Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots.

Eva H Stukenbrock,Julien Y Dutheil

doi:10.1534/genetics.117.300502

Abstract

Meiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation, and rates of adaptation. In many organisms, recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate and positions of recombination hotspot can be studied using population genomics data and statistical methods. In this study, we conducted population genomics analyses to address the evolution of recombination in two closely related fungal plant pathogens: the prominent wheat pathogen Zymoseptoria tritici and a sister species infecting wild grasses Z. ardabiliae. We specifically addressed whether recombination landscapes, including hotspot positions, are conserved in the two recently diverged species and if recombination contributes to rapid evolution of pathogenicity traits. We conducted a detailed simulation analysis to assess the performance of methods of recombination rate estimation based on patterns of linkage disequilibrium, in particular in the context of high nucleotide diversity. Our analyses reveal overall high recombination rates, a lack of suppressed recombination in centromeres, and significantly lower recombination rates on chromosomes that are known to be accessory. The comparison of the recombination landscapes of the two species reveals a strong correlation of recombination rate at the megabase scale, but little correlation at smaller scales. The recombination landscapes in both pathogen species are dominated by frequent recombination hotspots across the genome including coding regions, suggesting a strong impact of recombination on gene evolution. A significant but small fraction of these hotspots colocalize between the two species, suggesting that hotspot dynamics contribute to the overall pattern of fast evolving recombination in these species.

Highlights

Meiotic recombination is an important driver of evolution
These methods are based on genome-wide patterns of linkage disequilibrium (LD) among single nucleotide polymorphisms (SNPs) and have the potential to capture the history of recombination events in a population sample
After filtering we identified 1.48 million SNPs in Z. tritici and 1.07 million SNPs in Z. ardabiliae, which corresponds to the nucleotide diversities, measured as Watterson’s u, of 0.0139 in Z. tritici and 0.0087 in Z. ardabiliae (Table 1)

Summary

Introduction

Meiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation, and rates of adaptation. While experimental measures of recombination rate can be challenging in many species, advances in statistical analyses provide powerful tools to generate fine-scale recombination maps using population genomic data (e.g., Myers et al 2005; Chan et al 2012; Wang and Rannala 2014). These methods are based on genome-wide patterns of linkage disequilibrium (LD) among single nucleotide polymorphisms (SNPs) and have the potential to capture the history of recombination events in a population sample. The accessory chromosomes are partly conserved among several species in the genus Zymoseptoria, suggesting that these small chromosomes have been maintained over long evolutionary times, predating the divergence of species (Stukenbrock et al 2011)

Methods

Results

Conclusion