Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant PathogenVerticillium dahliae

Abstract

Transposable elements (TEs) are a major source of genetic and regulatory variation in their host genome and are consequently thought to play important roles in evolution. Many fungal and oomycete plant pathogens have evolved dynamic and TE-rich genomic regions containing genes that are implicated in host colonization and adaptation. TEs embedded in these regions have typically been thought to accelerate the evolution of these genomic compartments, but little is known about their dynamics in strains that harbor them. Here, we used whole-genome sequencing data of 42 strains of the fungal plant pathogen Verticillium dahliae to systematically identify polymorphic TEs that may be implicated in genomic as well as in gene expression variation. We identified 2,523 TE polymorphisms and characterize a subset of 8% of the TEs as polymorphic elements that are evolutionary younger, less methylated, and more highly expressed when compared with the remaining 92% of the total TE complement. As expected, the polyrmorphic TEs are enriched in the adaptive genomic regions. Besides, we observed an association of polymorphic TEs with pathogenicity-related genes that localize nearby and that display high expression levels. Collectively, our analyses demonstrate that TE dynamics in V. dahliae contributes to genomic variation, correlates with expression of pathogenicity-related genes, and potentially impacts the evolution of adaptive genomic regions.

Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi

“…3d ). This observation would corroborate the hypothesis of stress-driven TE de-repression observed in other patho-systems 43 – 45 . However, it also shows that in P. pachyrhizi only a small percentage of the TEs are highly expressed during early infection stages.…”

Highlight: Virtual Issue on Host–Pathogen Interactions and Antimicrobial Drug Resistance

“…A study by Wyka et al (2021) investigated the plant pathogen Claviceps and found that expansion of transposable elements and tandem gene duplications coincided with increased host range potential and speciation. According to Wyka et al, this indicates that “alterations of genomic architecture and plasticity can substantially influence and shape the evolutionary trajectory of fungal pathogens and their adaptability.” Consistent with this, Torres et al (2021) identified polymorphic transposable elements in the fungal plant pathogen Verticillium dahliae that colocalized near pathogenicity-related genes and correlated with high expression levels, suggesting that these elements may impact the evolution of adaptive genomic regions.…”

The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation

“…These damaging effects can be avoided and controlled by epigenetic silencing, such as through DNA methylation [193]. siRNAs are interconnected with various TEs and act as mediators and stimulate DNA methylation [252]. This DNA methylation may lead to suppression of transposition through transcription reduction, along with the formation of loops among DNA and histone methylations (Figure 4) through siRNAs [253].…”