Silenced retrotransposons are major rasiRNAs targets in Arabidopsis galls induced by Meloidogyne javanica

Abstract

Root-knot nematodes (RKNs, Meloidogyne spp.) are sedentary biotrophic pathogens that establish within the vascular cylinder of plant roots, forming a gall and inducing several feeding cells, giant cells (GCs), essential for completion of their life cycle. GCs suffer gene expression changes, repeated mitosis and endoreduplication events. Transcriptomics has revealed that an extensive down-regulation of transcripts, a molecular signature of early-developing galls and GCs that is conserved in tomato and Arabidopsis, may be achieved through small RNA (sRNA) gene silencing pathways. The role of some microRNAs (miRNAs) in plant-RKN interactions has recently been addressed, but little is known about the regulatory roles of other sRNA types. Here, we perform a differential accumulation analysis to show which repeat-associated small interfering RNAs (rasiRNAs) are distinctive or enriched in early Arabidopsis galls vs. uninfected roots. Those distinctive from galls are preferentially located in pericentromeric regions with predominant sizes of 24 and 22 nucleotides. Gall-distinctive rasiRNAs target primarily GYPSY and COPIA retrotransposons, which show a marked repression in galls vs. uninfected roots. Infection tests and phenotypic studies of galls from Meloidogyne javanica in Arabidopsis mutants impaired in post-transcriptional gene silencing and/or canonical RNA-directed DNA methylation (RdDM) pathways, as well as quantitative polymerase chain reaction analysis, suggest the implication of canonical and non-canonical RdDM pathways during gall formation, possibly through the regulation of retrotransposons. This process may be crucial for the maintenance of genome integrity during the reprogramming process of galls/GCs from their vascular precursor cells, and/or to ensure a faithful DNA replication during the repeated mitosis/endoreduplication that concurs with feeding site formation.

Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

“…These genes are, therefore, robust candidates for regulation by hc-siRNA, through RdDM, during the development of feeding sites induced by plant-parasitic nematodes. Recently, two Arabidopsis mutants rdr2-rdr6 and dcl2/dcl3/dcl4 deprived of key factors for RdDM were shown to have lower rates of infection with RKN highlighting the importance of siRNAs and RdDM in Arabidopsis-Meloidogyne interaction [52].…”

Biological Control of Plant-Parasitic Nematodes by Filamentous Fungi Inducers of Resistance: Trichoderma, Mycorrhizal and Endophytic Fungi

“…This heritability extends to the growth promotion induced by this fungus during its interaction with the plant that is accompanied by a significant reduction in the defenses dependent on the SA and JA pathways. In this respect, it is very interesting to highlight how fungal symbiosis and nematode infection induce epigenetic changes in the plants probably guided by small RNAs (Cabrera et al, 2016;de Medeiros et al, 2017;Medina et al, 2017;Ruiz-Ferrer et al, 2018), that includes changes in plants methylomes (Hewezi et al, 2018). It has been recently demonstrated how epigenetic and post-transcriptional modifications control the interactions between the plants and their surrounding microorganisms, that is, these regulatory mechanisms play a key role in promoting plant resistance to pathogens facilitating the establishment of symbiotic relationships.…”

MicroRNAs, New Players in the Plant–Nematode Interaction

“…Plant-parasitic nematodes induce the neoformation of feeding structures within host roots by inducing an extensive reprogramming of gene expression in the targeted root cells. The role of small noncoding RNAs in the plant–nematode interaction was established with the increased resistance to RKN and CN of A. thaliana mutants disrupted for miRNA or siRNA pathway (Hewezi et al, 2008; Medina et al, 2017; Ruiz-Ferrer et al, 2018). The development of sequencing technologies has made it possible to initiate studies of the role of plant miRNAs in this process in various plant species.…”

“…Most studies to date have focused on miRNAs, but few studies investigating the siRNAs expressed in roots infected with PPNs in Arabidopsis (Hewezi et al, 2017; Medina et al, 2018; Ruiz-Ferrer et al, 2018) have highlighted an overrepresentation in galls of 24 nt siRNAs known to be associated with RNA-directed DNA methylation. Two first studies of changes in DNA methylation have been performed in A. thaliana and soybean plants infected with CN (Rambani et al, 2015; Hewezi et al, 2017).…”