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Research article - Peer-reviewed, 2021

Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation

Van Poucke, Kris; Haegeman, Annelies; Goedefroit, Thomas; Focquet, Fran; Leus, Leen; Jung, Marilia Horta; Nave, Corina; Redondo, Miguel Angel; Husson, Claude; Kostov, Kaloyan; Lyubenova, Aneta; Christova, Petya; Chandelier, Anne; Slavov, Slavcho; de Cock, Arthur; Bonants, Peter; Werres, Sabine; Oliva Palau, Jonàs; Marçais, Benoit; Jung, Thomas;
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Abstract

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.

Keywords

Flow cytometry; GBS; Oomycete; Hybrid; Phylogeny; Polyploidy

Published in

IMA fungus

2021, volume: 12, number: 1, article number: 16

Authors' information

Van Poucke, Kris
Flanders Research Institute for Agriculture, Fisheries and Food
Haegeman, Annelies
Flanders Research Institute for Agriculture, Fisheries and Food
Goedefroit, Thomas
Flanders Research Institute for Agriculture, Fisheries and Food
Focquet, Fran
Flanders Research Institute for Agriculture, Fisheries and Food
Leus, Leen
Flanders Research Institute for Agriculture, Fisheries and Food
Jung, Marilia Horta
Mendel University Brno
Nave, Corina
Julius Kühn Institute (JKI)
Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology
Husson, Claude
French ministry for agriculture and food
Kostov, Kaloyan
AgroBioInstitute
Lyubenova, Aneta
AgroBioInstitute
Christova, Petya
AgroBioInstitute
Chandelier, Anne
Walloon Agricultural Research Centre
Slavov, Slavcho
AgroBioInstitute
de Cock, Arthur
Westerdijk Fungal Biodiversity Institute
Bonants, Peter
Wageningen University and Research
Werres, Sabine
Julius Kühn Institute (JKI)
Oliva Palau, Jonàs
Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology
Oliva Palau, Jonàs
University of Lleida
Marçais, Benoit
University of Lorraine
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UKÄ Subject classification

Biological Systematics

Publication Identifiers

DOI: https://doi.org/10.1186/s43008-021-00068-w

URI (permanent link to this page)

https://res.slu.se/id/publ/112633