Biology subjects

Dhakal, U.

Publications and source records attributed to Dhakal, U..

3 recordsLinked to original sources

bioRxiv2025

PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification

Whole genome sequencing (WGS) offers a comprehensive, organism-agnostic method that effectively meets the need for efficient, reliable, and standardized responses to emerging threats from pathogens and pests. Here, we present PathogenSurveillance, an open-source and automated Nextflow pipeline for population genomic analyses of WGS data. It is designed with features tailored for biosurveillance and is suitable for in-field or point-of-care diagnostics. PathogenSurveillance is flexible, accommodating short- and long-read datasets and mixed samples of prokaryotes and/or eukaryotes. It automates all steps, including reference identification and retrieval from the NCBI Assembly database, and produces customizable interactive reports with summaries, phylogenetic trees, and minimum spanning networks that enable species and subspecies level identification. It also outputs quality control metrics and carefully names and organizes output files to facilitate downstream analyses. The pipeline runs on any Linux-based system and minimizes the need for advanced computational expertise. Source code is available on GitHub under the open-source MIT license. The pipeline expands the toolkit for real-time biosurveillance, enabling rapid detection and monitoring of pathogens and pests for rapid response to novel variants.

bioinformatics↗

bioRxiv2025

Genome-wide association study of DMI fungicide sensitivity detects numerous small-effect variants in the major North American population of Fusarium graminearum

Fusarium head blight (FHB), a major disease of wheat, is primarily managed through applications of demethylation inhibitor (DMI) fungicides during anthesis. However, repeated use of DMIs has led to the emergence of Fusarium graminearum isolates with reduced sensitivity and, in some cases, resistance. In this study, we evaluated the sensitivity of 152 F. graminearum isolates to propiconazole and tebuconazole. While sensitivity varied among isolates, no resistant strains were detected. We also conducted a genome-wide association study (GWAS) to investigate the genetic basis of DMI sensitivity. GWAS identified 48 and 39 quantitative trait nucleotides (QTNs) associated with propiconazole and tebuconazole sensitivity, respectively, with 12 QTNs common to both fungicides--supporting their common mode of action. Candidate gene analysis highlighted genes encoding transporters, secondary metabolite synthesis enzymes, transcription factors, and a heat shock protein as potential candidates for DMI fungicide response. We propose that tolerance to DMIs in F. graminearum is linked to active fungicide efflux out of fungal cells, mediated by transporters, including those associated with secondary metabolite pathways. Data summaryInformation on all strains used in the experiments have been included in a supplemental file. All sequencing data used in this study are publicly available and were described in our previous publication, which has been cited. Additional supporting data (isolate genotype and phenotype files) and code written for the analyses described here are made available on GitHub: https://github.com/Toomajian-laboratory/files_fungicide_manuscript/ Impact statementIsolates from field populations of fungal plant pathogens vary in their sensitivity to DMI fungicides, though in most cases the genetic determinants of this variation are poorly understood. In this study, we measure the sensitivity of isolates from the main US population of Fusarium graminearum to two DMI fungicides. We used GWAS to identify genomic loci and candidate genes that might underlie variation in DMI sensitivity. Our work contributes to the broader effort to understand the evolution of fungicide tolerance and resistance in populations of plant pathogens. The candidate genes identified, most of which are novel, provide good targets for functional studies of the tools fungi use to survive fungicides. The identified variants can also be screened to monitor potential increases in fungicide tolerance. The high-throughput, rapid, and large-scale monitoring of fungicide sensitivity described here advances both fundamental research and resistance management efforts.

genetics↗

bioRxiv2025

Everything, everywhere, all at once - Surveillance and molecular epidemiology reveal Melissococcus plutonius is endemic among Michigan, US beekeeping operations of all sizes and present in some honey bee colonies year-round

European foulbrood (EFB) is a severe bacterial disease of honey bee brood often leading to significant declines in colony health and honey production. The dearth of data on this disease in the United States (US) complicates response efforts. In this study, we combine surveillance and molecular epidemiology to investigate prevalence, diversity, and transmission dynamics of Melissococcus plutonius, the causative agent of EFB, in US honey bee colonies. Rates of infection and disease were found to be seasonal, with prevalence peaking in June when over half the colonies screened were infected. Whole genome, single nucleotide polymorphism analysis revealed wide genetic diversity even within a single hive. Operations often had multiple genotypes present which varied from year to year, consistent with high rates of transmission and reinfection. Prevalence and whole genome data provided here will be critical in tracking the efficacy of mitigation efforts and underscore the necessity of additional epidemiological investigations.

genomics↗