Biology subjects

Negre, N.

Publications and source records attributed to Negre, N..

11 recordsLinked to original sources

bioRxiv2025

A characterization of piARNs, their biogenesis and their targets in Spodoptera frugiperda (Lepidoptera, Noctuidae)

PIWI-interacting RNAs (piRNAs) and PIWI proteins were initially described as involved in gametogenesis and preservation of genome integrity through the control of transposable elements (TE). Expressed also in the soma and able to regulate protein coding gene expression, they are involved in multiple biological pathways including host-pathogens interaction, sex determination, reproductive isolation. Spodoptera frugiperda is a major invasive insect pest species consisting of two strains with different host-plant ranges. In this paper, we characterized proteins and genomic regions involved in their biogenesis as well as TE and gene transcripts regulated by piRNAs. By phylogenetic analysis, we identified two new Piwi genes conserved in the genus Spodoptera, compared to the Lepidopteran model Bombyx mori, one more than in Drosophila. One of them, more expressed in gonads then soma could be a functional homolog of Drosophila PIWI or replace AGO3. A pool of 11 sRNA-Seq libraries was used to annotate piRNA clusters with Shortstack in the genomes of the two strains of Spodoptera frugiperda. Identification of TE targeted by piRNAs revealed that active transposons differ between the two strains of S. frugiperda despite of a similar TE content, as putative cause or consequence of reproductive isolation. GO analysis of genes targeted by piRNAs shows that some are involved in protein translation initiation. A piRNA cluster in the Masc gene suggests that sex determination is regulated by piRNAs in Spodoptera frugiperda. Our analysis supports that piRNAs have additional roles than silencing of transposable elements and contributes to functional annotation of the two strains genomes of Spodoptera frugiperda.

genomics↗

bioRxiv2025

Nested PCR to optimize rpoB metabarcoding for low-concentration and host-associated bacterial DNA

BackgroundHousekeeping genes have proved effective taxonomic markers for characterizing bacterial microbiota in short-read amplicon metabarcoding studies. A region of the rpoB gene, in particular, has been shown to minimize OTU overestimation bias with a high degree of accuracy, providing better species-level taxonomic resolution (Ogier et al. BMC Microbiol. 19:171). However, the primers for rpoB are highly degenerate, leading to potential problems in the amplification of bacterial DNA present at low concentration in the sample or embedded within eukaryotic matrices, as for the host-associated microbiota. We addressed these limitations by using a two-step PCR approach to optimize the rpoB procedure. The first PCR amplifies a 906-nucleotide region of the rpoB gene with the classical primers, referred to here as outer primers, and the second PCR then uses primers incorporating Illumina adapters, referred to here as inner primers, to amplify a 435-nucleotide subregion, the taxonomic marker for metabarcoding. ResultsWe first used in silico approaches to evaluate the universality of the outer and inner rpoB primers. We then tested the nested rpoB PCR method on commercial mock samples of known composition. The nested PCR approach increased amplification efficiency for dilute samples without biasing the bacterial composition of the mock sample revealed by metabarcoding relative to single-step PCR. We also tested the nested rpoB PCR method on field-collected samples of the lepidopteran Spodoptera frugiperda. The nested PCR outperformed single-step PCR, increasing amplification efficiency for bacterial DNA present at low concentrations (oral secretions from S. frugiperda) or embedded in eukaryotic DNA matrices (S. frugiperda larvae). ConclusionsThis method provides a promising new strategy for characterizing insect-associated microbiota that can also be applied to other host microbiomes.

microbiology↗

bioRxiv2024

Identification of a viral gene essential for the genome replication of a domesticated endogenous virus in ichneumonid parasitoid wasps

