakasato-Tagami G; Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands., Shi-Kunne X; Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands., Martinez de la Parte E; Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands., Chavarro-Carrero E; Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands., Meijer HJG; Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands.; Department Biointeractions and Plant Health, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands., Feurtey A; Christian-Albrechts University of Kiel, Christian-Albrechts-Platz 4, 24118, Kiel, Germany.; Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306, Plön, Germany.; Plant Pathology, Eidgenössische Technische Hochschule Zürich, Rämistrasse 101, 8092, Zürich, Switzerland., Maryani N; Biology Education, Universitas Sultan Ageng Tirtayasa, Jalan Raya Palka No.Km 3, 42163, Banten, Indonesia., Ordóñez N; Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands., Schneiders H; KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands., Nijbroek K; KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands., Wittenberg AHJ; KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands., Hofstede R; KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands., García-Bastidas F; KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands., Sørensen A; KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands., Swennen R; Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, Catholic University of Leuven, Oude Markt 13, 3000, Leuven, Belgium.; International Institute of Tropical Agriculture, Plot 15 Naguru E Rd, Kampala, PO Box 7878, Uganda., Drenth A; The University of Queensland, St Lucia, 4072, Brisbane, Queensland, Australia., Stukenbrock EH; Christian-Albrechts University of Kiel, Christian-Albrechts-Platz 4, 24118, Kiel, Germany.; Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306, Plön, Germany., Kema GHJ; Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands., Seidl MF; Department of Biology, Theoretical Biology & Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands.

Publikováno v: The New phytologist [New Phytol] 2024 Apr; Vol. 242 (2), pp. 610-625. Date of Electronic Publication: 2024 Feb 25.