Latest Articles

Section: Infections ; Topics: Evolution, Population biology

Population shifts in begomoviruses associated with tomato yellow leaf curl disease in western Mediterranean countries

Granier, Martine; Faize, Mohamed; Passera, Sandie; Urbino, Cica; Peterschmitt, Michel

10.24072/pcjournal.628 - Peer Community Journal, Volume 5 (2025), article no. e108
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Tomato yellow leaf curl disease (TYLCD) was reported in western Mediterranean basin since the late 1980s. Based on intensive plant samplings performed in Spain, Italy and Morocco at different periods between the 1990s and 2014, several begomoviruses (family Geminiviridae) were identified as the cause of TYLCD. They comprise the native Begomovirus solanumflavusardiniaense (Tomato yellow leaf curl Sardinia virus, TYLCSaV), two strains of Begomovirus coheni (Tomato yellow leaf curl virus, TYLCV) introduced from the Middle East, and several types of TYLCV/TYLCSaV recombinants, including the invasive recombinant TYLCV-IS76 in which the genome fragment inherited from TYLCSaV was unusually short. Although parental and recombinant TYLCD-associated begomoviruses were present in each country, country specificities were detected with respect to their relative prevalence, the infection profiles of individual tomato plants, and the recombination patterns of TYLCV/TYLCSaV recombinants. Considering geographic proximities and trade activities between these countries, and the efficient transmission of begomoviruses which are persistently transmitted by the polyphagous and tiny whitefly vector Bemisia tabaci, it was not known if these specificities would be maintained over time. To address this question, 105 tomato samples collected in the three countries between 2015 and 2019 were analysed with PCR tests previously designed to distinguish species, strains and recombinants of TYLCD associated begomoviruses, and with an original PCR test distinguishing emerging resistance-breaking recombinants bearing short TYLCSaV-inherited fragments like TYLCV-IS76 (Srec) from formerly reported recombinants with longer TYLCSaV fragments (Lrec). The results show that country specificities are still present, the most striking being the contrasted geographic distribution of Srec recombinants, with TYLCV-IS76 detected in Morocco but not in Italy, and TYLCV-IS141 and a new Srec recombinant (TYLCV-IMS60-2400) both detected in Italy and not in Morocco. Nevertheless, besides country specificities, a general population shift was revealed regarding TYLCV/TYLCSaV recombinants. Indeed, all the recombinant positive samples, irrespective of their geographic origin, were Srec-positive but Lrec-negative, which suggest that the emergence of Srec recombinants occurred at the expenses of the Lrec recombinants. These results are discussed in relation to the positive selection of Srec recombinants by Ty-1-resistant tomato plants.
Section: Genomics ; Topics: Genetics/genomics ; Conference: JOBIM

hdmax2, an R package to perform high dimension mediation analysis

Pittion, Florence; Jumentier, Basile; Nakamura, Aurélie; Lepeule, Johanna; François, Olivier; Richard, Magali

10.24072/pcjournal.564 - Peer Community Journal, Volume 5 (2025), article no. e107
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Mediation analysis plays a crucial role in epidemiology, unraveling the intricate pathways through which exposures exert influence on health outcomes. Recent advances in high-throughput sequencing techniques have generated growing interest in applying mediation analysis to explore the causal relationships between patient environmental exposure, molecular features (such as omics data) and various health outcomes. Mediation analysis handling high-dimensional mediators raise a number of statistical challenges. Despite the emergence of numerous methods designed to tackle these challenges, the majority are limited to continuous outcomes. Furthermore, these advanced statistical approaches have yet to find widespread adoption among epidemiologists and health data scientists in their day-to-day practices. To address this gap, we introduce a method specifically tailored for high-dimensional mediation analysis using the max-squared method (HDMAX2). This tool aims to bridge the current divide by providing a practical solution for researchers and practitioners eager to explore intricate causal relationships in health data involving complex molecular features. Here we improve the HDMAX2 method, and expand its capabilities to accommodate multivariate exposure and non-continuous outcomes. This improvement enables its application to a diverse array of mediation analysis scenarios, mirroring the complexity often encountered in healthcare data. To enhance accessibility for users with varying expertise, we release an R package called hdmax2. This package allows users to estimate the indirect effects of mediators, calculate the overall indirect effect of mediators, and facilitates the execution of high-dimensional mediation analysis. We demonstrate its application through two high-dimensional case studies examining DNA methylation and gene expression as mediators, with binary outcomes and both continuous and binary exposures. These examples illustrate practical aspects of the method, including latent factor selection and mediator identification.
Section: Genomics ; Topics: Agricultural sciences, Genetics/genomics

