Biology subjects

Gimenez, S.

Publications and source records attributed to Gimenez, S..

6 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↗

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↗

bioRxiv2021

NK cells acquire CCR5 and CXCR4 by trogocytosis in people living with HIV-1

NK cells play a major role in the antiviral immune response, including against HIV-1. HIV patients have impaired NK cell activity with decrease in CD56dim NK cells and increase in CD56-CD16+ subset and recently it has been proposed that a population of CD56+NKG2C+KIR+CD57+ cells represents antiviral memory NK cells. Antiretroviral therapy (ART) partly restores the functional activity of this lymphocyte lineage. NK cells when interacting with their targets can gain antigens from them by the process of trogocytosis. Here we show that NK cells can obtain CCR5 and CXCR4, but barely CD4, from T cell lines by trogocytosis in vitro. By UMAP (Uniform Manifold Approximation and Projection), we show that aviremic HIV patients have unique NK cell clusters that encompass for cells expressing CCR5, NKG2C and KIRs, but lack CD57 expression. Viremic patients have a larger proportion of CXCR4+ and CCR5+ NK cells than healthy donors (HD) and this is largely increased in CD107+ cells, suggesting a link between degranulation and trogocytosis. In agreement, UMAP identified a specific NK cell cluster in viremic HIV patients, which contains most of the CD107a+, CCR5+ and CXCR4+ cells. However, this cluster lacks NKG2C expression. Therefore, NK cells can gain CCR5 and CXCR4 by trogocytosis, which depends on degranulation. Author SummaryNK cells play a major role in the antiviral immune response, including against HIV-1. HIV-1 infection largely impacts NK cell lineage. However, identification of the NK cells fighting the virus and eliminating infected cells has remained elusive. By using FACs analysis and analyzing T cell markers, we identify specific NK cell subsets that have gained T cell antigen markers by trogocytosis. We show a strong association of degranulation and trogocytosis ex vivo suggesting that NK cells are eliminating or trying to eliminate HIV-1 infected cells. Moreover, we show that NK cells can obtain the HIV-1 coreceptors CCR5 and CXCR4, but barely CD4, from T cells. Therefore, by uncovering that NK cells gain CCR5 and CXCR4 by trogocytosis we show that NK cells are actively fighting against HIV-1 infection in viremic and aviremic patients. This should help to identify why certain patients better control the virus, to develop new anti-HIV-1, NK cell-based, immunotherapies and to understand if NK cells can be a new HIV-1 reservoir.

immunology↗

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↗

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↗

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↗