A whole genome scan of SNP data suggests a lack of abundant hard selective sweeps in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum.

Mark Charles Derbyshire,James K Hane,Mahsa Mousavi-Derazmahalleh,Lars G Kamphuis,Sylvain Raffaele,Lone Buchwaldt,Steven Chang,Matthew Denton-Giles,Tzen-Yuh Chiang

doi:10.1371/journal.pone.0214201

Abstract

The pathogenic fungus Sclerotinia sclerotiorum infects over 600 species of plant. It is present in numerous environments throughout the world and causes significant damage to many agricultural crops. Fragmentation and lack of gene flow between populations may lead to population sub-structure. Within discrete recombining populations, positive selection may lead to a ‘selective sweep’. This is characterised by an increase in frequency of a favourable allele leading to reduction in genotypic diversity in a localised genomic region due to the phenomenon of genetic hitchhiking. We aimed to assess whether isolates of S. sclerotiorum from around the world formed genotypic clusters associated with geographical origin and to determine whether signatures of population-specific positive selection could be detected. To do this, we sequenced the genomes of 25 isolates of S. sclerotiorum collected from four different continents–Australia, Africa (north and south), Europe and North America (Canada and the northen United States) and conducted SNP based analyses of population structure and selective sweeps. Among the 25 isolates, there was evidence for two major population clusters. One of these consisted of 11 isolates from Canada, the USA and France (population 1), and the other consisted of nine isolates from Australia and one from Morocco (population 2). The rest of the isolates were genotypic outliers. We found that there was evidence of outcrossing in these two populations based on linkage disequilibrium decay. However, only a single candidate selective sweep was observed, and it was present in population 2. This sweep was close to a Major Facilitator Superfamily transporter gene, and we speculate that this gene may have a role in nutrient uptake from the host. The low abundance of selective sweeps in the S. sclerotiorum genome contrasts the numerous examples in the genomes of other fungal pathogens. This may be a result of its slow rate of evolution and low effective recombination rate due to self-fertilisation and vegetative reproduction.

Highlights

Spread of a favourable allele through a population due to positive selective pressure is known as a selective sweep [1,2]
To gain further insight into positive selective pressure in plant pathogens, we examined the genome of the fungus Sclerotinia sclerotiorum for evidence of selective sweeps
To confirm that fungal isolates belonged to the species S. sclerotiorum, a phylogenetic tree was built using previously published heat shock protein 60 (HSP60) gene sequences in conjunction with sequences from de novo assemblies

Summary

Introduction

Spread of a favourable allele through a population due to positive selective pressure is known as a selective sweep [1,2]. When a favourable allele increases in frequency due to positive selective pressure, linked loci increase in frequency. Several tests for selective sweeps have been developed based on this understanding [4,5,6] Such tests have been applied to numerous organisms to study the footprints of positive selection in genomes [7]. 346 genomic regions in Drosophila melanogaster were found to exhibit a significantly high degree of fixation between populations from Europe and Africa. Genes within these regions were enriched for various functional activities including transcriptional regulation [8]. Numerous population specific signals of positive selection have been identified and linked with genes involved in processes such as skin pigmentation, immunity, heat shock and olfactory perception [9,10,11,12]

Objectives

Methods

Results

Conclusion