Biology subjects

CARRERE, S.

Publications and source records attributed to CARRERE, S..

5 recordsLinked to original sources

bioRxiv2026

A plant single nucleotide polymorphism impacts nectar sugar composition, microbial diversity and pollinator visits

Nectar is a hub for plant-pollinator interactions, yet gene-level causal links between plant genetic variation, pollinator foraging and nectar microbial assembly remain poorly resolved. Using near-isogenic lines, innovative field time-lapse monitoring of pollinator visits and long-read amplicon sequencing of nectar microbiota, we show that a natural single-nucleotide variant at a cell-wall invertase gene (HaCWINV2) controls sunflower nectar chemistry and influences both pollinators and microbes. Plants homozygous for a loss-of-function HaCWINV2 allele produce sucrose-rich nectar, resulting in fewer bee visits under field conditions, while bumblebee visitation remained unaffected. In pollinator-excluded flowers, invertase-deficient plants harboured greater fungal diversity and compositionally distinct communities, indicating that nectar sugar profiles act as ecological filters shaping the nectar microbiome. This loss-of-function allele was found rarely and only at the heterozygote state in wild sunflowers and was fixed in 35% of cultivated lines indicating a positive selection during domestication. Our findings establish a causal link between a single gene and nectar chemistry with cascading ecological effects in a plant-pollinator system, illustrating how subtle genetic changes scale up to alter nectar traits, microbial assembly and pollinator foraging behaviour.

genetics↗

bioRxiv2026

Fine mapping and genomic analyses reveal a tandem kinase-pseudokinase candidate underlying OrDeb2-mediated resistance to Orobanche cumana in sunflower

Sunflower broomrape (Orobanche cumana Wallr.) is a holoparasitic weed that parasitizes sunflower (Helianthus annuus L.) and severely constrains yield. The OrDeb2 gene confers resistance to broomrape race G in the sunflower line DEB2. It has been previously located within a 1.38-Mbp physical region in the H. annuus XRQ reference genome that contains a cluster of receptor-like proteins and receptor-like kinases (RLKs). In this study, an OrDeb2 candidate has been proposed though high-resolution genetic and physical mapping, multi-allelic comparisons across resistant and susceptible lines, and exclusion of other potential candidates based on their function and genetic features. OrDeb2 was delimited to a 219.4-kbp region in the DEB2 genome assembly that contained six annotated protein-coding genes belonging to two groups: three small heat shock proteins (HSP20) and three RLKs. Given that the only sunflower broomrape resistance gene cloned to date encodes an RLK, the key role of RLKs in resistance to biotic stresses in plants, and the similar genetic features between RLK-type resistance genes and OrDeb2 as major dominant genes in gene-for-gene interactions, RLKs in the interval emerged as the most plausible candidates. Within them, the RLK-2 gene encoding a root-expressed full-length kinase-pseudokinase protein belonging to the tandem kinase proteins (TKPs) family was prioritized, because the other two RLKs corresponded to a truncated TKP with a stop codon within the kinase domain. RLK-2 also carried sequence variants unique to DEB2 relative to multiple susceptible genotypes. The results of this research reveal the potential role of TKP genes as new players in resistance to parasitic plants and provide a framework to dissect the genetic dialog between O. cumana and sunflower in gene-for-gene interactions.

plant biology↗

bioRxiv2025

Phylogenomics of Plasmopara halstedii reveals genomic regions associated with the breakdown of sunflower downy mildew resistance genes

