The population genetics of adaptation through copy number variation in a fungal plant pathogen.

Autor: Stalder L; Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland., Oggenfuss U; Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland., Mohd-Assaad N; Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.; Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia., Croll D; Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
Jazyk: angličtina
Zdroj: Molecular ecology [Mol Ecol] 2023 May; Vol. 32 (10), pp. 2443-2460. Date of Electronic Publication: 2022 Apr 05.
DOI: 10.1111/mec.16435
Abstrakt: Microbial pathogens can adapt rapidly to changing environments such as the application of pesticides or host resistance. Copy number variations (CNVs) are a major source of adaptive genetic variation for recent adaptation. Here, we analyse how a major fungal pathogen of barley, Rhynchosporium commune, has adapted to the host environment and fungicide applications. We screen the genomes of 125 isolates sampled across a worldwide set of populations and identify a total of 7,879 gene duplications and 116 gene deletions. Most gene duplications result from segmental chromosomal duplications. Although CNVs are generally under negative selection, we find that genes affected by CNVs are enriched in functions related to host exploitation (i.e., effectors and cell-wall-degrading enzymes). We perform genome-wide association studies (GWAS) and identify a large segmental duplication of CYP51A that has contributed to the emergence of azole resistance and a duplication encompassing an effector gene affecting virulence. We show that the adaptive CNVs were probably created by recently active transposable element families. Moreover, we find that specific transposable element families are important drivers of recent gene CNV. Finally, we use a genome-wide single nucleotide polymorphism data set to replicate the GWAS and contrast it with the CNV-focused analysis. Together, our findings show how extensive segmental duplications create the raw material for recent adaptation in global populations of a fungal pathogen.
(© 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)
Databáze: MEDLINE
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