Thousands of endoparasitoid wasp species in the families Braconidae and Ichneumonidae harbor "domesticated endogenous viruses" (DEVs) in their genomes. This study focuses on ichneumonid DEVs, named ichnoviruses (IVs), which derive from an unknown virus and produce virions in ovary calyx cells during the pupal and adult stages of female wasps. Females inject IV virions into host insects when laying eggs. Virions infect cells which express IV genes with functions required for wasp progeny development. IVs have a dispersed genome consisting of two genetic components: proviral segment loci that serve as templates for circular dsDNAs that are packaged into capsids, and genes from an ancestral virus controlling virion production. Because of the lack of homology with known viral genes, the molecular control mechanisms of IV genome are largely uncharacterized. We generated a chromosome-scale genome assembly for Hyposoter didymator and identified a total of 67 H. didymator ichnovirus (HdIV) loci distributed across the 12 wasp chromosomes. By analyzing genomic DNA levels, we found that all HdIV loci were locally amplified in calyx cells during the wasp pupal stage, suggesting the implication of viral proteins in DNA replication. We tested a candidate HdIV gene, U16, encoding a protein with a conserved domain found in primases and which is transcribed in calyx cells during the initial stages of replication. Knockdown of U16 by RNA interference inhibited amplification of all HdIV loci, as well as HdIV gene transcription, circular molecule production and virion morphogenesis in calyx cells. Altogether, our results showed that viral DNA amplification is an early step of IV replication essential for virions production, and demonstrated the implication of the viral gene U16 in this process. Author SummaryParasitoid "domesticated endogenous viruses" (DEVs) provide a fascinating example of eukaryotes acquiring new functions through integration of a virus genome. DEVs consist of multiple loci in the genomes of wasps. Upon activation, these elements collectively orchestrate the production of virions or virus-like particles that are crucial for successful parasitism of host insects. Despite the significance of DEVs for parasitoid biology, the mechanisms regulating key steps in virion morphogenesis are largely unknown. In this study, we focused on the ichneumonid parasitoid Hyposoter didymator, which harbors an ichnovirus consisting of 67 proviral loci. Our findings reveal that all proviral loci are simultaneously amplified in ovary calyx cells of female wasps during the early pupal stage suggesting a hijacking of cellular replication complexes by viral proteins. We tested the implication of such a candidate, U16, encoding a protein with a weakly conserved primase C-terminal domain. Silencing U16 resulted in inhibited viral DNA amplification and virion production, underscoring the key role of this gene for ichnovirus replication. This study provides evidence that genes involved in viral DNA replication have been conserved during the domestication of viruses in the genomes of ichneumonid wasps.

microbiology↗

bioRxiv2022

Host-plant adaptation as a driver of incipient speciation in the fall armyworm (Spodoptera frugiperda)

BackgroundDivergent selection on host-plants is one of the main evolutionary forces driving ecological speciation in phytophagous insects. The ecological speciation might be challenging in the presence of gene flow and assortative mating because the direction of divergence is not necessarily the same between ecological selection (through host-plant adaptation) and assortative mating. The fall armyworm (FAW), a major lepidopteran pest species, is composed of two sympatric strains, corn and rice strains, named after two of their preferred host-plants. These two strains have been hypothesized to undergo incipient speciation, based on (i) several lines of evidence encompassing both pre- and post-zygotic reproductive isolation, and (ii) the presence of a substantial level of genetic differentiation. Even though the status of these two strains has been established a long time ago, it is still yet to be found whether these two strains indeed exhibit a marked level of genetic differentiation from a large number of genomic loci. Here, we analyzed whole genome sequences from 56 FAW individuals either collected from pasture grasses (a part of the favored host range of the rice strain) or corn to assess the role of host-plant adaptation in incipient speciation. ResultsPrincipal component analysis of whole genome data shows that the pattern of divergence in the fall armyworm is predominantly explained by the genetic differentiation associated with host-plants. The level of genetic differentiation between corn and rice strains is particularly marked in the Z chromosome. We identified one autosomal locus and two Z chromosome loci targeted by selective sweeps specific to rice strain and corn strain, respectively. The autosomal locus has both increased DXY and FST while the Z chromosome loci had decreased DXY and increased FST. ConclusionThese results show that the FAW population structure is dominated by the genetic differentiation between corn and rice strains. This differentiation involves divergent selection targeting at least three loci, which include a locus potentially causing reproductive isolation. Taken together, these results suggest the evolutionary scenario that host-plant speciation is a driver of incipient speciation in the fall armyworm.

