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Daviere, A.

Publications and source records attributed to Daviere, A..

4 recordsLinked to original sources
bioRxiv2026

Role of transposons in the specialization of Botrytis cinerea to grapevine: Insights into small RNAs and a new Starship

While transposable elements (TEs) are recognized as major drivers of fungal genome structure, evidence of their direct involvement in the interaction with host plants and the environment is only beginning to emerge. Retrotransposons can generate small RNA (sRNA) that act through cross-kingdom RNA interference, while giant DNA TEs called Starships carry dozens of cargo genes that enrich the accessory gene compartment of fungal genomes. In the polyphagous pathogen Botrytis cinerea, the Vv3 strain and other strains specialized on grapevine display a specific repertoire of TEs, including the retrotransposons BcCopia4, BcGypsy6, and BcGypsy7. This study first explored the putative role of sRNA generated from these retrotransposons in the interaction between the Vv3 strain and its host of origin, grapevine. Putative targets were identified among the host mRNAs, but predicted cleavage sites could not be experimentally validated. Moreover, Dicer mutants unable to produce retrotransposons-derived sRNA remained fully pathogenic on grapevine, indicating that these sRNAs do not act as virulence factors on this host. In parallel, this study provides an updated RNA-seq-based annotation of the accessory genes of the Vv3 strain, which revealed a new 93 kb-Starship harboring 43 cargo genes, some of which are related to arsenic resistance. A formal genetic approach confirmed that this locus confers resistance to this metalloid. This giant TE, named Ariane, was also detected in additional grapevine-specialized strains resistant to arsenic but not in strains isolated from other hosts such as tomato. In conclusion, this study highlights how a Starship giant transposon shaped the accessory genes compartment of the polyphagous fungus B. cinerea and may have contributed to its adaptation to vine cultivation by conferring resistance to arsenic, a compound widely used in vineyards during the last century. IMPACT STATEMENTFungal genomes contain many families of transposons whose functional role in adaptation to the environment and in biotic interactions remained hidden for a long time. In the grey mold fungus Botrytis cinerea, strains specialized on grapevine, such as Vv3, carry a specific repertoire of transposons which provides a valuable opportunity to investigate their role in niche adaptation. In this study, we first investigated retrotransposon-derived small RNA, previously described as effectors capable of manipulating the immunity of the model plant Arabidopsis thaliana. Although in silico analysis of the specific repertoire of small RNAs of the Vv3 strain suggested that some could target the expression of grapevine genes, a genetic approach demonstrated that they do not play a significant role in virulence on this host. In contrast, this study identified a new transposon, named Ariane, that carries 43 cargo genes and confers a selective advantage to the Vv3 strain. Ariane belongs to a family of giant transposons called Starships, recently discovered in fungi and considered to be responsible for horizontal genes transfers between unrelated species. Ariane was detected only in some B. cinerea strains isolated from grapevine, and a genetic cross showed that it provides these strains with the ability to grow in presence of arsenic. Arsenic was used in vineyards until the beginning of the 21st century to control fungal trunk diseases and insect pests. Therefore, Ariane appears to have played an important role in the adaptation of B. cinerea strains to cultivated grapevine. Overall, these results underline the importance of considering Starships when predicting emergence of resistance to antifungal compounds. DATA SUMMARYThe novel data described in this study, i.e., RNA-Seq data and the Starship element are accessible under NCBI GEO accession GSE327899 and at https://doi.org/10.57745/HYWRNM, respectively. All information related to Botrytis cinerea genomes used in this study are centralized and kept up to date at the Bioinfo Bioger genomic web portal: https://bioinfo.bioger.inrae.fr/portal/genome-portal/. Direct links to individual portals are respectively https://bioinfo.bioger.inrae.fr/portal/genome-portal/3/ for B. cinerea Vv3 genome, https://bioinfo.bioger.inrae.fr/portal/genome-portal/2/ for B. cinerea Sl3 genome, and https://bioinfo.bioger.inrae.fr/portal/genome-portal/4/ for B. cinerea populations isolated on tomato or grapevine. Each portal provides: (i) a centralized access to public genomic resources, including the genome, transposon, and RNA repositories; (ii) a data browser to download the genomic files; (iii) a genome browser that enables visualization of features within their genomic context, along with associated expression data. As a summary, the prior main public B. cinerea genomic accessions and resources used in this study are: GCA_039644125 for VV3 genome, GCA_022560135 for Sl3 genome, GCA_000143535 for B05.10 genome, PRJNA624742 for populations, https://doi.org/10.57745/HYWRNM for transposons, and GSE181592 for small RNAs. Furthermore, table S1 summarizes the list and characteristics of the 64 B. cinerea genomes publicly available to date. The genomic data for Vitis vinifera genome PN40024.v4 used in this study are available at: https://integrape.eu/resources/genes-genomes/genome-accessions/.

