Biology subjects

Coursol, S.

Publications and source records attributed to Coursol, S..

4 recordsLinked to original sources

bioRxiv2026

How to be dispensable: genomic and transcriptomic determinants in maize genes

BackgroundPlant genomes harbour a substantial proportion of dispensable genes - present only in a subset of individuals - that differ from ubiquitously shared core genes in multiple genomic and expression features. While these differences have been repeatedly documented, the factors shaping gene dispensability remain poorly understood. ResultsWe assembled a pan-gene set from eight maize inbred lines from American and European germplasms, together with their transcriptomic profile across 22 tissues/conditions, revealing the genomic and transcriptomic determinants of maize gene dispensability. Multivariate analysis demonstrates that gene expression level and purifying selection - rather than gene size - are the primary factors distinguishing core from dispensable genes. Dispensable genes overlap Helitrons at 4.6 times the rate of core genes, implicating Helitron-mediated gene capture as a major mechanism of dispensable gene formation. Classifying genes into stably expressed, variably expressed, and on-off categories shows that all three classes contain dispensable genes, though in different proportions than for core genes. Contrary to previous assumptions, we show that dispensable genes can participate in basal biological functions just as core genes, and that gene duplication likely provides only a partial mechanism for functional complementation of accessory genes absence. ConclusionsOur results provide novel insights into the molecular and evolutionary factors distinguishing core from dispensable genes and into the biological mechanisms shaping gene dispensability in maize, and demonstrate that classifying genes by transcriptional patterns provides a powerful framework for understanding the biological functions and evolutionary dynamics of both core and dispensable genes.

plant biology↗

bioRxiv2024

Cell wall digestibility outperforms ear in maintaining digestibility even under severe combined water and heat stress

CONTEXT OR PROBLEMForage maize is a central pillar of dairy cow feeding in France, directly influencing milk production. Drought significantly affects both maize yield and digestibility, which are both key parameters required for hybrid registration purposes. OBJECTIVE OR RESEARCH QUESTIONResearch on maize inbred lines has revealed droughts notable effect on dry matter and cell wall digestibilities due to changes in cell wall composition, directly impacting forage quality. No such studies have been performed on forage maize hybrids however, which are the main seed type used in the agricultural sector. In this paper, we aimed to understand the impact of water and heat stress on forage maize digestibility, and to uncover the factors controlling it. METHODSWe grew a range of modern forage maize hybrids for two years under four different controlled water stress modalities. These plants were agronomically, biochemically and histologically assayed, allowing us to perform a multiscale analysis to determine the traits responsible for variations in digestibility. RESULTSBy establishing a comprehensive heat and water stress index, we classified the environmental conditions. We demonstrated that under severe stress, ear production decreases significantly, but dry matter digestibility can be maintained through increased cell wall digestibility. This boost in cell wall digestibility was due to a reduction in p-hydroxycinnamic acid content and changes in lignin distribution, while lignin content and structure remained stable. The significant impact of lignin distribution on cell wall digestibility increased with the severity of the stress, reaching an extreme threshold where biochemical parameters solely account for digestibility variations. CONCLUSION AND IMPLICATIONSTo improve maize digestibility, it will be necessary to better understand how the reduction in carbon flux under stress affects p-hydroxycinnamic acid levels without greatly impacting lignin content. Finally, our work suggests that the inclusion of moderate stress conditions in future maize breeding programs will be necessary to better adapt forage maize hybrids to climate change.

plant biology↗

bioRxiv2022

Plant-PLMview: a database for identifying cis-regulatory sequences with preferential positions in gene-proximal regions of plants

BackgroundEstablishing relationships between transcription factors and target genes is essential for understanding the mechanisms regulating gene expression, which play a fundamental role in plant adaptation to the local environment. Despite the importance of this research area and the tremendous progress in sequencing methods such as ChIP-seq and DAP-seq, we are still far from a complete reconstruction of the cis-regulatory landscape. Only a small number of transcription factors can be assessed from experimental data to identify their cis-regulatory binding sites. This highlights the role that in silico approaches can play to complement experimental data. ResultsWe have developed Plant-PLMview, a web-accessible database for detecting preferentially cis-regulatory sequences in the gene-proximal regions of 20 plant species. Users of Plant-PLMview can (i) access the proximal regions of controlled genes from 20 plant species, (ii) query their own DNA motifs or access 840 cis-regulatory sequences from various plant resources, and (iii) use a tool called PLMdetect to search for preferentially located motifs in the gene-proximal regions of a list of genes. Results are displayed via a web interface with a list of DNA motifs preferentially located in a region near the start or end of genes, the distribution of these motifs and associated annotations. In addition, a graphical map of the preferential locations of the motifs in the 5 and 3-proximal regions of genes provides an overview of all motifs and genes examined. ConclusionPlant-PLMview provides the opportunity to study the proximal landscape of gene regulation in 20 plant genomes. The originality of the database lies in its ease of use thanks to the curated data (cis-regulatory sequences and proximal regions of genes) and the possibility to search through PLMdetect in the 5-gene-proximal region, but also in the 3-gene-proximal region, which is rarely explored. The web interface provides numerous graphical views that allow the users to get an overview and interpret the results more easily.

bioinformatics↗

bioRxiv2022

Genome-wide identification of preferentially located motifs in gene-proximal regions provides new insights into cis-regulatory sequences in plants

The identification of cis-regulatory elements controlling gene expression is an arduous challenge that is being actively explored to discover the key genetic factors responsible for traits of agronomic interest. Here, we have used a de novo and genome-wide approach for preferentially located motif (PLM) detection to investigate the proximal cis-regulatory landscape of Arabidopsis thaliana and Zea mays. We report three groups of PLMs in each gene-proximal region and emphasize conserved PLMs in both species, particularly in the 3-gene-proximal region. Comparison with resources of transcription factor and microRNA binding sites indicates that 79% of the identified PLMs are unassigned, although some are supported by MNase-defined cistrome occupancy analysis. Enrichment analyses further reveal that unassigned PLMs provide functional predictions distinct from those inferred by transcription factor and microRNA binding sites. Our study provides a comprehensive map of PLMs and points at their potential utility for future characterization of orphan genes in plants.

genomics↗