Biology subjects

Genissel, A.

Publications and source records attributed to Genissel, A..

6 recordsLinked to original sources

bioRxiv2026

Adaptive evolution of transcriptome and transcriptomic plasticity in stable and fluctuating environments

Adaptation to new environments often involves multiple genes and can induce substantial changes in biological systems, but the overall consequences of the genetic response to specific environmental pressures remain poorly understood. Here, we investigate the large-scale effects of adaptation to new temperature regimes on the whole transcriptome from experimental evolution carried on the fungus Zymoseptoria tritici. Two distinct strains from the wild were grown in constant cool (17{degrees}C), constant warm (23{degrees}C), and fluctuating temperature environments, for about 250 clonal generations. The expression of > 10,000 genes was estimated by RNA-seq before and after evolution at several temperatures. We observed massive convergent change in both gene expression and gene expression plasticity. Fluctuating environments did not favor plastic gene expression in general, although fluctuating populations did evolve towards the optimal reaction norms. Some of our observations were at odds with common expectations; adaptive mutations were highly pleiotropic, and adaptation to stable temperature conditions did not match gene expression plasticity. We thus showed that the evolution of complex biological systems follow some general patterns which challenge gene-centered or quantitative genetics predictions.

evolutionary biology↗

bioRxiv2024

Association between gene expression plasticity and regulatory network topology

Over the past two decades, a large body of theoretical and empirical work has been conducted with the aim of identifying the gene regulatory network topologies responsible for gene expression dynamics. Some studies have linked gene expression plasticity to specific network motifs such as feedforward loops, diamond motifs, or feedback loops. However, both theoretical and empirical work have produced equivocal results, as the same topologies have also been associated with expression robustness. As a step toward understanding the regulatory basis of gene expression plasticity, our goal is to understand how local regulatory topologies may contribute to it. To this end we compared theoretical predictions from a simulated network evolution model with empirical data based on Escherichia coli regulatory network. We investigated the link between network topology and gene expression at three levels: the number of regulators, the number and the proportion of loops (feedback loops, feedforward loops and diamond loops), and the proportion of unique motifs (here characterized by the position of up- or down-regulations within loops). Consistent results from our empirical and theoretical approaches revealed that plastic genes are, on average, regulated by a greater number of genes. In addition, our theoretical predictions showed that selection, as opposed to genetic drift, strongly biases the distribution of network motifs. However, similar results were observed when comparing plastic and non-plastic genes. Overall, this work illustrates that our current understanding of network topology may be insufficient to fully explain or predict gene expression plasticity.

systems biology↗

bioRxiv2024

Evolutionary impact of in vitro adaptation on virulence in the pathogen Zymoseptoria tritici

O_LIAll species are living in variable environments. integrating the impact of changing environments into plant-pathogen studies becomes essential. This integration is key to expanding our understanding of the evolutionary dynamics governing plant-pathogen interactions. C_LIO_LIAfter subjecting Zymoseptoria tritici to 500 generations of experimental evolution in vitro under various temperature regimes, we assessed the evolved lineages virulence levels across six wheat cultivars. Additionally, we performed whole-genome sequencing on ten evolved lineages to identify accumulated mutations C_LIO_LIOur study revealed a reduction in virulence among several evolved lineages, with variability based on the host genotype. We observed trans-lineage segregating mutations in the genome, encompassing both synonymous and non-synonymous mutations within the secretome. Intriguingly, despite 500 generations of experimental evolution, no loss of dispensable chromosomes was detected C_LIO_LIThese findings suggest that the abiotic environment can significantly influence the dynamic evolution of the plant pathogen Z. tritici. C_LI

evolutionary biology↗

bioRxiv2023

Improved gene annotation of the fungal wheat pathogen Zymoseptoria tritici based on combined Iso-Seq and RNA-Seq evidence