genomics↗
bioRxiv2026

Apoplast multi-omics profiling during fungal infection uncovers new players of basal and early induced immunity

The extracellular space in plant tissues, known as the apoplast, remains one of the least characterized cellular compartments. The apoplastic fluid (APF), akin to mammalian extracellular fluid, serves as the primary interface between pathogens and their host. It allows the exchange of signalling molecules, coordinates host cell responses, and enables the circulation of pathogen effectors that modulate the immune response. We describe here the first multi-omics analysis of the APF content just 6 h after the onset of A. thaliana infection with B. cinerea, a fast-killing necrotrophic fungus. By varying plant nitrogen nutrition, known to affect both plant defenses and pathogen virulence, we identify candidates that do not stand out under optimal conditions. Our analysis uncovers novel nitrogen-dependent mechanisms that regulate both basal and early induced apoplastic immunity, revealing the presence of previously unidentified, potentially protective apoplastic metabolites as well as the intercellular transport of nuclear proteins, thereby offering new insights into early apoplastic immune responses.

plant biology↗
bioRxiv2024

Apoplast metabolomics reveals that plant-pathogen crosstalk is modulated by nitrogen supply

In the present study, we analyzed the role played by the apoplast in the crosstalk between biotic and abiotic stress conditions. In particular, we studied the crosstalk between nitrogen (N) limitation and infection of the model plant Arabidopsis thaliana by E. amylovora, an apoplastic bacterium. Our previous findings indicated that low N (LN) conditions increase E. amylovora in planta titers and expression of virulence factors. In this work, we extracted the apoplast wash fluids (AWF) from plants grown under low N or high N (HN) conditions and applied them to bacteria in vitro. We observed that LN-AWF induced stronger virulence gene expression than HN-AWF. Metabolomic analysis of both apoplast extracts revealed the presence of common metabolites, however, their proportions were distinct, indicating a direct effect of N availability on apoplast content. Interestingly, changes in the apoplast metabolite proportions were also observed early after bacterial infection, but only in plants grown under LN conditions. To evaluate the effect of single metabolites on virulence gene expression, we selected 43 metabolites and observed that 29 of them were activators whereas two, GABA and citrate, acted as repressors. This study shows that environmental constraints, such as N availability, impact plant-pathogen interactions by altering the apoplastic content.

plant biology↗
bioRxiv2024

Unravelling the Interplay of Nitrogen Nutrition and the Botrytis cinerea pectin lyase BcPNL1 in Modulating Arabidopsis thaliana Susceptibility

In this study, we investigated the intricate interplay between nitrogen nutrition, and the dynamics of pectin degradation during plant-pathogen interactions, using Arabidopsis thaliana and Botrytis cinerea as a model pathosystem. Our findings revealed a noteworthy impact of nitrogen availability on the pectin degrading activity of the B. cinerea pectin lyase 1 (PNL) for which the mutant strains presented a reduced pathogenicity restored by complementation. More precisely, infected nitrogen-sufficient (high N) plants exhibited an increased release of PNL-derived oligogalacturonides compared to infected nitrogen-deficient (low N) plants. This correlated with an elevated expression of jasmonic acid repressor genes in high N plants, rendering them more susceptible to B. cinerea. Using{Delta} Bcpnl1 deletion mutants, we demonstrated that the increased production of BcPNL1 -derived oligogalacturonides under high N conditions was responsible for the increased expression of jasmonic acid repressor genes, significantly contributing to the higher susceptibility of high N plantsto B. cinerea. In conclusion, we demonstrated that BcPNL1 is a major pathogenicity factor during B. cinerea interaction that is affected by the plants N nutrition conditions.

plant biology↗