O_LIUnderstanding the genetic diversity and evolutionary history of plant pathogens is crucial for effective disease management strategies. Sunflower downy mildew, caused by the oomycete Plasmopara halstedii, is a worldwide threat to the sunflower oil crop. We aimed to explain through phylogenomic studies how downy mildew resistance breakdown occurred recurrently in the last decades in France, leading to new virulence profiles. C_LIO_LIWe assembled high-quality genomes of three founder pathotypes of Pl. halstedii. Performing comparative genomic analyses, population genetics, and phylogenomic analyses, we studied the genomic structure among the 16 reference French pathotypes of Pl. halstedii. C_LIO_LIWe revealed a conserved genomic organisation among pathotypes and a strong synteny with other Peronosporales species. The history of Pl. halstedii invasion in France over the last 60 years was documented by identifying founder strains and their admixture patterns. The emergence of pathotypes with broader virulence spectra and therefore capable of overcoming host resistance was associated with genomic reshuffling. We highlighted genomic mosaicism in admixed pathotypes and identified regions associated with the breakdown of host resistance genes harbouring putative effector genes. C_LIO_LIOur findings provide insights into evolutionary mechanisms underlying plant pathogen host adaptation, which has implications for a sustainable deployment of multiple resistance genes. C_LI

plant biology↗

bioRxiv2024

The relative effects of abiotic and biotic factors in explaining the structure of soil bacterial communities at diverse taxonomic levels

Soil microbes play pivotal roles in the multifunctioning of terrestrial ecosystems. In the context of global changes, there is an urgent need to protect soil microbial diversity, which relies on determining the abiotic and biotic factors that influence the diversity, composition, and assemblage of soil microbiota. A large number of informative studies have reported edaphic properties and climate factors as key drivers of soil bacteria microbiota. However, these studies were mainly conducted at the phylum level and based on a restricted number of non-microbial variables. In this study, we aimed to estimate the relative effects of abiotic and biotic factors in shaping soil bacterial communities at diverse taxonomic levels by focusing on 160 natural sites located in the southwest of France for which a large and unique set of non-microbial variables is available. After characterizing soil bacterial communities with the highly taxonomically resolving gyrB gene, we identified that in addition to pH, temperature, and precipitations, soil bacterial communities at the lowest taxonomic levels appear strongly structured by soil micronutrients, notably manganese. On the other hand, soil bacterial communities at the highest taxonomic levels appear strongly structured by the interplay between descriptors of plant communities and edaphic properties. Similar to previous observations on microbial pathogens, the strong and positive associations between soil bacterial species and the presence of particular plant species suggest host specificity for soil commensal bacteria. Altogether, a deeper characterization of both abiotic and biotic factors could help fuel programs designed for protecting and restoring soil ecosystem functions.

ecology↗

bioRxiv2022

Investigating genetic diversity within the most abundant and prevalent non-pathogenic leaf-associated bacteria interacting with Arabidopsis thaliana in natural habitats

Plants interact simultaneously with highly diversified microbes defined as the plant microbiota. Microbiota modulates plant health and appears as a promising lever to develop innovative, sustainable and eco-friendly agro-ecosystems. Key patterns of microbiota assemblages in plants have been revealed by an extensive number of studies based on taxonomic profiling by metabarcoding. However, understanding the functionality of microbiota and identifying the genetic and molecular mechanisms underlying the interplay between plants and their microbiota are still in its infancy and relies on reductionist approaches primarily based on the establishment of representative microbial collections. In Arabidopsis thaliana, most of these microbial collections include one strain per OTU isolated from a limited number of habitats, thereby neglecting the ecological potential of genetic diversity within microbial species to affect the plant-microbiota molecular dialog. With this study, we aimed at estimating the extent of genetic variation between strains within the most abundant and prevalent leaf-associated non-pathogenic bacterial species in 163 natural populations of A. thaliana located south-west of France. By combining a culture-based collection approach consisting of the isolation of more than 7,000 bacterial colonies with an informative-driven approach, we isolated 35 pure strains from eight non-pathogenic bacterial species. We detected significant intra-specific genetic variation at the genomic level and for growth rate in synthetic media. In addition, significant host genetic variation was detected in response to most bacterial strains in in vitro conditions, with the presence of both negative and positive responses on plant growth. Our study provides new genetic and genomic resources for a better understanding of the plant-microbe ecological interactions at the microbiota level. We also highlight the need of considering genetic variation in both non-pathogenic bacterial species and A. thaliana to decipher the genetic and molecular mechanisms involved in the ecologically relevant dialog between hosts and leaf microbiota.

microbiology↗