HaploCharmer: a Snakemake workflow for read-scale haplotype calling adapted to polyploids

Rio, Simon; Abdallah, Sophie; Durand, Théo; D'Hont, Angélique; Garsmeur, Olivier

10.24072/pcjournal.631 - Peer Community Journal, Volume 5 (2025), article no. e106
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The advent of next-generation sequencing (NGS) has revolutionized the study of single nucleotide polymorphisms (SNPs), making it increasingly cost-effective. Haplotypes, which combine alleles from adjacent variants, offer several advantages over bi-allelic SNPs, including enhanced information content, reduced dimensionality, and improved statistical power in genomic studies. These benefits are particularly significant for polyploid species, where distinguishing all homologous copies using SNP markers alone can be challenging. This article introduces HaploCharmer, a flexible workflow designed for read-scale haplotype calling from NGS data. HaploCharmer identifies haplotypes within preconfigured genomic regions smaller than a sequencing read, ensuring direct comparability across individuals. It integrates a series of processing steps including mapping, haplotype identification, filtration, and reporting of haplotype sequences, as presence-absence, in the panel of accessions analyzed. The performance of HaploCharmer was validated by building a genetic map using whole-genome sequencing data from a highly polyploid sugarcane cultivar (R570) and its self-progeny, and performing a diversity analysis in the polyploid Saccharum genus using targeted sequencing data. The workflow successfully identified a large number of high-quality haplotypes, with less than 1% of false positives. The dense genetic map obtained using single-dose haplotypes accurately depicted the known genome architecture of the R570 cultivar, including large chromosome rearrangements. The diversity analysis accurately reflected the known genetic structure within this genus. It also allowed inferring ancestral origins to mapped haplotypes and the corresponding chromosome segments in the R570 genetic map. HaploCharmer provides a robust method for diversity, genetic mapping, and quantitative genetics studies in both diploid and polyploid species.
Section: Infections ; Topics: Biology of interactions, Biophysics and computational biology, Health sciences

The potential of attractive insecticide-treated nets (ITNs) in reducing malaria transmission: a modeling study

Moiroux, Nicolas; Pennetier, Cédric

10.24072/pcjournal.632 - Peer Community Journal, Volume 5 (2025), article no. e105
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Recent studies suggest that insecticide-treated nets (ITNs) may actively attract malaria vectors, increasing their likelihood of coming into contact with the insecticide while potentially reducing personal protection. The impact of such attractive ITN on malaria transmission at the community level remains unclear. In this study, we developed a model to compare the effectiveness of attractive, inert and deterrent ITNs under varying levels of human usage and different degrees of physiological or behavioral resistance to insecticides in malaria vectors. We developed a model to simulate the host-seeking, feeding and mortality (HSFM) of mosquito vectors facing ITNs. This model allows mosquitoes to choose between two rooms based on the presence and remote influence (attractive, inert or deterrent) of ITNs. The HSFM model was then integrated into a malaria transmission model to compare the Plasmodium transmission potential of mosquitoes exposed to these different type of ITNs under various scenarios of ITN coverage, physiological resistance, quantitative behavioral resistance, and qualitative behavioral resistance. The model predicts that attractive ITNs consistently reduce malaria transmission potential of vectors more effectively than inert or deterrent ITNs, even in the presence of resistant vector phenotypes. For instance, at intermediate use rate (50%), strongly attractive ITNs are expected to reduce transmission by up to 67% compared to deterrent ITNs. In resistant vector populations, attractive ITNs remained more effective overall, though the reduction in transmission were less pronounced. Our findings suggest that both inert and attractive ITNs could enhance malaria control efforts, outperforming current deterrent ITNs, even in resistant vector populations. Shifting from deterrent to inert or attractive ITNs could significantly improve vector control strategies, warranting further research and product development to fully explore and optimize this approach.

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The network image was drawn by Martin Grandjean: A force-based network visualization CC BY-SA