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Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen

View ORCID ProfileMarina Pais, Kentaro Yoshida, View ORCID ProfileArtemis Giannakopoulou, Mathieu A. Pel, View ORCID ProfileLiliana M. Cano, Ricardo F. Oliva, Kamil Witek, View ORCID ProfileHannele Lindqvist-Kreuze, Vivianne G. A. A. Vleeshouwers, View ORCID ProfileSophien Kamoun
doi: https://doi.org/10.1101/116012
Marina Pais
1The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
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Kentaro Yoshida
1The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
2Graduate School of Agricultural Science, Kobe University, Japan
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Artemis Giannakopoulou
1The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
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Mathieu A. Pel
3Wageningen UR Plant Breeding, Wageningen, The Netherlands
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Liliana M. Cano
1The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
4Institute of Food and Agricultural Sciences, Department of Plant Pathology, Indian River Research and Education Center, University of Florida, Fort Pierce, FL, USA
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Ricardo F. Oliva
1The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
5Genetics and Biotechnology Division, International Rice Research Institute, Los Banos, Philippines
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Kamil Witek
1The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
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Hannele Lindqvist-Kreuze
6International Potato Center, Lima, Peru
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Vivianne G. A. A. Vleeshouwers
2Graduate School of Agricultural Science, Kobe University, Japan
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Sophien Kamoun
1The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
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  • ORCID record for Sophien Kamoun
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Abstract

Outbreaks caused by asexual lineages of fungal and oomycete pathogens are an expanding threat to crops, wild animals and natural ecosystems (Fisher et al. 2012,Kupferschmidt 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl and Thomma 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Cooke et al. 2012, Yoshida et al. 2013,Yoshida et al. 2014). Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by compared sibling strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Forbes et al. 1997, Oyarzun et al. 1998, Delgado et al. 2013, Yoshida et al. 2013, Yoshida et al. 2014). We detected numerous examples of structural variation, nucleotide polymorphisms and gene conversion within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. These results highlight the exceptional genetic and phenotypic plasticity that underpins host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen.

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Posted March 11, 2017.
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Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen
Marina Pais, Kentaro Yoshida, Artemis Giannakopoulou, Mathieu A. Pel, Liliana M. Cano, Ricardo F. Oliva, Kamil Witek, Hannele Lindqvist-Kreuze, Vivianne G. A. A. Vleeshouwers, Sophien Kamoun
bioRxiv 116012; doi: https://doi.org/10.1101/116012
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Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen
Marina Pais, Kentaro Yoshida, Artemis Giannakopoulou, Mathieu A. Pel, Liliana M. Cano, Ricardo F. Oliva, Kamil Witek, Hannele Lindqvist-Kreuze, Vivianne G. A. A. Vleeshouwers, Sophien Kamoun
bioRxiv 116012; doi: https://doi.org/10.1101/116012

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