A modern genome and transcriptomics database for Onthophagus taurus
Davidson Lab · Department of Biological Sciences · Mississippi State University
(DB)² is an open, web-based genome and transcriptomics database for the dung beetle Onthophagus taurus (Schreber, 1759) — a model organism for studying the genomic basis of developmental plasticity, sexual selection, and horn polyphenism. The platform centralizes chromosome-level genome assemblies for four species, NCBI and Davidson Lab custom gene annotations, RNA-seq expression datasets, global biodiversity occurrence data, and real-time scientific literature in a single, visually immersive research interface.
O. taurus exhibits striking male-limited horn polyphenism, in which large males develop prominent cephalic horns used in combat for female access while small males remain hornless. This conditional strategy has made the species a powerful system for understanding how genomes encode alternative phenotypes, and (DB)² is designed to support this research by making genome-level data accessible at every level of biological inquiry.
| Feature | Detail |
|---|---|
| Species | Onthophagus taurus (Schreber, 1759) |
| Family | Scarabaeidae |
| Subfamily | Scarabaeinae (dung beetles) |
| NCBI Taxon ID | 166361 |
| Research focus | Horn polyphenism, sexual selection, developmental plasticity, genome evolution |
| Native range | Mediterranean Europe, North Africa, Middle East |
| Introduced range | North America, Australia |
| Species | Assembly | Level | Size | Annotation |
|---|---|---|---|---|
| Onthophagus taurus | GCF_036711975.1 (Otau_3.2) | Chromosome | ~295 Mb | NCBI + Davidson Lab v1 |
| Onthophagus sagittarius | Osag_1.3 | Scaffold | ~561 Mb | AUGUSTUS |
| Digitonthophagus gazella | Dgaz_1.3 | Scaffold | ~346 Mb | AUGUSTUS |
| Onthophagus binodis | Obin_1.0 | Scaffold | ~843 Mb | AUGUSTUS |
All assemblies are hosted on Cloudflare R2 and served to JBrowse 2 via HTTP byte-range requests. No server-side processing required at browse time.
A cinematic scroll-animated landing page featuring a frame-by-frame biological dissection sequence: from an intact O. taurus beetle rotating on its axis, through progressive exoskeletal transparency and internal anatomy, to a luminous DNA double helix at the genomic level. Built with HTML5 canvas and requestAnimationFrame — no video element, no scroll event listeners.
Powered by JBrowse 2 embedded as a React component. A species dropdown switches between all four assemblies, remounting JBrowse with the correct config for each. All genomic data streams client-side on demand from Cloudflare R2.
Tracks available:
- Reference sequence (BgzipFastaAdapter)
- NCBI Gene Annotation Release — O. taurus (Gff3TabixAdapter)
- Davidson Lab Custom Annotation v1 — O. taurus (Gff3TabixAdapter)
- AUGUSTUS Gene Annotation — O. sagittarius, D. gazella, O. binodis (Gff3TabixAdapter)
- RNA-seq tracks (coming in v2)
Interactive biodiversity map on Leaflet.js with live iNaturalist API data. Switches between heatmap tiles at low zoom and individual clickable observation markers at zoom ≥ 10, each showing species name, observer, date, quality grade, photo, and direct iNaturalist link. Covers 122,000+ global Scarabaeinae observations.
Real-time academic search via Europe PMC REST API. Server-side Next.js proxy resolves CORS and bot-detection issues. Returns title, authors, year, journal, citation count, abstract, open-access PDF links, and DOI for every result. Default query tuned for Onthophagus research. No curation required — newly indexed papers appear automatically.
Genomic data downloads for all four species organized by species and file type: genome assembly FASTA, GTF gene annotations, repeat-masked genome, protein sequences, and nucleotide sequences. All files hosted on Cloudflare R2 with zero egress fees.
Curated Davidson Lab publications and dung beetle genomics literature with DOI links and dataset cross-references.
Lab directory for the Davidson Lab and four collaborating principal investigators across Boston University, Indiana University, Southwest University, and UC San Diego.
Filterable, sortable table of 28,456+ predicted gene models with search by gene ID, chromosome, coordinate range, annotation source, and RNA-seq availability.
RNA-seq datasets linked to biological features including horn development, leg morphology, and developmental stage series.
| Layer | Technology | Purpose |
|---|---|---|
| Framework | Next.js 14 (App Router) | Full-stack React, SSR/SSG, API routing |
| Language | TypeScript 5 | Type-safe development |
| Styling | Tailwind CSS + CSS variables | Dark-theme UI system |
| Genome browser | JBrowse 2 | Multi-species embedded genomic visualization |
| Distribution map | Leaflet.js + iNaturalist API v1 | Biodiversity occurrence mapping |
| Literature | Europe PMC REST API (server-side proxy) | Real-time academic literature search |
| Scroll animation | HTML5 Canvas + rAF | Frame-by-frame beetle dissection hero |
| Cinematic visuals | Higgsfield AI + ffmpeg | Background videos and loading animations |
| File hosting | Cloudflare R2 | Zero-egress genomic file CDN |
| Deployment | Vercel | CI/CD + global edge hosting |
All genomic files are preprocessed before deployment to enable efficient byte-range HTTP access in JBrowse.
