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Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation

Affiliation
Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Belgium
Van Poucke, Kris;
Affiliation
Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Belgium
Haegeman, Annelies;
Affiliation
Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Belgium
Goedefroit, Thomas;
Affiliation
Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Belgium
Focquet, Fran;
Affiliation
Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Belgium
Leus, Leen;
Affiliation
Mendel University, Phytophthora Research Centre (PRC), Czech Republic. ; University of Algarve, Laboratory of Molecular Biotechnology and Phytopathology, Centre for Mediterranean Bioresources and Food, Portugal
Jung, Marília Horta;
Affiliation
Julius Kühn-Institute (JKI), Institute for Plant Protection in Horticulture and Forests, Germany
Nave, Corina;
Affiliation
Swedish University of Agricultural Sciences (SLU), Department of Forest Mycology and Plant Pathology, Sweden
Redondo, Miguel Angel;
Affiliation
Ministère de l’agriculture et de l’alimentation, Direction générale de l’alimentation (DGAL), Sous Direction de la Qualité et de la Protection des Végétaux (SDQPV), Département de la Santé des Forêts, France
Husson, Claude;
Affiliation
Agricultural Academy, AgroBioInstitute (ABI), Bulgaria
Kostov, Kaloyan;
Affiliation
Agricultural Academy, AgroBioInstitute (ABI), Bulgaria
Lyubenova, Aneta;
Affiliation
Agricultural Academy, AgroBioInstitute (ABI), Bulgaria
Christova, Petya;
Affiliation
Walloon Agricultural Research Centre (CRAW), Life Sciences Department, Belgium
Chandelier, Anne;
Affiliation
Agricultural Academy, AgroBioInstitute (ABI), Bulgaria
Slavov, Slavcho;
Affiliation
Westerdijk Fungal Biodiversity Institute, The Netherlands
de Cock, Arthur;
Affiliation
Wageningen University & Research, Business Unit Biointeractions & Plant Health, The Netherlands
Bonants, Peter;
GND
1058984977
Affiliation
Julius Kühn-Institute (JKI), Institute for Plant Protection in Horticulture and Forests, Germany
Werres, Sabine;
Affiliation
Swedish University of Agricultural Sciences (SLU), Department of Forest Mycology and Plant Pathology, Sweden ; University of Lleida, Spain
Palau, Jonàs Oliva;
Affiliation
Université de Lorraine – Institut National de la Recherche Agronomique (INRAe), L’Unité Mixte de Recherche Interactions arbres/microorganismes (UMR IAM, France
Marçais, Benoit;
Affiliation
Mendel University, Phytophthora Research Centre (PRC), Czech Republic ; University of Algarve, Laboratory of Molecular Biotechnology and Phytopathology, Centre for Mediterranean Bioresources and Food, Portugal
Jung, Thomas;
Affiliation
Swedish University of Agricultural Sciences (SLU), Department of Forest Mycology and Plant Pathology, Sweden
Stenlid, Jan;
Affiliation
Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Belgium
Ruttink, Tom;
Affiliation
Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Belgium
Heungens, Kurt

The genus Phytophthora comprises many economically and ecologically important plant pathogens. Hybrid species have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a wider host range and display enhanced vigour compared to their progenitors. Phytophthora hybrids therefore pose a serious threat to agriculture as well as to natural ecosystems. Early and correct identification of hybrids is therefore essential for adequate plant protection but this is hampered by the limitations of morphological and traditional molecular methods. Identification of hybrids is also important in evolutionary studies as the positioning of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we have combined genotyping-by-sequencing (GBS) and genome size estimation on a genus-wide collection of 614 Phytophthora isolates. Analyses based on locus- and allele counts and especially on the combination of species-specific loci and genome size estimations allowed us to confirm and characterize 27 previously described hybrid species and discover 16 new hybrid species. Our method was also valuable for species identification at an unprecedented resolution and further allowed correct naming of misidentified isolates. We used both a concatenation- and a coalescent-based phylogenomic method to construct a reliable phylogeny using the GBS data of 140 non-hybrid Phytophthora isolates. Hybrid species were subsequently connected to their progenitors in this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations.

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License Holder: The Author(s). 2021

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