Biology subjects

Vacherie, B.

Publications and source records attributed to Vacherie, B..

3 recordsLinked to original sources

bioRxiv2026

Mosaic selection and gene flow at the onset of grain beetle domestication

Domestication is an evolutionary process that can begin before deliberate breeding, when association with humans reshapes gene flow and selection. The yellow mealworm, Tenebrio molitor, is undergoing this transition from a synanthropic pest of stored grain to farmed species. We asked whether gene flow between farmed populations contributes to adaptation to captivity and whether selection extends to production traits. We combined population genomics of 320 beetles from eight farmed and wild populations with genetic mapping of 15 production traits from 3,575 individuals. Farm stocks retained high diversity and weak differentiation, with Netherlands-related ancestry connecting populations across Europe and Canada. Farm-restricted sweep-like signatures were 2.06-fold enriched within regions of excess allele sharing, suggesting local selection on introgressed variation. Across 305 production-trait QTLs, overlaps with selection and introgression signals showed no significant enrichment or depletion, suggesting that adaptive gene flow may primarily contribute to adaptation to captivity rather than broadly shaping growth, development and fertility. Nevertheless, egg-hatching-rate and development-time QTLs overlapped regions of reduced nucleotide diversity and low Tajima's D. These findings support a model in which gene flow supplies variation for unintended selection under intensive rearing. Crowding and physiological stress may favour adaptation to captive environments before sustained breeding establishes a broad genomic response at production loci.

evolutionary biology↗

bioRxiv2024

Nitrogen metabolism in the picoalgae Pelagomonas calceolata: disentangling cyanate lyase function under different nutrient conditions.

Cyanate (OCN-) is potentially an important organic nitrogen source in aquatic environments given the prevalence and activity of cyanate lyase genes in microalgae. However, the conditions under which these genes are expressed and the actual capacity of microalgae to assimilate cyanate remain underexplored. Here, we studied the nitrogen metabolism of the cosmopolitan picoalga Pelagomonas calceolata (Pelagophyceae, Stramenopiles) in environmental metatranscriptomes and transcriptomes from culture experiments under different nitrogen sources and concentrations. We observed that cyanate lyase is over-expressed in nitrate-poor oceanic regions, suggesting that cyanate is an important molecule contributing to the persistence of P. calceolata in oligotrophic environments. In the laboratory, we confirmed that this gene is over-expressed in low-nitrate medium together with several genes involved in nitrate recycling from endogenous molecules. Non-axenic cultures of P. calceolata were capable of growing on various nitrogen sources, including nitrate, urea and cyanate, but not ammonium. RNA sequencing of these cultures revealed that cyanate lyase was under-expressed in the presence of cyanate, indicating that this gene in not involved in the catabolism of extracellular cyanate to ammonia. Conversely, axenic P. calceolata cultures were not able to grow on cyanate, suggesting that the bacterial community consumes cyanate and provides an available form of nitrogen for growth of the alga. Based on environmental datasets and laboratory experiments, we propose that cyanate lyase is important in nitrate-poor environments to reduce the toxicity of intracellular cyanate produced by endogenous nitrogenous compound recycling, rather than being used to metabolise imported extracellular cyanate as an alternative nitrogen source.

genomics↗

bioRxiv2021

Male differentiation in the marine copepod Oithona nana reveals the development of a new nervous ganglion linked to Lin12-Notch-Repeat protein-associated proteolysis

BackgroundCopepods are among the most numerous animals, and play an essential role in the marine trophic web and biogeochemical cycles. The genus Oithona is described as having the highest density of copepods, and as being the most cosmopolite copepods. The Oithona male paradox describes the activity states of males, which are obliged to alternate between immobile and mobile phases for ambush feeding and mate searching, respectively, while the female is typically less mobile and often feeding. To characterize the molecular basis of this sexual dimorphism, we combined immunofluorescence, genomics, transcriptomics, and protein-protein interaction approaches. ResultsImmunofluorescence of {beta}3- and -tubulin revealed two male-specific nervous ganglia in the lateral first segment of the Oithona nana males prosome. In parallel, transcriptomic analysis showed male-specific enrichment for nervous system development-related transcripts. Twenty-seven Lin12-Notch Repeat domain-containing protein coding genes (LDPGs) of the 75 LDPGs identified in the genome were specifically expressed only in males. Furthermore, most of the LDPGs (27%) coded for proteins having predicted proteolytic activity, and non-LDPG proteolysis-associated transcripts showed a male-specific enrichment. Using yeast double-hybrid assays, we constructed a protein-protein interaction network involving two LDPs with proteases, extracellular matrix proteins, and neurogenesis-related proteins. ConclusionsFor the first time, our study describes the lateral nervous ganglia of O. nana males, unique to copepods. We also demonstrated a role of LDPGs and their associated proteolysis in male-specific physiology, and we hypothesize a role of the LDPGs in the development of the lateral ganglia through directed lysis of the extracellular matrix for the growth of neurites and genesis of synapses.

molecular biology↗