Biology subjects

Bournaud, C.

Publications and source records attributed to Bournaud, C..

3 recordsLinked to original sources

bioRxiv2026

A miniaturized Arabidopsis thaliana - Botrytis cinerea seedling pathosystem and the GreenDayz workflow for longitudinal image-based phenotyping

Plant-pathogen interactions are strongly influenced by host developmental stage, yet many Arabidopsis thaliana-Botrytis cinerea assays remain centred on mature rosette leaves and rely on inoculum loads that may exceed those involved in a primary infection. We established a miniaturized in vitro A. thaliana-B. cinerea seedling pathosystem initiated with a very low conidial dose (nominally ~25 conidia per plate) compatible with both destructive molecular sampling and repeated, non-destructive RGB imaging. The pathosystem was coupled to a low-cost smartphone photo station and to GreenDayZ Phenotyping, a guided image-analysis application with an intuitive graphical interface that standardizes longitudinal RGB image processing and extracts quantitative colour-based phenotypes. Together, the pathosystem and GreenDayZ Phenotyping provide an accessible and reproducible framework for longitudinal phenotyping of low-inoculum seedling infections, in which image-derived trajectories can be aligned with independent molecular readouts.

pathology↗

bioRxiv2025

DNA-protein interactions in Meloidogyne incognita

BackgroundThe root-knot nematode Meloidogyne incognita, is a highly destructive parasite that manipulates host plant processes through effector proteins, affecting agriculture globally. Despite advances in genomic and transcriptomic studies, the regulatory mechanisms controlling effector gene expression, especially at the chromatin level, are still poorly understood. Gene regulation studies in plant-parasitic nematodes (PPN) face several challenges, including the absence of transformation systems and technical barriers in chromatin preparation, particularly for transcription factors (TFs) expressed in secretory gland cells. Conventional methods like Chromatin Immunoprecipitation (ChIP) are limited in PPN due to low chromatin yields, the impermeability of nematode cuticles, and difficulties in producing antibodies for low-abundance TFs. These issues call for alternative approaches, such as dCas9-based CAPTURE (CRISPR Affinity Purification in siTU of Regulatory Elements) that allows studying chromatin interactions by using a catalytically inactive dCas9 protein to target specific genomic loci without relying on antibodies. ResultsThis study presents an optimized in vitro dCas9-based CAPTURE for M. incognita that addresses key challenges in chromatin extraction and stability. The protocol focuses on the promoter region of the effector gene 6F06, a critical gene for parasitism. Several optimizations were made, including improvements in nematode disruption, chromatin extraction, and protein-DNA complex stability. This method successfully isolated chromatin-protein complexes and identified four putative chromatin-associated proteins, including BANF1, linked to chromatin remodelling complexes like SWI/SNF. ConclusionThe optimized in vitro dCas9-based CAPTURE protocol offers a new tool for investigating chromatin dynamics and regulatory proteins in non-transformable nematodes. This method expands the scope of effector gene regulation research and provides new insights into parasitism in M. incognita. Future research will aim to validate these regulatory proteins and extend the method to other effector loci, potentially guiding the development of novel nematode control strategies.

molecular biology↗

bioRxiv2021

Genome expression dynamics reveals parasitism regulatory landscape of the root-knot nematode Meloidogyne incognita and a promoter motif associated with effector genes

Root-knot nematodes are the major contributor to the crop losses caused by nematodes. Root-knot nematodes secrete effectors into the plant, derived from two sets of pharyngeal gland cells, to manipulate host physiology and immunity. Successful completion of the life cycle, involving successive molts from egg to adult, covers morphologically and functionally distinct stages and will require precise control of gene expression, including effectors. The details of how root-knot nematodes regulate transcription remain sparse. Here, we report a life stage-specific transcriptome of Meloidogyne incognita. Combined with an available annotated genome, we explore the spatio-temporal regulation of gene expression. We reveal gene expression clusters and predicted functions that accompany the major developmental transitions. Focusing on effectors, we identify a putative cis-regulatory motif associated with expression in the dorsal glands: providing an insight into effector regulation. We combine the presence of this motif with several other criteria to predict a novel set of putative dorsal gland effectors. Finally, we show this motif, and thereby its utility, is broadly conserved across the Meloidogyne genus and termed it Mel-DOG. Taken together, we provide the first genome-wide analysis of spatio-temporal gene expression in a root-knot nematode, and identify a new set of candidate effector genes that will guide future functional analyses.

genomics↗