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Genomewide signatures of selection in Epichloë reveal candidate genes for host specialization.
Journal article

Genomewide signatures of selection in Epichloë reveal candidate genes for host specialization.

  • Schirrmann MK Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland.
  • Zoller S Genetic Diversity Centre (GDC), ETH Zürich, Zürich, Switzerland.
  • Croll D Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
  • Stukenbrock EH Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany.
  • Leuchtmann A Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland.
  • Fior S Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland.
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  • 2018-04-11
Published in:
  • Molecular ecology. - 2018
endophytic fungi
host specialization
pathogens
population genomics
positive selection
secreted proteins
Endophytes
Epichloe
Genetic Variation
Genetics, Population
English Host specialization is a key process in ecological divergence and speciation of plant-associated fungi. The underlying determinants of host specialization are generally poorly understood, especially in endophytes, which constitute one of the most abundant components of the plant microbiome. We addressed the genetic basis of host specialization in two sympatric subspecies of grass-endophytic fungi from the Epichloë typhina complex: subsp. typhina and clarkii. The life cycle of these fungi entails unrestricted dispersal of gametes and sexual reproduction before infection of a new host, implying that the host imposes a selective barrier on viability of the progeny. We aimed to detect genes under divergent selection between subspecies, experiencing restricted gene flow due to adaptation to different hosts. Using pooled whole-genome sequencing data, we combined FST and DXY population statistics in genome scans and detected 57 outlier genes showing strong differentiation between the two subspecies. Genomewide analyses of nucleotide diversity (π), Tajima's D and dN/dS ratios indicated that these genes have evolved under positive selection. Genes encoding secreted proteins were enriched among the genes showing evidence of positive selection, suggesting that molecular plant-fungus interactions are strong drivers of endophyte divergence. We focused on five genes encoding secreted proteins, which were further sequenced in 28 additional isolates collected across Europe to assess genetic variation in a larger sample size. Signature of positive selection in these isolates and putative identification of pathogenic function supports our findings that these genes represent strong candidates for host specialization determinants in Epichloë endophytes. Our results highlight the role of secreted proteins as key determinants of host specialization.
Language
  • English
Open access status
closed
Identifiers
Persistent URL
https://sonar.ch/global/documents/113089
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