# Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen

## TL;DR

A fungal wheat pathogen adapts to different climates through gene copy number changes, especially involving a mobile genetic element linked to climate tolerance.

## Contribution

The study identifies a conserved Sirtuin gene within a mobile element as a key driver of global thermal adaptation in a fungal pathogen.

## Key findings

- Gene copy number variation (CNV) facilitates climate adaptation in Zymoseptoria tritici.
- A conserved Sirtuin gene within a Starship mobile element is strongly associated with climatic adaptation.
- Gene loss and CNVs in secondary metabolite pathways likely aid in continental colonization and climate tolerance.

## Abstract

Copy number variation (CNV) can drive rapid evolution in changing environments. In microbial pathogens, such adaptation is a key factor underpinning epidemics and colonization of new niches. However, the genomic determinants of such adaptation remain poorly understood. Here, we systematically investigate CNVs in a large genome sequencing dataset spanning a worldwide collection of 1104 genomes from the major wheat pathogen Zymoseptoria tritici. We found overall strong purifying selection acting on most CNVs. Genomic defense mechanisms likely accelerated gene loss over episodes of continental colonization. Local adaptation along climatic gradients was likely facilitated by CNVs affecting secondary metabolite production and gene loss in general. One of the strongest loci for climatic adaptation is a highly conserved gene of the NAD-dependent Sirtuin family. The Sirtuin CNV locus localizes to an ~68-kb Starship mobile element unique to the species carrying genes highly expressed during plant infection. The element has likely lost the ability to transpose, demonstrating how the ongoing domestication of cargo-carrying selfish elements can contribute to selectable variation within populations. Our work highlights how standing variation in gene copy numbers at the global scale can be a major factor driving climatic and metabolic adaptation in microbial species.

The deletion and duplication of genes can be major facilitators of evolution. Here, the role of such variation was investigated in over a thousand genomes characterizing the global spread of a major fungal pathogen of wheat. The study suggests that gene loss likely facilitated the pathogen’s colonization of new continents by modulating climate tolerance and metabolic capabilities.