Biology subjects

De Rouck, S.

Publications and source records attributed to De Rouck, S..

5 recordsLinked to original sources

bioRxiv2026

Multiparental RNA-seq driven eQTL screening identifies loci underlying host plant fitness in a generalist herbivore

The two-spotted spider mite (Tetranychus urticae) is an extremely polyphagous pest, yet the genetic basis of this adaptive potential remains to be fully elucidated. Since expression quantitative trait loci (eQTLs) provide the genetic basis of numerous phenotypes, we aimed to identify trans-eQTL hotspots underlying T. urticae fitness upon transfer from a common (bean) to a challenging (tomato) host plant. Nonetheless, the identification of trans-eQTLs is complex and often constrained by methodological challenges and high costs. Therefore, we employed a multiparental mapping strategy driven by RNA-seq, enabling us to leverage extensive genetic variation in a cost-efficient manner. A randomly mating population was generated on bean from a small number of genetically diverse, often heterozygous parents, and subsequently transferred to tomato prior to RNA-seq. Upon whole genome sequencing of the parents, RNA-seq of the mapping population individuals was sufficient to reconstruct their genomes as a combination of parental haploblocks. Subsequent eQTL mapping identified 23 distinct trans-eQTL hotspot regions associated with the expression of numerous target genes. The most prominent hotspot on chromosome 3 was associated with approximately 900 genes and showed enrichment for functions related to detoxification and digestion. Furthermore, 4 of these trans-eQTL hotspot genotypes explained significant variation in mite fitness on the challenging host plant. This contrasted a traditional QTL mapping approach, where these genotypes could not be detected due to multiple testing correction. Our study hence offers a powerful strategy for trans-eQTL hotspot screening and the discovery of trait-associated loci in complex, multiparental genetic backgrounds.

bioinformatics↗

bioRxiv2026

Genome sequence and efficient CRISPR/Cas9 gene editing in the solanacea specialist pest Tetranychus evansi

Tetranychus evansi is an invasive spider mite pest of solanaceous crops worldwide. Its global expansion and ability to rapidly develop acaricide resistance highlight the need for robust genomic resources and functional genetic tools to design custom control strategies. Here, we deliver a high-quality genome assembly and establish efficient CRISPR/Cas9 editing in T. evansi to enable mechanistic studies of host adaptation and pesticide resistance. Using an inbred line and Oxford Nanopore Technologies (ONT) long-read sequencing ([~]36x), we assembled an 89 Mb genome into 13 contigs (N50 = 18.6 Mb) with high completeness and annotated 14,246 protein-coding genes. We manually curated the principal detoxification gene families (P450s, CCEs, GSTs, UGTs, ABC transporters and DOGs), revealing consistently smaller repertoires than in the highly polyphagous relative Tetranychus urticae. To enable reverse genetics, we adapted SYNCAS (saponin + branched amphiphilic peptide capsules) for maternal delivery of CRISPR/Cas9 in T. evansi. Targeting the phytoene desaturase (PD) pigmentation marker produced reliable knockouts with visible albinism and mean editing efficiencies of [~]9.6-14.7%, allowing establishment of stable mutant lines. We further applied precision gene editing to knock-in (KI) the M918T and M918L substitutions into the voltage-gated sodium channel (VGSC). While M918L was lethal in T. evansi, we generated multiple homozygous lines for M918T (mean KI [~]4.4%). Bioassays demonstrated that while the mutation caused extremely high levels of bifenthrin resistance (RR>1000), this was less so for cyfluthrin (RR=164), revealing the independent and specific role of M918T in pyrethroid resistance. Collectively, these resources establish T. evansi as a tractable system for reverse genetic analysis and provide a reference for future comparative and population genomics.

genetics↗

bioRxiv2025

SYNCAS-Mediated CRISPR-Cas9 Genome Editing in the Jewel Wasp, Nasonia vitripennis

