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

Clémence Medina,Marc Magliano,Pierre Abad,Bruno Favery,Nathalie Marteu,Martine Da Rocha,Kevin Lebrigand,Alizée Raptopoulo,Stéphanie Jaubert-Possamai

doi:10.1186/s12864-018-5296-3

Abstract

BackgroundRoot-knot nematodes (RKN), genus Meloidogyne, are plant parasitic worms that have the ability to transform root vascular cylinder cells into hypertrophied, multinucleate and metabolically over-active feeding cells. Redifferentiation into feeding cells is the result of a massive transcriptional reprogramming of root cells targeted by RKN. Since RKN are able to induce similar feeding cells in roots of thousands of plant species, these worms are thought to manipulate essential and conserved plant molecular pathways.ResultsSmall non-coding RNAs of uninfected roots and infected root galls induced by M. incognita from Arabidopsis thaliana were sequenced by high throughput sequencing. SiRNA populations were analysed by using the Shortstack algorithm. We identified siRNA clusters that are differentially expressed in infected roots and evidenced an over-representation of the 23–24 nt siRNAs in infected tissue. This size corresponds to heterochromatic siRNAs (hc-siRNAs) which are known to regulate expression of transposons and genes at the transcriptional level, mainly by inducing DNA methylation.ConclusionsCorrelation of siRNA clusters expression profile with transcriptomic data identified several protein coding genes that are candidates to be regulated by siRNAs at the transcriptional level by RNA directed DNA methylation (RdDM) pathway either directly or indirectly via silencing of neighbouring transposable elements.

Highlights

Root-knot nematodes (RKN), genus Meloidogyne, are plant parasitic worms that have the ability to transform root vascular cylinder cells into hypertrophied, multinucleate and metabolically over-active feeding cells
Identification of predicted Small interfering RNA (siRNA) clusters in galls and uninfected roots We sequenced small RNAs expressed in uninfected root inter-nodes and galls 7 and 14 dpi induced by the RKN M. incognita
We identified five genes at 7 dpi and two genes at 14 dpi with i) promoter regions displaying some sequence identity to transposable elements ii) differential expression in galls and an inverse correlation of expression with differentially expressed (DE) siRNA clusters located in the promoter region of the genes concerned and iii) promoter regions differentially methylated in cyst nematode (CN) feeding sites

Summary

Introduction

Root-knot nematodes (RKN), genus Meloidogyne, are plant parasitic worms that have the ability to transform root vascular cylinder cells into hypertrophied, multinucleate and metabolically over-active feeding cells. Redifferentiation into feeding cells is the result of a massive transcriptional reprogramming of root cells targeted by RKN. Since RKN are able to induce similar feeding cells in roots of thousands of plant species, these worms are thought to manipulate essential and conserved plant molecular pathways. There are two principal classes of small RNAs in plants, classified according to their biogenesis: microRNAs (miRNAs) and small interfering RNAs (siRNAs) [2, 3]. They induce post-transcriptional gene silencing (PTGS) principally by triggering messenger RNA (mRNA) degradation, but Transcriptional gene silencing (TGS) takes place in two phases with different specific actors. The pre-establishment phase involves a DNA-dependent RNA polymerase (Pol) II producing aberrant transcripts, RDR6, which produces dsRNAs that are processed by Dicer-like protein 2 (DCL2) and DCL4 to produce 21–22 nt siRNAs that induce DNA methylation by DOMAINS REARRANGED

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