Abstract
In model organisms, epigenome dynamics underlies a plethora of biological processes. The role of epigenetic modifications in development and parasitism in nematode pests remains unknown. The root-knot nematode Meloidogyne incognita adapts rapidly to unfavorable conditions, despite its asexual reproduction. However, the mechanisms underlying this remarkable plasticity and their potential impact on gene expression remain unknown. This study provides the first insight into contribution of epigenetic mechanisms to this plasticity, by studying histone modifications in M. incognita. The distribution of five histone modifications revealed the existence of strong epigenetic signatures, similar to those found in the model nematode Caenorhabditis elegans. We investigated their impact on chromatin structure and their distribution relative to transposable elements (TE) loci. We assessed the influence of the chromatin landscape on gene expression at two developmental stages: eggs, and pre-parasitic juveniles. H3K4me3 histone modification was strongly correlated with high levels of expression for protein-coding genes implicated in stage-specific processes during M. incognita development. We provided new insights in the dynamic regulation of parasitism genes kept under histone modifications silencing. In this pioneering study, we establish a comprehensive framework for the importance of epigenetic mechanisms in the regulation of the genome expression and its stability in plant-parasitic nematodes.
Highlights
Crops are continually attacked by a wide range of pests and parasites
These antibodies gave single bands on western blots and saturated signals on ChIP-titration (Supplementary Figure S1 and Supplementary Table S1). They were raised against H3K27ac, H4K20me1, H3K9me3 and H3K27me3, and were added to the first previously validated antibody raised against H3K4me3 (Perfus-Barbeoch et al, 2014)
ChIP-Seq data were obtained for two Root knot nematodes (RKN) developmental stages, eggs and pre-parasitic juveniles 2 (J2s), and were mapped to the most complete annotated M. incognita genome publicly available (Blanc-Mathieu et al, 2017)
Summary
Crops are continually attacked by a wide range of pests and parasites. Plant-parasitic nematodes are thought to be one of the main causes of damages in food crops, resulting in yield losses of more than $150 billion worldwide (Singh et al, 2013). Root knot nematodes (RKN), Meloidogyne spp., are among the most rapidly spreading of all crop pests and pathogens (Bebber et al, 2014). Their rapid spread may have been facilitated by their wide host range, high fecundity, and parthenogenetic reproduction, allowing infestations to become established with relatively few individuals (Singh et al, 2013). Understanding the determinants of the extreme adaptive capacity of RKN is crucial for the development of effective and sustainable control methods.
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