Diverse selective sweeps in the genome of the fungal phytopathogen Sclerotinia sclerotiorum

Mark Derbyshire 1 Matthew Denton-Giles 1 James K. Hane 1 Steven Chang 1 Mahsa Mousavi-Derazmahalleh 1,2 Sylvain Raffaele 4 Lone Buchwaldt 3 Lars G. Kamphuis 1
1Centre for Crop and Disease Management, Curtin University, Perth, WA, Australia
2UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
3Agriculture and Agrifood Canada, Saskatoon Research and Development Centre, Saskatoon, Saskatchewan, Canada
4Laboratoire des Interactions Plantes-Micro-Organisms, Institut National de la Recherche Agronomique (INRA), Toulouse, France

The phytopathogenic fungus Sclerotinia sclerotiorum causes disease in more than 400 host species, including several economically important crops. We used single nucleotide polymorphism (SNP) data from 25 re-sequenced isolates of S. sclerotiorum to identify genetically distinct global populations. We then used an approach not commonly applied to plant pathogenic fungi to detect recent selective sweeps based on SNP frequency spectra. In addition, we characterised numerous presence / absence polymorphisms among gene models of the genome of the reference isolate 1980 (1).

We found that among the isolates there were two major global clades of S. sclerotiorum, corresponding to individuals from Europe and North America (population 1), and Australia and Africa (population 2). We found 41 putative selective sweeps in population 1 and 21 in population 2. By considering non-synonymous SNPs in these regions, we identified several candidate genes that may have undergone recent adaptive evolution. We highlight a methyltransferase, two secreted proteins, and a putative secondary metabolite biosynthesis cluster. The latter three of these were significantly up-regulated during infection of Brassica napus based on previously published RNA sequencing data (2).

We also found numerous presence / absence polymorphisms among reference genes and highlight a 200 Kb stretch of chromosome 11 that has been deleted in several isolates. This region contains genes with domains that have previously been associated with fungal vegetative incompatibility. We hypothesise that it may be involved in prevention of hyphal fusion between unrelated isolates of S. sclerotiorum.

1. Derbyshire M, Denton-Giles M, Hegedus D, Seifbarghi S, Rollins J, Kan JV, et al. The complete genome sequence of the phytopathogenic fungus Sclerotinia sclerotiorum reveals insights into the genome architecture of broad host range pathogens. Genome Biol Evol. 2017;9(3):593–618.

2. Seifbarghi S, Borhan MH, Wei Y, Coutu C, Robinson SJ, Hegedus DD. Changes in the Sclerotinia sclerotiorum transcriptome during infection of Brassica napus. BMC Genomics. 2017 Mar 29;18:266.