evolutionary biology↗

bioRxiv2020

Genomic balancing selection is key to the invasive success of the fall armyworm

A successful biological invasion involves survival in a newly occupied environment. If a population bottleneck occurs during an invasion, the resulting depletion of genetic variants could cause increased inbreeding depression and decreased adaptive potential, which may result in a fitness reduction. How invasive populations survive in the newly occupied environment despite reduced heterozygosity and how, in many cases, they maintain moderate levels of heterozygosity are still contentious issues1. The Fall armyworm (FAW; Lepidoptera: Spodoptera frugiperda), a polyphagous pest, is native to the Western hemisphere. Its invasion in the Old World was first reported from West Africa in early 2016, and in less than four years, it swept sub-Saharan Africa and Asia, finally reaching Australia. We used population genomics approaches to investigate the factors that may explain the invasive success of the FAW. Here we show that genomic balancing selection played a key role in invasive success by restoring heterozygosity before the global invasion. We observe a drastic loss of mitochondrial polymorphism in invasive populations, whereas nuclear heterozygosity exhibits a mild reduction. The population from Benin in West Africa has the lowest length of linkage disequilibrium amongst all invasive and native populations despite its reduced population size. This result indicates that balancing selection increased heterozygosity by facilitating the admixture of invasive populations from distinct origins and that, once heterozygosity was sufficiently high, FAW started spreading globally in the Old World. As comparable heterozygosity levels between invasive and native populations are commonly observed1, we postulate that the restoration of heterozygosity through balancing selection could be widespread among successful cases of biological invasions.

evolutionary biology↗

bioRxiv2020

Whole genome sequencing of global Spodoptera frugiperda populations: evidence for complex, multiple introductions across the Old World

Native to the Americas, the invasive Spodoptera frugiperda (fall armyworm; FAW) was reported in West Africa in 2016, followed by chronological order of detections across the Old World and the hypothesis of an eastward Asia expansion. We explored population genomic signatures of American and Old World FAW and identified 12 maternal mitochondrial DNA genome lineages across the invasive range, while from 870 high-quality nuclear single nucleotide polymorphic DNA markers five distinct New World population clusters were identified, broadly reflected their native geographical ranges and absence of host-plant preferences. We identified unique admixed Old World populations, and admixed and non-admixed Asian FAW individuals, all of which suggested multiple introductions underpinned the pests global spread. Directional gene flow from the East into eastern Africa was also detected, in contrast to the west-to-east spread hypothesis. Our study demonstrated population genomic approaches via international partnership to address global emerging pest threats and biosecurity challenges.

genomics↗

bioRxiv2019

Adaptation by copy number variation increases insecticide resistance in fall armyworms

Insecticide resistance is a major main challenge in pest control, and understanding its genetic basis is a key topic in agricultural ecology. Detoxification genes are well-known genetic elements that play a key role in adaptation to xenobiotics. The adaptive evolution of detoxification genes by copy number variations has been interpreted as a cause of insecticide resistance. However, the same pattern can be generated by the adaptation to host-plant defense toxins as well. In this study, we tested in fall armyworms (Lepidoptera Spodoptera frugiperda) if adaptation by copy number variation is the cause of the increased level of insecticide resistance from two geographic populations with different levels of resistance and two strains with different host plants. Following the generation of an assembly with chromosome-sized scaffolds (N50 = 13.2Mb), we observed that these two populations show a significant allelic differentiation of copy number variations, which is not observed between strains. In particular, a locus with almost complete allelic differentiation (Fst > 0.8) includes a cluster of P450 genes, which are well-known key players in detoxification. Detoxification genes are overrepresented in the genes with copy number variations, and the observed copy number variation appears to have beneficial effects in general. From this result, we concluded that copy number variation of detoxification genes in fall armyworms plays a key role in the insecticide resistance but not in the adaptation to host-plants, suggesting that the evolution of insecticide resistance may occur independently from host-plant adaptation.

evolutionary biology↗

bioRxiv2019

Partner-specific induction of Spodoptera frugiperda immune genes in response to the entomopathogenic nematobacterial complex Steinernema carpocapsae-Xenorhabdus nematophila

