RNA silencing proteins and small RNAs in oomycete plant pathogens and biocontrol agents

Abstract

IntroductionOomycetes cause several damaging diseases of plants and animals, and some species also act as biocontrol agents on insects, fungi, and other oomycetes. RNA silencing is increasingly being shown to play a role in the pathogenicity of Phytophthora species, either through trans-boundary movement of small RNAs (sRNAs) or through expression regulation of infection promoting effectors.MethodsTo gain a wider understanding of RNA silencing in oomycete species with more diverse hosts, we mined genome assemblies for Dicer-like (DCL), Argonaute (AGO), and RNA dependent RNA polymerase (RDRP) proteins from Phytophthora plurivora, Ph. cactorum, Ph. colocasiae, Pythium oligandrum, Py. periplocum, and Lagenidium giganteum. Moreover, we sequenced small RNAs from the mycelium stage in each of these species.Results and discussionEach of the species possessed a single DCL protein, but they differed in the number and sequence of AGOs and RDRPs. SRNAs of 21nt, 25nt, and 26nt were prevalent in all oomycetes analyzed, but the relative abundance and 5’ base preference of these classes differed markedly between genera. Most sRNAs mapped to transposons and other repeats, signifying that the major role for RNA silencing in oomycetes is to limit the expansion of these elements. We also found that sRNAs may act to regulate the expression of duplicated genes. Other sRNAs mapped to several gene families, and this number was higher in Pythium spp., suggesting a role of RNA silencing in regulating gene expression. Genes for most effector classes were the source of sRNAs of variable size, but some gene families showed a preference for specific classes of sRNAs, such as 25/26 nt sRNAs targeting RxLR effector genes in Phytophthora species. Novel miRNA-like RNAs (milRNAs) were discovered in all species, and two were predicted to target transcripts for RxLR effectors in Ph. plurivora and Ph. cactorum, indicating a putative role in regulating infection. Moreover, milRNAs from the biocontrol Pythium species had matches in the predicted transcriptome of Phytophthora infestans and Botrytis cinerea, and L. giganteum milRNAs matched candidate genes in the mosquito Aedes aegypti. This suggests that trans-boundary RNA silencing may have a role in the biocontrol action of these oomycetes.

Isolation of a Novel Pythium Species, P. thermoculicivorax, and Trichoderma sp. from Natural Enzootic Mosquito Larval Infections

“…Chemical pesticides continue to be the most widely used method for mosquito control, although alternatives, including natural products, gene targeting, sterile insect techniques, and biological agents such as mosquito pathogenic viruses, bacteria, and fungi, are actively being examined and sometimes even commercialized for mosquito control [ 15 , 44 , 45 , 46 , 47 , 48 , 49 ]. Methods for the facile isolation of microbial mosquito larval pathogens ranging from fungi to oomycetes have led to identification of several new species [ 50 , 51 , 52 ].…”

Histone (de)acetylation in epigenetic regulation of Phytophthora pathobiology

“…As discussed by Piombo et al. ( 2023 ), the form of gene regulation mediated by non‐coding small RNAs (sRNAs) is involved in the pathogenicity of the oomycete by transboundary movement of sRNAs or regulation of the expression of effectors. For example, in P. sojae , sRNA regulated transcription of the effector Avr3a , which led to transgenerational silencing (Qiao et al., 2013 ), while the maintenance of the silenced state of the effector gene Avr1b required H3K27me3 deposition (Wang, Chen, et al., 2020 ).…”