Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen
- Luigi Faino1,3,
- Michael F. Seidl1,3,
- Xiaoqian Shi-Kunne1,
- Marc Pauper1,
- Grardy C.M. van den Berg1,
- Alexander H.J. Wittenberg2 and
- Bart P.H.J. Thomma1
- 1Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, The Netherlands;
- 2Keygene N.V., 6708 PW Wageningen, The Netherlands
- Corresponding author: bart.thomma{at}wur.nl
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↵3 These authors contributed equally to this work.
Abstract
Genomic plasticity enables adaptation to changing environments, which is especially relevant for pathogens that engage in “arms races” with their hosts. In many pathogens, genes mediating virulence cluster in highly variable, transposon-rich, physically distinct genomic compartments. However, understanding of the evolution of these compartments, and the role of transposons therein, remains limited. Here, we show that transposons are the major driving force for adaptive genome evolution in the fungal plant pathogen Verticillium dahliae. We show that highly variable lineage-specific (LS) regions evolved by genomic rearrangements that are mediated by erroneous double-strand repair, often utilizing transposons. We furthermore show that recent genetic duplications are enhanced in LS regions, against an older episode of duplication events. Finally, LS regions are enriched in active transposons, which contribute to local genome plasticity. Thus, we provide evidence for genome shaping by transposons, both in an active and passive manner, which impacts the evolution of pathogen virulence.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.204974.116.
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Freely available online through the Genome Research Open Access option.
- Received January 30, 2016.
- Accepted June 17, 2016.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
