Biology subjects

Deremarque, T.

Publications and source records attributed to Deremarque, T..

3 recordsLinked to original sources

bioRxiv2026

A 23-copy tandem repeat of a cytochrome P450 gene underlies an adaptive introgression breakthrough in Ciona intestinalis

Introgression between highly divergent species is generally selected against, yet some foreign alleles can break through species barriers when they provide a sufficient selective advantage, a process known as adaptive introgression. Here, we characterize the structural variant underlying adaptive introgression from Ciona robusta into C. intestinalis, two species separated by 14.5% net molecular divergence. Previous work identified a narrow peak of C. robusta ancestry on chromosome 5 that reached high frequency in several C. intestinalis populations despite otherwise restricted introgression. Using whole-genome Nanopore sequences from 15 C. intestinalis and three C. robusta individuals, together with short-read datasets including parent-offspring trios, we narrowed down the core introgressed segment from 16 to three genes and characterized copy-number variation affecting the cytochrome P450 gene CYP2U1c. The introgressed haplotype carries a tandem amplification of a 5,173-bp segment containing CYP2U1c, with 23 consecutive copies and conserved repeat boundaries. The nearly 120-kb array could not be fully resolved by long-read sequencing, but coverage consistently supported approximately 23 copies per introgressed haplotype. Despite its extreme size and repetitive structure, the allele showed Mendelian inheritance. CYP2U1c copy number was also polymorphic in C. robusta. Long reads fully resolved two structurally distinct haplotypes in one individual, carrying either a duplication encompassing adjacent CYP2U1b and CYP2U1c genes or five CYP2U1c copies. Their distinct breakpoints indicate independent origins. Our results reveal independently arising CYP2U1c amplifications in the donor species and show that an extreme high-copy-number allele was subsequently favoured following introgression into C. intestinalis.

evolutionary biology↗

bioRxiv2025

Evaluating the roles of testosterone and sex-linked genes in territorial aggression of sex-reversed XY females in the African pygmy mouse

Sex differences in social aggression are widespread across the animal kingdom, with males typically displaying greater territoriality. While this dimorphism has traditionally been attributed to sex hormones, sex chromosomes can also contribute to it independently of hormonal influence. In the African pygmy mouse Mus minutoides, naturally occurring sex-reversed XY females (named X*Y due to a mutation on the X chromosome) are highly territorial in comparison to the other female genotypes present in the population (XX and XX*). However, the molecular basis of this phenotype remains unknown. Here, we evaluate molecular factors, known to correlate with aggressiveness, following a standardized behavioural assessment of aggression. We focus on i) the androgen pathway by quantifying testosterone serum levels and expression of its receptor in the brain; ii) the brain dopaminergic system through expression of dopamine-regulating genes, including the sex-determining Sry gene; and iii) neuroendocrine circuits, via vasopressin and oxytocin expression. These systems, although distinct, converge on hypothalamic-limbic circuits that regulate social behaviour and threat responses, providing an integrated framework for the modulation of aggression. Contrary to earlier reports, we found reduced level of aggression in X*Y females, likely to reflect a breeding facility effect. We also observe no correlations between aggressiveness and androgen levels or gene expression of the tested factors. However, our results support a stimulation of the dopaminergic system and of the oxytocin pathway following the agonistic assay suggesting their potential involvement in aggression-related responses. This further supports the idea that aggression is multifactorial. It is shaped by the interaction of several neuroendocrine and neurotransmitter pathways rather than a single determinant.

evolutionary biology↗

bioRxiv2021

ONTdeCIPHER: An amplicon-based nanopore sequencing pipeline for tracking pathogen variants

MotivationAmplicon-based nanopore sequencing is increasingly used for molecular surveillance during epidemics (e.g. ZIKA, EBOLA) or pandemics (e.g. SARS-CoV-2). However, there is still a lack of versatile and easy-to-use tools that allow users with minimal bioinformatics skills to perform the main steps of downstream analysis, from quality testing to SNPs effect to phylogenetic analysis. ResultsHere, we present ONTdeCIPHER, an amplicon-based Oxford Nanopore Technology (ONT) sequencing pipeline to analyze the genetic diversity of SARS-CoV-2 and other pathogenes. Our pipeline integrates 13 bioinformatics tools. With a single command line and a simple configuration file, users can pre-process their data and obtain the sequencing statistics, reconstruct the consensus genome, identify variants and their effects for each viral isolate, infer lineage and, finally perform multi-sequence alignments and phylogenetic analyses. Availability and implementationONTdeCIPHER is available at https://github.com/emiracherif/ONTdeCIPHER Contactemira.cherif@ird.fr Supplementary informationSupplementary data are available at ...

bioinformatics↗