Despite large omics datasets, the establishment of a reliable gene annotation is still challenging for eukaryotic genomes. Here, we used the reference genome of the major fungal wheat pathogen Zymoseptoria tritici (isolate IPO323) as a case study to develop methods to improve eukaryotic gene prediction. Four previous IPO323 annotations identified 10,933 to 13,260 gene models, but only one third of these coding sequences (CDS) have identical structures. To resolve these discrepancies and improve gene models, we generated full-length transcripts using long-read sequencing. This dataset was used together with other evidence (RNA-Seq transcripts and protein sequences) to generate novel ab initio gene models. The selection of the best structure among novel and existing gene models was performed according to transcript and protein evidence using InGenAnnot, a novel bioinformatics suite. Overall, 13,414 re-annotated gene models (RGMs) were predicted, including 671 new genes among which 53 encoded effector candidates. This process corrected many of the errors (15%) observed in previous gene models (coding sequence fusions, false introns, missing exons). While fungal genomes have poor annotations of untranslated regions (UTRs), our Iso-Seq long-read sequences outlined 5 and 3UTRs for 73% of the RGMs. Alternative transcripts were identified for 13% of RGMs, mostly due to intron retention (75%), likely corresponding to unprocessed pre-mRNAs. A total of 353 genes displayed alternative transcripts with combinations of previously predicted or novel exons. Long non-coding transcripts (lncRNAs) and double-stranded RNAs from two fungal viruses were also identified. Most lncRNAs corresponded to antisense transcripts of genes (52%). lncRNAs that were up or down regulated during infection were enriched in antisense transcripts (70%), suggesting their involvement in the control of gene expression. Our results showed that combining different ab initio gene predictions and evidence-driven curation using InGenAnnot improved the quality of gene annotations of a compact eukaryotic genome. Our analysis also provided new insights into the transcriptional landscape of Z. tritici, helping develop an increasingly complex picture of its biology.

genomics↗

bioRxiv2022

A thousand-genome panel retraces the global spread and climatic adaptation of a major crop pathogen

Human activity impacts the evolutionary trajectories of many species worldwide. Global trade of agricultural goods contributes to the dispersal of pathogens reshaping their genetic makeup and providing opportunities for virulence gains. Understanding how pathogens surmount control strategies and cope with new climates is crucial to predicting the future impact of crop pathogens. Here, we address this by assembling a global thousand-genome panel of Zymoseptoria tritici, a major fungal pathogen of wheat reported in all production areas worldwide. We identify the global invasion routes and ongoing genetic exchange of the pathogen among wheat-growing regions. We find that the global expansion was accompanied by increased activity of transposable elements and weakened genomic defenses. Finally, we find significant standing variation for adaptation to new climates encountered during the global spread. Our work shows how large population genomic panels enable deep insights into the evolutionary trajectory of a major crop pathogen.

genomics↗

bioRxiv2019

Evolution and plasticity of the transcriptome under temperature fluctuations in the fungal plant pathogen Zymoseptoria tritici

- Background. Species are subjected to variable environment in nature. While the ability to cope with changes has been studied through theoretical approaches, the small number of empirical studies limits our understanding of the evolutionary molecular mechanisms underlying adaptation to fluctuations - Results. Whole transcriptome sequencing of the fungal wheat pathogen Zymoseptria tritici revealed the evolution of gene expression after 48 weeks of experimental evolution under stable or fluctuating temperature. We found that although there is a strong genetic signature of gene expression, fluctuating regime could have a large and pervasive effect on the transcriptome evolution. Results show a few hot spots of significantly differentially expressed genes in the genome, in regions enriched with transposable elements (TE), including on dispensable chromosomes. Further, our results evidenced gene evolution towards robustness associated with the fluctuating regime, suggesting robustness is adaptive in changing environment. Last, an analysis on gene expression correlation revealed a significant set of genes that could act as trans-regulators. - Conclusions. This study is the first evolve and re-sequence experiment of a fungal pathogen, with the goal to describe the potential ability to evolve to changing environment and the molecular changes occurring in response to fluctuating selection. In addition to explore the evolutionary potential of the pathogen under temperature fluctuation this work highlights the important role of transcriptional rewiring that can adjust regulation of cell growth and multiplication.

evolutionary biology↗