Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation
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...
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2021-07-01
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| Online Access: | https://doi.org/10.1186/s43008-021-00068-w |
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| author | Kris Van Poucke Annelies Haegeman Thomas Goedefroit Fran Focquet Leen Leus Marília Horta Jung Corina Nave Miguel Angel Redondo Claude Husson Kaloyan Kostov Aneta Lyubenova Petya Christova Anne Chandelier Slavcho Slavov Arthur de Cock Peter Bonants Sabine Werres Jonàs Oliva Palau Benoit Marçais Thomas Jung Jan Stenlid Tom Ruttink Kurt Heungens |
| author_facet | Kris Van Poucke Annelies Haegeman Thomas Goedefroit Fran Focquet Leen Leus Marília Horta Jung Corina Nave Miguel Angel Redondo Claude Husson Kaloyan Kostov Aneta Lyubenova Petya Christova Anne Chandelier Slavcho Slavov Arthur de Cock Peter Bonants Sabine Werres Jonàs Oliva Palau Benoit Marçais Thomas Jung Jan Stenlid Tom Ruttink Kurt Heungens |
| author_sort | Kris Van Poucke |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-9a987cda08104cc0afd655760da2760a |
| institution | Kabale University |
| issn | 2210-6359 |
| language | English |
| publishDate | 2021-07-01 |
| publisher | BMC |
| record_format | Article |
| series | IMA Fungus |
| spelling | doaj-art-9a987cda08104cc0afd655760da2760a2025-02-02T19:58:12ZengBMCIMA Fungus2210-63592021-07-0112112410.1186/s43008-021-00068-wUnravelling hybridization in Phytophthora using phylogenomics and genome size estimationKris Van Poucke0Annelies Haegeman1Thomas Goedefroit2Fran Focquet3Leen Leus4Marília Horta Jung5Corina Nave6Miguel Angel Redondo7Claude Husson8Kaloyan Kostov9Aneta Lyubenova10Petya Christova11Anne Chandelier12Slavcho Slavov13Arthur de Cock14Peter Bonants15Sabine Werres16Jonàs Oliva Palau17Benoit Marçais18Thomas Jung19Jan Stenlid20Tom Ruttink21Kurt Heungens22Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences UnitFlanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences UnitFlanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences UnitFlanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences UnitFlanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences UnitPhytophthora Research Centre (PRC), Mendel UniversityJulius Kühn Institute (JKI) – Federal Research Center for Cultivated Plants, Institute for Plant Protection in Horticulture and Forestry (GF)Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences (SLU)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 ForêtsAgroBioInstitute (ABI), Agricultural AcademyAgroBioInstitute (ABI), Agricultural AcademyAgroBioInstitute (ABI), Agricultural AcademyLife Sciences Department, Walloon Agricultural Research Centre (CRAW)AgroBioInstitute (ABI), Agricultural AcademyWesterdijk Fungal Biodiversity InstituteWageningen University & Research, Business Unit Biointeractions & Plant HealthJulius Kühn Institute (JKI) – Federal Research Center for Cultivated Plants, Institute for Plant Protection in Horticulture and Forestry (GF)Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences (SLU)Université de Lorraine – Institut National de la Recherche Agronomique (INRAe), L’Unité Mixte de Recherche Interactions arbres/microorganismes (UMR IAM)Phytophthora Research Centre (PRC), Mendel UniversityDepartment of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences (SLU)Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences UnitFlanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences UnitAbstract 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.https://doi.org/10.1186/s43008-021-00068-wFlow cytometryGBSOomyceteHybridPhylogenyPolyploidy |
| spellingShingle | Kris Van Poucke Annelies Haegeman Thomas Goedefroit Fran Focquet Leen Leus Marília Horta Jung Corina Nave Miguel Angel Redondo Claude Husson Kaloyan Kostov Aneta Lyubenova Petya Christova Anne Chandelier Slavcho Slavov Arthur de Cock Peter Bonants Sabine Werres Jonàs Oliva Palau Benoit Marçais Thomas Jung Jan Stenlid Tom Ruttink Kurt Heungens Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation IMA Fungus Flow cytometry GBS Oomycete Hybrid Phylogeny Polyploidy |
| title | Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation |
| title_full | Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation |
| title_fullStr | Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation |
| title_full_unstemmed | Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation |
| title_short | Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation |
| title_sort | unravelling hybridization in phytophthora using phylogenomics and genome size estimation |
| topic | Flow cytometry GBS Oomycete Hybrid Phylogeny Polyploidy |
| url | https://doi.org/10.1186/s43008-021-00068-w |
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