The Steinernema carpocapsae-Xenorhabdus nematophila association is a nematobacterial complex (NBC) used in biological control of insect crop pests. The ability of this dual pathogen to infest and kill an insect strongly depends on the dialogue between the hosts immune system and each partner of the complex. Even though this dialogue has been extensively studied from the two partners points of view in several insect models, still little is known about the structure and the molecular aspects of the insects immune response to the dual infection. Here, we used the lepidopteran pest Spodoptera frugiperda as a model to analyze the respective impact of each NBC partner in the spatiotemporal immune responses that are induced after infestation. To this aim, we first analyzed the expression variations of the insects immune genes in the fat bodies and hemocytes of infested larvae by using previously obtained RNAseq data. We then selected representative immune genes for RT-qPCR investigations of the temporal variations of their expressions after infestation and of their induction levels after independent injections of each partner. We found that the fat body and the hemocytes both produce potent and stable immune responses to the infestation by the NBC, which correspond to combinations of bacterium- and nematode-induced ones. Consistent with the nature of each pathogen, we showed that X. nematophila mainly induces genes classically involved in antibacterial responses, whereas S. carpocapsae is responsible for the induction of lectins and of genes expected to be involved in melanization and cellular encapsulation. In addition, we found that two clusters of unknown genes dramatically induced by the NBC also present partner-specific induction profiles, which paves the way for their functional characterization. Finally, we discuss putative relationships between the variations of the expression of some immune genes and the NBCs immunosuppressive strategies.\n\nAuthor summaryEntomopathogenic nematodes (EPNs) are living in the soil and prey upon insect larvae. They enter the insect by the natural orifices, and reach the hemocoel through the intestinal epithelium. There, they release their symbiotic bacteria that will develop within the insect and eventually kill it. Nematodes can then feed and reproduce on the insect cadaver. By using transcriptomic approaches, we previously showed that Lepidoptera larvae (caterpillars of the fall armyworm Spodoptera frugiperda) produce a strong immune response in reaction to infestation by EPNs. However, we do not know if this immune reaction is triggered by the nematode itself -Steinernema carpacapsae - or its symbiotic bacteria - Xenorhabdus nematophila. To answer this question, we present in this work a careful annotation of immunity genes in S. frugiperda and surveyed their activation by quantitative PCR in reaction to an injection of the bacteria alone, the axenic nematode or the associated complex. We found that the immune genes are selectively activated by either the bacteria or the nematode and we discuss the implication of which pathway are involved in the defense against various pathogens. We also show that a cluster of newly discovered genes, present only in Lepidoptera, is activated by the nematode only and could represent nematicide genes.

immunology↗

bioRxiv2019

Spodoptera frugiperda transcriptional response to infestation by Steinernema carpocapsae

Steinernema carpocapsae is an entomopathogenic nematode (EPN) used in biological control of agricultural pest insects. It enters the hemocoel of its host via the intestinal tract and releases its symbiotic bacterium Xenorhabdus nematophila, which kills the insect in less than 48 hours. Although several aspects of its interactions with insects have been extensively studied, still little is known about the immune and physiological responses of its different hosts. In order to improve this knowledge, we examined the transcriptional responses to EPN infestation of the fat body, the hemocytes and the midgut in the lepidopteran pest model Spodoptera frugiperda (Lepidoptera: Noctuidae).\n\nOur results indicate that the tissues poorly respond to the infestation at an early time post-infestation of 8 h, even though the proliferation of the bacterial symbiont within the hemocoel is detected. Only 5 genes are differentially expressed in the fat body of the caterpillars. However, strong transcriptional responses are observed at a later time point of 15 h post-infestation in all three tissues. While few genes are differentially expressed in the midgut, tissue-specific panels of induced metalloprotease inhibitors, immune receptors and antimicrobial peptides together with several uncharacterized genes are up-regulated in the fat body and the hemocytes. In addition, among the most up-regulated genes, we identified new potential immune effectors, unique to Lepidoptera, for which we present evidence of acquisition by Horizontal Gene Transfer from bacteria.\n\nAltogether, these results pave the way for further functional studies of the mobilized genes involvement in the interaction with the EPN.\n\nAuthor summaryThe Fall Armyworm, Spodoptera frugiperda, is a major agricultural pest. The caterpillars cause extensive damage to crops of importance such as corn, rice, sorghum and cotton. Originally from the Americas, it is currently becoming invasive in other parts of the world, first in Africa in 2016, then in India and now in south-east Asia. Programs of biological control against insect pests are increasingly encouraged around the world and include the use of pathogens. Entomopathogenic nematodes such as Steinernema carpocapsae are already commercialized as organic pesticides. These nematodes live in the soil and enter the body of their insect preys. Once within the insects, they release their symbiotic bacteria (Xenorhabdus nematophila in this case), which infect and kill the host in a few hours. The nematodes can then feed on the dead insects, reproduce and resume their life cycle. It is a major challenge to understand how EPN achieve their pathogenicity as well as how the insects can resist them. Here we provide the foundation for such an interaction between EPN and a Lepidoptera. We analyzed the dynamic of transcriptional response in three insect tissues (midgut, fat body and hemocytes) upon infestation by EPN. Not many studies have been performed genome-wide on such an interaction, and none on a Lepidopteran model of economical importance. Our transcriptomic approach revealed some specificities of the Lepidopteran defense mechanisms. In particular, we discovered a set of genes, acquired in Lepidoptera from bacteria by Horizontal Gene Transfer, that probably encode proteins with antibiotic activity.

