Percorrer por autor "Webster, Matthew"
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- Bioinformatics pipeline to evaluate patterns of diversity in detoxification genes in the Western honey bee (Apis mellifera)Publication . Barbosa, Daniela; Li, Fernanda; Bashir, Sana; Lopes, Ana Rita; Yadró Garcia, Carlos A.; Quaresma, Andreia; Rufino, José; Rosa-Fontana, Annelise; Verbinnen, Gilles; de Graaf, Dirk C.; De Smet, Lina; Taliadoros, Demetris; Webster, Matthew; Pinto, M. Alice; Henriques, DoraThe Western honey bee, Apis mellifera, displays significant genetic diversity in detoxification genes, which is pivotal for environmental adaptation and resilience. Herein, we developed a bioinformatics pipeline to investigate patterns of diversity in these genes, focusing on single nucleotide polymorphisms (SNPs) across A. mellifera populations, with variant annotation performed using both snpEff and the Variant Effect Predictor (VEP). Our pipeline integrates GATK, VCFtools, PLINK, bcftools, snpEff, and VEP to process genomic data systematically. Regions of interest were defined in a BED file for variant filtering. Using GATK, SNPs were extracted from a VCF file and conversion to PLINK format for population genetics analyses. Variants were filtered by minor allele frequency (MAF) and population differentiation (FST index) to identify SNPs with considerable. Variants were annotated with snpEff and VEP to predict functional impacts, enabling a comparative analysis of their annotation consistency and depth. Custom scripts were developed to map SNPs to detoxification genes, quantify SNP density, and integrated gene descriptions and lineage data. The resulting data were visualized using a combination of and generate different graphs using ggplot2 and chromoMap for chromossomal maps. Quality control steps were applied through the pipeline ensuring data reliability. Our findings reveal distinct SNP patterns in detoxification genes, highlighting candidate SNPs associated with A. mellifera subspecies-specific adaptations. The comparison of snpEff and VEP annotations provides insights into their strengths and limitations, which can help optimize software selection for genomic studies. This pipeline offers a reproducible framework for studying genetic diversity in A. mellifera that is adaptable to other species, advancing conservation and evolutionary genomics.
- Evaluating the consequences of plant protection products in the Western honey bee (Apis mellifera) genomePublication . Barbosa, Daniela; Li, Fernanda; Bashir, Sana; Yadró Garcia, Carlos A.; Taliadoros, Demetris; Webster, Matthew; Rufino, José; Roessink, Ivo; Buddendorf, Bas; van der Steen, Jozef; Murcia, Maria; Fernández-Alba, Amadeo Rodríguez; Pinto, M. Alice; Henriques, DoraThe Western honey bee (Apis mellifera)is a key model organism for evaluating risks from Plant Protection Products (PPPs). Despite well-documented impacts of PPPs on honey bees survival and behaviour, their molecular consequences remain underexplored. Herein, over 472 whole genomes from samples collected across Europe in the framework of the project Better-B were used to investigate the genetic basis of PPP exposure through Genomic-Environment Association (GEA) analysis. By integrating genomic data from honey bee colonies with processed PPP exposure data collected in the framework of the project INSIGNIAEU and from the PEST-CHEMGRIDS database as well as from environmental datasets from CORINE land cover, this study used SAMBADA (a spatial analysis tool) and Redundancy Analysis (RDA) scripts to identify candidate genes potentially linked to pesticide stress. This research addresses a knowledge gap, offering a pathway to mitigate PPPrelated molecular effects and support sustainable beekeeping, and can inform breeding programs to bolster honey bee resilience. Ultimately, this work advances our understanding of PPP impacts at the molecular level, fostering resilience in a key pollinator essential for global food security.
