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Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation

Van Poucke, Kris and Haegeman, Annelies and Goedefroit, Thomas and Focquet, Fran and Leus, Leen and Jung, Marilia Horta and Nave, Corina and Redondo, Miguel Angel and Husson, Claude and Kostov, Kaloyan and Lyubenova, Aneta and Christova, Petya and Chandelier, Anne and Slavov, Slavcho and de Cock, Arthur and Bonants, Peter and Werres, Sabine and Oliva Palau, Jonàs and Marçais, Benoit and Jung, Thomas and Stenlid, Jan and Ruttink, Tom and Heungens, Kurt (2021). Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation. IMA fungus. 12 , 16
[Research article]

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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.

Authors/Creators:Van Poucke, Kris and Haegeman, Annelies and Goedefroit, Thomas and Focquet, Fran and Leus, Leen and Jung, Marilia Horta and Nave, Corina and Redondo, Miguel Angel and Husson, Claude and Kostov, Kaloyan and Lyubenova, Aneta and Christova, Petya and Chandelier, Anne and Slavov, Slavcho and de Cock, Arthur and Bonants, Peter and Werres, Sabine and Oliva Palau, Jonàs and Marçais, Benoit and Jung, Thomas and Stenlid, Jan and Ruttink, Tom and Heungens, Kurt
Title:Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation
Series Name/Journal:IMA fungus
Year of publishing :2021
Volume:12
Article number:16
Number of Pages:24
ISSN:2210-6340
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Biological Systematics
Keywords:Flow cytometry, GBS, Oomycete, Hybrid, Phylogeny, Polyploidy
URN:NBN:urn:nbn:se:slu:epsilon-p-112633
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-112633
Additional ID:
Type of IDID
DOI10.1186/s43008-021-00068-w
ID Code:24889
Faculty:S - Faculty of Forest Sciences
Department:(NL, NJ) > Dept. of Forest Mycology and Plant Pathology
(S) > Dept. of Forest Mycology and Plant Pathology
Deposited By: SLUpub Connector
Deposited On:13 Aug 2021 08:25
Metadata Last Modified:13 Aug 2021 08:31

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