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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>HoneyGDB Poster</title>
<!-- Bootstrap CSS -->
<link href="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/css/bootstrap.min.css" rel="stylesheet">
<style>
/* Custom Navbar Styles */
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background-color: #E6A400;
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display: none;
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<!-- Poster Content -->
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<h1>HoneyGDB: Comprehensive Genomic Database for Apis Species</h1>
<h4>Advancing Honeybee Health and Varroa Resistance Research</h4>
<p><strong>Authors:</strong> Ankush Sharma<sup>1,3</sup>, Lewis J. Bartlett<sup>2</sup>, Jessica Kissinger<sup>3,4,5</sup>, Andrew H. Paterson<sup>1,3,4</sup></p>
<p><strong>Affiliations:</strong></p>
<ul class="list-unstyled">
<li>1. Plant Genome Mapping Lab, University of Georgia, Athens, GA, USA</li>
<li>2. Center for Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA</li>
<li>3. Institute of Bioinformatics, University of Georgia, Athens, GA, USA</li>
<li>4. Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA</li>
<li>5. Department of Genetics, University of Georgia, Athens, GA, USA</li>
</ul>
</div>
<!-- SVG Poster Image -->
<div class="text-center">
<img src="HoneyGDB.svg" alt="HoneyGDB Poster" class="poster-svg">
</div>
<!-- Abstract Section -->
<div class="content-section">
<h2 class="section-title">Abstract</h2>
<p>Honeybees (Apis species) are essential for global agriculture and ecosystems, providing crucial pollination services [1]. <strong>HoneyGDB</strong> (<a href="http://chibba.agtec.uga.edu/HoneyGDB">http://chibba.agtec.uga.edu/HoneyGDB</a>) is a user-friendly web platform that integrates genomic, transcriptomic, and proteomic data across major Apis species [2]. It addresses gaps in existing databases by offering comprehensive multi-omics integration, supporting research on honeybee health and Varroa mite resistance [3]. HoneyGDB facilitates advancements in sustainable agriculture, improved pollination practices, and conservation efforts [4].</p>
</div>
<!-- Introduction Section -->
<div class="content-section">
<h2 class="section-title">Introduction</h2>
<p>Advancements in genome sequencing have made large-scale genomic data for honeybees readily available [5]. However, existing databases like BeeBase lack comprehensive multi-omics integration [6]. <strong>HoneyGDB</strong> consolidates genomic, transcriptomic, and proteomic data for species including <em>A. mellifera</em>, <em>A. cerana</em>, <em>A. dorsata</em>, <em>A. florea</em>, and <em>A. laboriosa</em> [7]. This platform democratizes data access, enabling researchers and beekeepers to explore honeybee biology, behavior, and health effectively [8].</p>
</div>
<!-- Materials and Methods Section -->
<div class="content-section">
<h2 class="section-title">Materials & Methods</h2>
<h5>Genome Data</h5>
<p>HoneyGDB aggregates genome assemblies and gene sets for various Apis species, annotated using NCBI RefSeq, Gene Ontology, UniProt, and InterPro [9]. Cross-references are managed via IntersectBed to ensure accurate gene identification [10].</p>
<h5>Transcriptome Data</h5>
<p>RNA-Seq datasets from NCBI SRA are processed with Trimmomatic and aligned using HISAT2 [11][12]. Gene expression is quantified using StringTie and BedTools, providing FPKM and RPKM values for comprehensive analysis [13].</p>
<h5>Genetic Variations</h5>
<p>Whole-genome sequencing data are aligned to reference genomes using Freebayes, and variants are annotated with SNPeff [14][15]. This dataset aids in studying population structure and resistance traits [16].</p>
<h5>Proteomics Integration</h5>
<p>Data from the HoneyBee Protein Atlas are linked via gene identifiers, offering detailed proteomic information across honeybee castes and tissues [17].</p>
<h5>Functional Annotation</h5>
<p>Gene models are re-annotated using InterProScan and KAAS for KEGG orthology [18][19]. BLASTP comparisons with <em>A. mellifera</em> ensure accurate functional predictions [20].</p>
<h5>Synteny & Phylogenomics</h5>
<p>Using Diamond BLAST, MCScanX, and Orthofinder, HoneyGDB provides synteny and phylogenomic data, facilitating evolutionary studies within Hymenoptera [21][22].</p>