genomics↗

bioRxiv2018

Genomic differentiation is initiated without physical linkage among targets of divergent selection in Fall armyworms

The process of speciation involves whole genome differentiation by overcoming gene flow between diverging populations. We have ample knowledge which evolutionary forces may cause genomic differentiation, and several speciation models have been proposed to explain the transition from genetic to genomic differentiation. However, it is still unclear what are critical conditions enabling genomic differentiation in nature. The Fall armyworm, Spodoptera frugiperda, is observed as two sympatric strains that have different host-plant ranges, suggesting the possibility of ecological divergent selection. In our previous study, we observed that these two strains show genetic differentiation across the whole genome with an unprecedentedly low extent, suggesting the possibility that whole genome sequences started to be differentiated between the strains. In this study, we analyzed whole genome sequences from these two strains from Mississippi to identify critical evolutionary factors for genomic differentiation. The genomic Fst is low (0.017) while 91.3% of 10kb windows have Fst greater than 0, suggesting genome-wide differentiation with a low extent. We identified nearly 400 outliers of genetic differentiation between strains, and found that physical linkage among these outliers is not a primary cause of genomic differentiation. Fst is not significantly correlated with gene density, a proxy for the strength of selection, suggesting that a genomic reduction in migration rate dominates the extent of local genetic differentiation. Our analyses reveal that divergent selection alone is sufficient to generate genomic differentiation, and any following diversifying factors may increase the level of genetic differentiation between diverging strains in the process of speciation.

evolutionary biology↗

bioRxiv2018

Transcriptional plasticity evolution in two strains of Spodoptera frugiperda (Lepidoptera: Noctuidae) feeding on alternative host-plants

AO_SCPLOWBSTRACTC_SCPLOWSpodoptera frugiperda, the fall armyworm (FAW), is an important agricultural pest in the Americas and an emerging pest in sub-Saharan Africa, India, East-Asia and Australia, causing damage to major crops such as corn, sorghum and soybean. While FAW larvae are considered polyphagous, differences in diet preference have been described between two genetic variants: the corn strain (sf-C) and the rice strain (sf-R). These two strains are sometimes considered as distinct species, raising the hypothesis that ost plant specialization might have driven their divergence. To test this hypothesis, we irst performed controlled reciprocal transplant (RT) experiments to address the impact of plant diet on several traits linked to the fitness of the sf-C and sf-R strains. The phenotypical data suggest that sf-C is specialized to corn. We then used RNA-Se to identify constitutive transcriptional differences between strains, regardless of diet, in laboratory as well as in natural populations. We found that variations in mitochon rial transcription levels are among the most substantial and consistent differences between the two strains. Since mitochondrial genotypes also vary between the strains, we believe the mitochondria may have a significant role in driving strain divergence.

evolutionary biology↗