Biology subjects

Justy, F.

Publications and source records attributed to Justy, F..

4 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

Recombination, truncation and horizontal transfer shape the diversity of cytoplasmic incompatibility patterns

Wolbachia are endosymbiotic bacteria inducing various reproductive manipulations of which cytoplasmic incompatibility (CI) is the most common. CI leads to reduced embryo viability in crosses between males carrying Wolbachia and uninfected females or those carrying an incompatible symbiont strain. In the mosquito Culex pipiens, the Wolbachia wPip causes highly complex crossing patterns. This complexity is linked to the amplification and diversification of the CI causal genes, cidA and cidB, with polymorphism located in the CidA-CidB interaction regions. We previously showed correlations between the identity of gene variants and CI patterns. However, these correlations were limited to specific crosses, and it is still unknown whether cid gene polymorphism in males and females Wolbachia can explain and predict the wide range of crossing types observed in C. pipiens. Taking advantage of a new method enabling full-gene acquisition, we sequenced complete cid repertoires from 45 wPip strains collected worldwide. We demonstrated that the extensive diversity of cid genes arises from recombination and horizontal transfers. We uncovered further cidB polymorphism outside the interface regions and strongly correlated with CI patterns. Most importantly, we showed that in every wPip genome, all but one cidB variant are truncated. Truncated cidBs located in palindromes are partially or completely deprived of their deubiquitinase domain, crucial for CI. The identity of the sole full-length cidB variant seems to dictate CI patterns, irrespective of the truncated cidBs present. Truncated CidBs exhibit reduced toxicity and stability in Drosophila cells, which potentially hinders their loading into sperm, essential for CI induction.

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↗

bioRxiv2018

Sharing cells with Wolbachia: the transovarian vertical transmission of Culex pipiens densovirus

Originality-Significance StatementThis contribution provides a window into the study of a densovirus called CpDV infecting Culex pipiens mosquitoes. The originality of the study lies in the fact that CpDV, a DNA virus, was to date almost unstudied, its interaction with its hosts and its transmission mode were unknown. Considering that all Cx. pipiens are infected with Wolbachia, we studied the influence of this bacterial endosymbiont on CpDV density and transmission. Although Wolbachia-RNA virus interactions, especially in non-native Wolbachia-host associations have been widely studied, Wolbachia-DNA virus interactions were rarely investigated.\n\nIn this natural tripartite Cx. pipiens-Wolbachia-CpDV system: O_LIWe revealed the wide prevalence of CpDV, mostly at low densities, in Cx. pipiens laboratory lines.\nC_LIO_LIWe monitored CpDV presence in several cell types in ovaries including the oocytes where they co-exist with the bacterial endosymbiont Wolbachia.\nC_LIO_LIWe demonstrated that CpDV density in ovaries was influenced by Wolbachia presence and strain variations\nC_LIO_LIWe studied CpDV vertical transmission depending on Wolbachia presence and strain variations\nC_LI\n\nWe report for the first time the occurrence of widely distributed covert CpDV infections in Cx. pipiens laboratory colonies. CpDV is maintained by both vertical and horizontal transmission and under the influence of the vertically transmitted bacterial endosymbiont Wolbachia. Taken together our results suggest that CpDV could be very prevalent in nature putatively influencing natural Cx. pipiens populations dynamics.\n\nSUMMARYCulex pipiens densovirus (CpDV), a single stranded DNA virus, has been isolated from Culex pipiens mosquitoes but differs from other mosquito densoviruses in terms of genome structure and sequence identity. Its transmission from host to host, the nature of its interactions with both its host and hosts endosymbiotic bacteria Wolbachia are not known. Here we report the presence of CpDV in the ovaries and eggs of Cx. pipiens mosquitoes in close encounters with Wolbachia. In the ovaries, CpDV quantity significantly differed between mosquito lines harboring different strains of Wolbachia and these differences were not linked to variations in Wolbachia densities. CpDV was vertically transmitted in all laboratory lines to 17%-20% of the offspring. For some females, however, the vertical transmission reached 90%. Antibiotic treatment that cured the host from Wolbachia also significantly affected both CpDV quantity and vertical transmission suggesting an impact of host microbiota, including Wolbachia, on CpDV transmission. Overall our results show that CpDV is transmitted vertically via transovarian path along with Wolbachia with which it shares the same cells. Our results are primordial to understand the dynamics of densovirus infection, their persistence and spread in populations considering their potential use in the regulation of mosquito vector populations.

microbiology↗