Small RNAs from the plant pathogenic fungus Sclerotinia sclerotiorum highlight candidate host target genes associated with quantitative disease resistance

Abstract

Plant pathogenic fungi secrete effector proteins and secondary metabolites to cause disease.Additionally, some produce small RNAs (sRNAs) that silence transcripts of host immunity genes through RNA interference. The fungus Sclerotinia sclerotiorum infects over 600 plant species, but little is known about its molecular interactions with its hosts. In particular, the role of sRNAs in S. sclerotiorum pathogenicity has not been determined. By sequencing sRNAs in vitro and during infection of two host species, we found that S. sclerotiorum produces at least 374 highly abundant sRNAs. These sRNAs mostly originated from polymorphic repeat-rich genomic regions. Predicted gene targets of these sRNAs, from 10 different host species, were enriched for immunity-related functional domains. Predicted A. thaliana gene targets of S. sclerotiorum sRNAs were significantly more down-regulated during infection than other genes. A. thaliana gene targets were also more likely to contain single nucleotide polymorphisms (SNPs) associated with quantitative disease resistance. In conclusion, sRNAs produced by S. sclerotiorum are likely capable of silencing immunity components in multiple hosts. Prediction of fungal sRNA targets in host plant genomes can be combined with other global approaches, such as genome wide association studies and transcriptomics, to assist identification of plant genes involved in disease resistance.

Small RNA inhibits infection by downy mildew pathogen Hyaloperonospora arabidopsidis

“…In general, two classes of small non‐coding RNAs exist in plant cells: miRNAs (encoded by the genome) and siRNAs (derived from dsRNA produced by multiple sources) (Khraiwesh et al ., ). In addition, the size of sRNAs in organisms can be different (Derbyshire et al , ). Several studies revealed that, in plants and animals, each sRNA (acting as a guide) binds to an Argonaute family protein and a sequence‐specific gene silencing ribonucleoprotein (RNP) is formed by base pairing between the sRNA and its target mRNA; this is known as the RNA‐induced silencing complex (RISC) in miRNA and siRNA pathways (Budak and Akpinar, ; Vargason et al , ; Wilson and Doudna, ).…”

Nonproteinaceous effectors: the terra incognita of plant–fungal interactions

“…Indeed, a single B. cinerea sRNA Bc ‐siR37 targets at least three A. thaliana genes involved in diverse aspects of plant defence (Wang et al ., ). In addition, recent evidence from S. sclerotiorum suggests that sRNAs target many genes in phylogenetically diverse host species (Derbyshire et al ., ). A priority now is to determine how widely the deployment of sRNA effectors is conserved among plant‐associated fungi with contrasting lifestyles, including endophytes and symbionts.…”

“…tritici (Wang et al ., , ). In silico predictions in the genomes of Sclerotinia sclerotiorum and Blumeria graminis suggest they produce sRNA effectors that putatively target genes in their plant hosts (Derbyshire et al ., ; Kusch et al ., ). Such genomic analyses indicate that expressing sRNA effectors to target plant host genes could be a widespread strategy in fungal plant pathogens.…”

Different Genetic Sources Contribute to the Small RNA Population in the Arbuscular Mycorrhizal Fungus Gigaspora margarita

“…Interestingly, the 23-26 nt range also corresponded to the group of the most expressed sRNAs (Figure 5), with the only exception of the endobacterium and the Giardia-like virus, the latter however characterized by very few total mapped reads. The 5 -ends enrichment in uracil, which is a rather common feature of fungal sRNA (Nicolás et al, 2003;Dumesic et al, 2013;Mueth et al, 2015;Nguyen et al, 2018;Derbyshire et al, 2019;Silvestri et al, 2019), for the 23-26nt long G. margarita sRNAs (the most expressed ones), could be a further indication of a functional role. Remarkably, the nucleotide composition of the 5 -end of sRNAs affects their ability to be loaded onto different classes of AGO proteins; in A. thaliana the uracil at the 5 -end is indeed associated with the sRNA loading onto AGO1 and AGO10, while cytosine is associated with AGO5, and adenine with AGO2, AGO4, AGO6, AGO7, and AGO9 (Borges and Martienssen, 2015).…”

“…This result is not surprising considering that the length of the sRNAs seems not to be a conserved trait in fungi, even among species from the same genus, such as Fusarium oxysporum and Fusarium graminearum (Chen et al, 2014(Chen et al, , 2015. For example N. crassa mainly produces 25-nt long sRNAs (Fulci and Macino, 2007), M. circinelloides 21and 25-nt (Nicolás et al, 2003), Aspergillus nidulans 25-nt (Hammond and Keller, 2005), M. oryzae 19-23-nt (Kadotani et al, 2003), Cryptococcus neoformans 22-nt (Dumesic et al, 2013), Trichoderma atroviride 20-21-and 24-nt (Carreras-Villaseñor et al, 2013), F. graminearum 27-and 28-nt (Chen et al, 2015), F. oxysporum 19-and 21-nt (Chen et al, 2014), Sclerotinia sclerotiorum 22-nt (Derbyshire et al, 2019), and Puccinia striiformis 22-nt (Mueth et al, 2015).…”