- Genetic Diversity of Detoxification Genes in 18 Honey Bee SubspeciesPublication . Li, Fernanda; Barbosa, Daniela; Bashir, Sana; Moreira de Sá, Leandro; Yadró Garcia, Carlos A.; Rufino, José; Rosa-Fontana, Annelise; Verbinnen, Gilles; de Graaf, Dirk; de Smet, Lina; Taliadoros, Demetris; Webster, Matthew; Pinto, M. Alice; Henriques, DoraThe honey bees (Apis mellifera) is a key pollinator that is exposed to a wide array of xenobiotics, both natural (plant allelochemicals) and synthetic (pesticides), while foraging or through contaminated food within the hive. These compounds have both lethal and sub-lethal effects, impairing foraging activity and negatively affecting bee development and colony health. Similar to other insects, honey bees rely on detoxification pathways to metabolise xenobiotics into less toxic or more readily excretable forms. This process is a key mechanism underlying insecticide resistance and is influenced by genetic variation. Therefore, investigating polymorphisms in detoxification-related genes is a promising approach to predict species-specific responses to pesticide exposure. Five major gene families are involved in xenobiotic detoxification: cytochrome P450 monooxygenases (CYPs), carboxyl/cholinesterases (CCEs), glutathione Stransferases (GSTs), ATP-binding cassette transporters (ABCs), and uridine 5′-diphospho-glucuronosyltransferases (UGTs). In this study, we examined the genomic detoxification inventory of over 1,600 individuals representing 18 A. mellifera subspecies representing the four main evolutionary lineages. For each lineage and subspecies, single-nucleotide polymorphism (SNP) loci were identified within these genes, allele frequency and FST (fixation index) were calculated. Additionally, all variants were annotated to assess their potential impact on protein function. Findings from this study have the potential to inform breeding and conservation strategies by identifying populations more vulnerable to chemical stressors, ultimately supporting honey bee health in changing environments.
- Genetic variation of detoxification genes: from genes to proteinsPublication . Henriques, Dora; Li, Fernanda; Bashir, Sana; Quaresma, Andreia; Lopes, Ana Rita; Taliadoros, Demetris; Webster, Matthew; Shiraishi, Carlos S.H.; Yadró Garcia, Carlos A.; Abreu, Rui M.V.; Rufino, José; Rosa-Fontana, Annelise; Verbinnen, Gilles; Graaf, Dirk C. de; De Smet, Lina; Pinto, M. AliceHoney bees (Apis mellifera) are exposed to natural and synthetic xenobiotics, requiring genetic adaptations for survival. Several gene families have been implicated in insect pesticide resistance, including cytochrome P450s, glutathione-S-transferases (GSTs), esterases, and uridine diphosphate (UDP)-glycosyltransferases. This study investigates genetic variation in these detoxification gene families and predicts the structural and functional effects of non-synonymous SNPs (single nucleotide polymorphisms) on protein structure and function. We analyzed SNPs mapped to these detoxification genes extracted from over 1,500 whole genomes representing 15 subspecies and the four main honey bee lineages: M, C, A, and O. Functional annotation and variant effects were predicted using SnpEff. Allele frequencies and each SNP’s fixation index (FST) were calculated per population and evolutionary lineage. Bioinformatics and molecular modeling techniques were employed to evaluate non-synonymous SNPs’ structural and functional consequences. Protein structures were generated from FASTA files using AlphaFold3, converted from mmCIF to PDB format, and visualized in PyMOL. Functional site predictions were performed using Proteins Plus, and molecular dynamics simulations were conducted in YASARA to assess stability and conformational changes in proteins. Our results indicate many non-synonymous SNPs in some subspecies, such as A. m. jemenitica and A. m. intermissa. The genes with the highest number of non-synonymous mutations belong to the CYP family, particularly Probable cytochrome P450 6a14 and CYP9Q1. Conversely, genes such as Cytochrome P450 6k1 and Methyl farnesoate epoxidase exhibit no non-synonymous SNPs. By understanding intraspecific genetic variation, we move closer to reliably predicting how honey bee populations will respond to pesticide exposure.
