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

Abstract

RNA interference (RNAi) is a key regulatory pathway of gene expression in almost all eukaryotes. This mechanism relies on short non-coding RNA molecules (sRNAs) to recognize in a sequence-specific manner DNA or RNA targets leading to transcriptional or post-transcriptional gene silencing. To date, the fundamental role of sRNAs in the regulation of development, stress responses, defense against viruses and mobile elements, and cross-kingdom interactions has been extensively studied in a number of biological systems. However, the knowledge of the "RNAi world" in arbuscular mycorrhizal fungi (AMF) is still limited. AMF are obligate mutualistic endosymbionts of plants, able to provide several benefits to their partners, from improved mineral nutrition to stress tolerance. Here we described the RNAi-related genes of the AMF Gigaspora margarita and characterized, through sRNA sequencing, its complex small RNAome, considering the possible genetic sources and targets of the sRNAs. G. margarita indeed is a mosaic of different genomes since it hosts endobacteria, RNA viruses, and nonintegrated DNA fragments corresponding to mitovirus sequences. Our findings show that G. margarita is equipped with a complete set of RNAi-related genes characterized by the expansion of the Argonaute-like (AGO-like) gene family that seems a common trait of AMF. With regards to sRNAs, we detected populations of sRNA reads mapping to nuclear, mitochondrial, and viral genomes that share similar features (25-nt long and 5 -end uracil read enrichments), and that clearly differ from sRNAs of endobacterial origin. Furthermore, the annotation of nuclear loci producing sRNAs suggests the occurrence of different sRNA-generating processes. In silico analyses indicate that the most abundant G. margarita sRNAs, including those of viral origin, could target transcripts in the host plant, through a hypothetical cross-kingdom RNAi.

Marine Oomycetes of the Genus Halophytophthora Harbor Viruses Related to Bunyaviruses

“…While vic and mating systems serve as antiviral defense mechanisms at the population level, RNA silencing or RNA interference (RNAi) provides a fungal antiviral defense response at the cellular level (Nuss, 2011). Antiviral RNA silencing has been demonstrated in different types of fungi including the chestnut pathogen Cryphonectria parasitica (Segers et al, 2007) or the arbuscular mycorrhizal fungus Gigaspora margarita (Silvestri et al, 2020) but also in oomycetes (Fahlgren et al, 2013). Since the RNAi machinery targets possible detrimental non-self-nucleic acids, virus-infected host organisms are normally enriched with viral small interfering (si) RNA.…”

Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungusRhizophagus irregularis

“…The genome of R. irregularis is particularly interesting because it contains over 2000 kinases and 30 Argonaute (AGO) genes, the highest numbers of these genes recorded so far in any species (6, 7, 8, 9 13, 14). As all superfamilies of transposons are capable of duplicating genes or gene fragments (30), we hypothesized that TE activity may have caused these gene expansions.…”

“…In eukaryotes, RdRPs are recruited to target RNAs, which they use as a template to produce complementary RNAs which trigger a secondary amplification mechanism to generate more sRNAs and enhance silencing activity (39). Examination of RNAi pathway genes in the genomes of mycorrhizal fungi revealed that AM species harbour AGO and RdRP gene expansions, and have maintained the sRNA methyltransferase ( HEN1 ) gene (Figure S4B, 6, 13, 14). For RNAi pathways to be functional in spores, proteins involved in sRNA biogenesis and function must be expressed.…”

“…Genomic analyses of these species have revealed contents of repetitive sequences ranging from 23 to 43% (9, 12). These repeats consist of transposable elements (TE) and expanded gene families that occasionally form tandemly repeated arrays of duplicate genes (6, 7, 8, 9, 13, 14). Expanded family genes are either orphans (no significant homologs can be identified), or contain protein domains related to signalling and RNA interference (RNAi), such as kinase, BTB/POZ (Broad-Complex, Tramtrack and Bric a brac/Pox virus and Zinc finger) domains, Sel1 tetratricopeptide repeats, Kelch-repeats and P-element Induced WImpy testis (PIWI) domains.…”

Mycorrhizal Interventions for Sustainable Potato Production in Africa

“…They can upregulate defense mechanisms upon herbivore attack against disease vectors such as aphids (Rizzo et al, 2020), as in the case with PVY. AM fungi have also been reported to contain silencing RNA, enabling negative regulation of pathogen gene expression and thus conferring plant protection (Silvestri et al, 2020).…”