Genetic engineering is a formidable approach to study biology. The development of CRISPR-Cas9 has allowed the genetic engineering of insect species from several orders, and in some species, this tool is used routinely for genetic research. However, insect gene editing often relies on the delivery of CRISPR-Cas9 components via embryo injection. This technique has a limitation: some species lay their eggs inside hard substrates or living hosts, making embryo collection impossible or labour-intensive. Recently, a variety of techniques that exploit maternal injection of nucleases have been developed to circumvent embryo injection. Yet, despite this variety of maternal delivery techniques, some insects remain refractory to gene editing. One of these is the parasitoid wasp, Nasonia vitripennis, an important hymenopteran model species. In this study, a recently developed method termed SYNCAS was used to perform knock-out (KO) of the cinnabar gene in this wasp, obtaining KO efficiencies up to ten times higher than reported for other maternal injection approaches. We found up to 2.73% of all offspring to display a KO phenotype, and we obtained up to 68 KO offspring per 100 injected mothers. The optimal timing of injection and provision of hosts for egg laying was determined. With this protocol, routine applications of CRISPR-Cas9 become feasible in this species, allowing reverse genetics studies of genes with unknown associated phenotypes and paving the way for more advanced editing techniques. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=63 SRC="FIGDIR/small/643426v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@170bdd6org.highwire.dtl.DTLVardef@bf3cbaorg.highwire.dtl.DTLVardef@12be928org.highwire.dtl.DTLVardef@1d85e6a_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIMaternal injection of Cas9 RNP together with BAPC and saponins (SYNCAS) results in efficient gene editing of Nasonia vitripennis offspring C_LIO_LITiming of injection and egg collection is important for maximising efficiency and reducing screening effort C_LIO_LIThe efficient genetic engineering of Nasonia vitripennis suggests the applicability of SYNCAS to other parasitoid wasps, a category of insects particularly difficult to genetically engineer with embryonic Cas9 injections. C_LI

molecular biology↗

bioRxiv2022

Next-generation large-scale binary protein interaction network for Drosophila

Generating reference maps of the interactome networks underlying most cellular functions can greatly illuminate genetic studies by providing a protein-centric approach to finding new components of existing pathways, complexes, and processes. Here, we applied state-of-the-art experimental and bioinformatics methods to identify high-confidence binary protein-protein interactions (PPIs) for Drosophila melanogaster. We performed four all-by-all yeast two-hybrid (Y2H) screens of >10,000 Drosophila proteins, resulting in the FlyBi dataset of 8,723 PPIs among 2,939 proteins. As part of this effort, we tested subsets of our data and data from previous PPI datasets using an orthogonal assay, which allowed us to normalize data quality across datasets. Next, we integrated our FlyBi data with previous PPI data, resulting in an expanded, high-confidence binary Drosophila reference interaction network, DroRI, comprising 17,232 interactions among 6,511 proteins. These data are accessible through the Molecular Interaction Search Tool (MIST) and other databases. To assess the utility of the PPI resource, we used novel interactions from the FlyBi dataset to generate an autophagy interaction network that we validated in vivo using two different autophagy-related assays. We found that deformed wings (dwg) encodes a protein that is both a regulator and a target of autophagy. Altogether, the resources generated in this project provide a strong foundation for building high-confidence new hypotheses regarding protein networks and function.

cell biology↗

bioRxiv2019

A reference map of the human protein interactome

Global insights into cellular organization and function require comprehensive understanding of interactome networks. Similar to how a reference genome sequence revolutionized human genetics, a reference map of the human interactome network is critical to fully understand genotype-phenotype relationships. Here we present the first human \"all-by-all\" binary reference interactome map, or \"HuRI\". With ~53,000 high-quality protein-protein interactions (PPIs), HuRI is approximately four times larger than the information curated from small-scale studies available in the literature. Integrating HuRI with genome, transcriptome and proteome data enables the study of cellular function within essentially any physiological or pathological cellular context. We demonstrate the use of HuRI in identifying specific subcellular roles of PPIs and protein function modulation via splicing during brain development. Inferred tissue-specific networks reveal general principles for the formation of cellular context-specific functions and elucidate potential molecular mechanisms underlying tissue-specific phenotypes of Mendelian diseases. HuRI thus represents an unprecedented, systematic reference linking genomic variation to phenotypic outcomes.

systems biology↗