</div>
<!-- Results Section -->
<div class="content-section">
<h2 class="section-title">Results</h2>
<p><strong>HoneyGDB</strong> employs a robust MySQL-based schema accessible via an Apache server [23]. The responsive front-end, built with PHP, JavaScript, and Bootstrap, offers interactive tools like JBrowse2 for genome browsing, BLAST for sequence alignment, and synteny viewers for comparative genomics [24]. Key features include:</p>
<ul>
<li><strong>BeeHub:</strong> Centralized portal for genetic and genomic data [25].</li>
<li><strong>MarkerHub:</strong> Database of validated genetic markers for trait mapping [26].</li>
<li><strong>Functional Annotation Search:</strong> Tools for protein family and pathway analysis [27].</li>
<li><strong>BeeCyc:</strong> Metabolic pathway database tailored for honeybees [28].</li>
<li><strong>HomologFinder & OrthologSearch:</strong> Tools for identifying gene conservation across species [29].</li>
<li><strong>BEEBLAST:</strong> Integrated BLAST server with seamless navigation to detailed gene pages [30].</li>
<li><strong>Pangenomes:</strong> Access to non-reference genes and genomic diversity [31].</li>
</ul>
<img src="workflow.svg" alt="HoneyGDB Architecture" class="poster-svg">
</div>
<!-- Discussion Section -->
<div class="content-section">
<h2 class="section-title">Discussion</h2>
<p><strong>HoneyGDB</strong> significantly enhances honeybee genomics research by providing integrated multi-omics data in an accessible format [32]. It supports studies on species-specific adaptations, gene regulation, and evolutionary biology, overcoming limitations of previous databases [33]. The platform's tools facilitate comprehensive analyses, promoting advancements in understanding honeybee health, Varroa resistance, and responses to environmental stressors [34].</p>
<h5>Impact on Varroa Resistance</h5>
<p>The variome and diversity datasets enable identification of genetic variants linked to Varroa mite resistance, aiding in the development of targeted breeding programs [35]. Transcriptomic integration allows exploration of gene expression under stress, supporting studies on colony health [36].</p>
<h5>Addressing Colony Collapse Disorder (CCD)</h5>
<p>By providing access to multi-omics data, HoneyGDB facilitates investigation into molecular pathways involved in CCD, promoting sustainable strategies to mitigate its effects and ensuring pollination services remain robust [37].</p>
</div>
<!-- Future Directions Section -->
<div class="content-section">
<h2 class="section-title">Future Directions</h2>
<p><strong>1. Expanding Omics Integration:</strong> Incorporate epigenomic and metabolomic data to deepen understanding of gene regulation and metabolic processes in honeybees [38].</p>
<p><strong>2. Enhancing Population Genomics:</strong> Expand datasets to include diverse honeybee populations, enabling studies on local adaptations and climate resilience [39].</p>
<p><strong>3. Implementing Machine Learning:</strong> Integrate advanced analytics for predictive modeling of gene-trait associations and environmental impacts on honeybee health [40].</p>
<p><strong>4. Fostering Collaboration:</strong> Encourage community contributions and partnerships to enrich HoneyGDB's data and toolset, supporting large-scale research initiatives [41].</p>
<p><strong>5. Expanding to Other Hymenoptera:</strong> Extend the database framework to include ants, wasps, and other Hymenoptera, enhancing comparative genomics and evolutionary studies [42].</p>
</div>
<!-- Conclusion Section -->
<div class="content-section">
<h2 class="section-title">Conclusion</h2>
<p><strong>HoneyGDB</strong> revolutionizes honeybee genomics by integrating diverse omics data into a unified, user-friendly platform [43]. It supports critical research on honeybee health, Varroa resistance, and ecological sustainability, making significant contributions to agriculture and conservation [44]. Future enhancements will further solidify HoneyGDB's role as an indispensable resource for the global honeybee research community [45].</p>
</div>
<!-- References Section -->
<div class="content-section">
<h2 class="section-title">References</h2>
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