- Human-mediated rapid evolutionary change in european honey beesPublication . Li, Fernanda; Taliadoros, Demetris; Costa, Maíra; Yadró Garcia, Carlos A.; Cunha, Larissa; Henriques, Dora; Martin-Hernandez, Raquel; de Graaf, Dirk; Webster, Matthew; Pinto, M. AliceIn its vast distributional range, spanning Africa, Europe, the Middle East, and western Asia, the honey bee Apis mellifera diversified into 30 subspecies grouped into four major evolutionary lineages. Two of these lineages, M (western/northern European) and C (southeastern European), are parapatric in Europe. However, increasingly intensified queen trading is likely eroding the natural genetic boundaries and altering the continent’s diversity patterns. To evaluate the impact of this recent human-mediated gene flow, we conducted an unprecedented survey spanning 33 countries and sampling more than 1,300 colonies, including 139 from conservation apiaries of the M-lineage subspecies A. m. mellifera. We used a dual-marker approach combining the hypervariable mitochondrial tRNALeu–cox2 intergenic region with nuclear genome-wide single-nucleotide polymorphisms (SNPs). Both markers were highly concordant at the lineage level and European scale, showing that in the native area of M-lineage, which covers western and northern Europe, C-lineage ancestry is now predominant. This pattern is congruent with widespread commercial dissemination of C-lineage subspecies (A. m. carnica, A. m. ligustica), which is leading to introgressive hybridisation and, in many regions, to almost complete replacement of native subspecies. The exceptions to this trend are the Iberian Peninsula, Ireland, and conservation apiaries, which retain almost exclusively native M-lineage ancestry. Remarkably, even within the native C-lineage range in the Mediterranean and southeastern Europe, the Italian subspecies A.m. ligustica, the most widely favoured subspecies worldwide, shows worrying levels of introgression from its C-lineage neighbour A.m. carnica. Equally striking is the widespread presence of African-lineage mitotypes, whose routes of introduction remain unclear. Altogether, these findings raise serious concerns about the genetic integrity of native subspecies and the consequences of admixture for adaptation in a rapidly changing environment shaped by climate change and emerging parasites and pathogens. Further, these changes may affect the gene pools of wild A. mellifera populations, recently classified as Endangered by the IUCN.
- Landscape-scale genomic responses of the western honey bee (Apis mellifera) to pesticide pressurePublication . Lima, Daniela; Li, Fernanda; Yadró Garcia, Carlos A.; Taliadoros, Demetris; Webster, Matthew; Rufino, José; Roessink, I.; Buddendorf, Bas; Van der Steen, Jozef; Murcia-Morales, María; Fernández-Alba, Amadeo R.; Graaf, Dirk C. de; Lopes, Ana Rita; Pinto, M. Alice; Henriques, DoraWidespread pesticide use associated with intensive agriculture has been proven to impact the Western honey bee (Apis mellifera). However, despite evidence of declines in survival, development, foraging efficiency, and overall colony health, the genomic underpinning of this abiotic stressor is largely unknown. This study involved 102 whole-genome sequences from honey bee colonies from across Europe, sampled under the Better-B project, to search for genetic correlations to pesticide exposure using Genomic-Environment Association (GEA) analyses. The environmental exposure data were collected within the framework of the INSIGNIA-EU project, which used APIStrips (in-hive pesticide-adsorbing strips) to quantify pesticide residues brought into the hive by foraging in many of the sampled colonies. The APISTRIP data were complemented by modelled exposure grids from PEST-CHEMGRIDS and agriculture zones from the CORINE Land Cover. Employing three complementary GEA approaches-SAMBADA (spatial analysis tool), LFMM (latent factor mixed models), and RDA (Redundancy Analysis)—we identified SNPs in the bee’s genome significantly correlated with agricultural pressure and pesticide use. Notably, several genes with known roles in detoxification and stress response, including venom carboxylesterase6 and CYP336A1, were highlighted. These variants point to molecular pathways targeted by agrochemical toxicity, offering insights into the consequences of pesticide use. Such findings may, in the future and upon further validation, help refine risk assessment frameworks, support the development of resilience-oriented breeding programs, and promote sustainable apicultural practices.