Abstract
SummaryFungal plant pathogens secrete effector proteins and metabolites to cause disease. Additionally, some species transfer small RNAs (sRNAs) into plant cells to silence host mRNAs through complementary base pairing and suppress plant immunity. The fungus Sclerotinia sclerotiorum infects over 600 plant species, but little is known about the molecular processes that govern interactions with its many hosts. In particular, evidence for the production of sRNAs by S. sclerotiorum during infection is lacking. We sequenced sRNAs produced by S. sclerotiorum in vitro and during infection of two host species, Arabidopsis thaliana and Phaseolus vulgaris. We found that S. sclerotiorum produces at least 374 distinct highly abundant sRNAs during infection, mostly originating from repeat‐rich plastic genomic regions. We predicted the targets of these sRNAs in A. thaliana and found that these genes were significantly more down‐regulated during infection than the rest of the genome. Predicted targets of S. sclerotiorum sRNAs in A. thaliana were enriched for functional domains associated with plant immunity and were more strongly associated with quantitative disease resistance in a genome‐wide association study (GWAS) than the rest of the genome. Mutants in A. thaliana predicted sRNA target genes SERK2 and SNAK2 were more susceptible to S. sclerotiorum than wild‐type, suggesting that S. sclerotiorum sRNAs may contribute to the silencing of immune components in plants. The prediction of fungal sRNA targets in plant genomes can be combined with other global approaches, such as GWAS, to assist in the identification of plant genes involved in quantitative disease resistance.
Highlights
Fungal phytopathogens largely rely on small secreted proteins, termed effectors, to infect and cause disease [1]
To identify S. sclerotiorum small RNAs (sRNAs) expressed during infection of host plants, we conducted sRNA sequencing on S. sclerotiorum growing in vitro and during infection of the two host species A. thaliana and P. vulgaris
We filtered out reads that matched exactly (i) the sense strands of plant transcripts, (ii) plant non-coding RNAs, (iii) plant sRNAs (either a mock inoculated A. thaliana sample or a P. vulgaris sRNA data set obtained from [33]), (iv) the sense strands of S. sclerotiorum transcripts, (v) S. sclerotiorum non-coding RNAs from Rfam
Summary
Fungal phytopathogens largely rely on small secreted proteins, termed effectors, to infect and cause disease [1]. Effectors can enter plant cells or act in the apoplast to manipulate host cell functions and promote fungal invasive growth [2].Necrotrophic fungi, which actively kill host cells, may secrete various secondary metabolites to facilitate plant colonization [3]. Small RNAs produced by the plant pathogenic fungus Botrytis cinerea were shown to be transferred into host tissues, where they silence host genes to facilitate infection [4].
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