# Block-compress with bgzip (required for random access)
bgzip -k genome.fasta
# Generate FASTA index and bgzip block index
samtools faidx genome.fasta.gz
# produces: genome.fasta.gz.fai + genome.fasta.gz.gzi# Sort by chromosome and start position, then block-compress
sort -k1,1 -k4,4n annotations.gtf | bgzip > annotations.sorted.gtf.gz
# Generate tabix index for coordinate-based random access
tabix -p gff annotations.sorted.gtf.gz
# produces: annotations.sorted.gtf.gz.tbi# Compress for download hosting (no indexing needed)
bgzip -k proteins.fasta
bgzip -k nucleotides.fasta
bgzip -k masked_genome.fastaAll processed files and indexes are hosted on Cloudflare R2 with CORS configured for browser-side byte-range requests:
[{
"AllowedOrigins": ["*"],
"AllowedMethods": ["GET", "HEAD"],
"AllowedHeaders": ["Range", "Accept-Ranges", "Content-Range"],
"ExposeHeaders": ["Content-Length", "Content-Range", "Accept-Ranges"],
"MaxAgeSeconds": 3600
}]db2-platform/
├── app/
│ ├── layout.tsx # Root layout with navbar
│ ├── page.tsx # Scroll-animated homepage
│ ├── components/home/ # Homepage section components
│ │ ├── ScrollHero.tsx # Canvas-based beetle dissection
│ │ ├── StatsBar.tsx
│ │ ├── SpeciesSection.tsx
│ │ ├── FeaturesSection.tsx
│ │ ├── AssemblyCard.tsx
│ │ └── ClosingCTA.tsx
│ ├── genome-browser/ # Multi-species JBrowse 2 browser
│ ├── distribution/ # iNaturalist map
│ ├── literature/ # Europe PMC live search
│ ├── publications/ # Curated publications
│ ├── directory/ # Lab directory
│ ├── downloads/ # File downloads (4 species)
│ ├── expression/ # RNA-seq data (v2)
│ ├── genes/ # Gene search (v2)
│ └── api/
│ └── literature/ # Server-side Europe PMC proxy
│
├── components/
│ ├── genome/
│ │ ├── JBrowseWrapper.tsx # SSR-safe dynamic import
│ │ ├── JBrowseViewInner.tsx # JBrowse React component
│ │ └── JBrowseLoader.tsx # Cinematic loading animation
│ ├── map/
│ │ └── DistributionMap.tsx # Leaflet + iNaturalist
│ └── site/
│ ├── Navbar.tsx
│ └── Footer.tsx
│
├── lib/
│ └── jbrowse-config.ts # All 4 species assembly + track configs
│
└── public/
├── media/Logo.png
├── frames/ # Beetle dissection animation frames
├── loading-frames/ # JBrowse loading animation frames
├── genome-bg.mp4 # Genome browser background loop
├── publications-bg.mp4 # Publications page header video
├── directory-bg.mp4 # Directory page header video
└── downloads-bg.mp4 # Downloads page header video
- Node.js 18+
- npm
git clone https://github.com/researchingadi/db2-platform.git
cd db2-platform
npm install
npm run devOpen http://localhost:3000.
- Scroll-animated cinematic homepage with beetle dissection sequence
- JBrowse 2 genome browser with 4-species dropdown switcher
- Chromosome assembly + NCBI and Davidson Lab annotation tracks
- Interactive global distribution map (iNaturalist live API)
- Real-time literature search (Europe PMC server-side proxy)
- Publications page with cinematic header
- Lab directory with collaborating PIs and cinematic header
- Downloads page for all 4 species with cinematic header
- Cinematic genome browser background loop
- Premium JBrowse loading animation
- GitHub repository
- Deploy to Vercel (live public URL)
- RNA-seq tracks in JBrowse (BAM/BigWig)
- Gene search table with multi-field filtering
- Gene detail pages with mini-browser and expression data
- Biological feature pages: Horns, Legs, Development, Reproduction
- Expression heatmap visualizations
- PostgreSQL database for gene models
- BLAST sequence search (NCBI BLAST+, FastAPI)
- Ortholog search across Onthophagus species
- Additional species support
- Advanced expression visualizations (volcano plots, PCA)
- Resource paper publication
All genomic data is scoped by species in both the R2 bucket structure and the JBrowse config:
R2 bucket: db2-genomics/
├── otaurus/ # O. taurus genome + annotations
├── osagittarius/ # O. sagittarius genome + annotations + sequences
├── dgazella/ # D. gazella genome + annotations + sequences
└── obinodis/ # O. binodis genome + annotations + sequences
All four species configs are defined in lib/jbrowse-config.ts as SPECIES_CONFIGS. Switching species in the browser remounts JBrowse with the correct assembly and tracks via React key prop — no page navigation required.
| Data | Source | Version / Accession |
|---|---|---|
| O. taurus genome assembly | NCBI | GCF_036711975.1 (IU_Otau_3.0) |
| O. taurus NCBI annotations | NCBI Annotation Release | GFF3 + GTF |
| O. taurus custom annotations | Davidson Lab, MSU | v1 |
| O. sagittarius assembly + annotations | Davidson Lab, MSU | Osag_1.3 |
| D. gazella assembly + annotations | Davidson Lab, MSU | Dgaz_1.3 |
| O. binodis assembly + annotations | Davidson Lab, MSU | Obin_1.0 |
| RNA-seq data | Davidson Lab, MSU | In preparation |
| Biodiversity occurrences | iNaturalist | Live API — Taxon ID 125819 |
| Scientific literature | Europe PMC | Live REST API |
If you use (DB)² or any genome resources from this platform in your research, please cite:
Davidson Lab (2025). (DB)² — Dung Beetle Database: a genomic and transcriptomic resource for Onthophagus taurus and related species. Mississippi State University. https://github.com/researchingadi/db2-platform
O. taurus genome assembly:
NCBI Assembly GCF_036711975.1 — Onthophagus taurus IU_Otau_3.0. National Center for Biotechnology Information.
Biodiversity occurrence data:
iNaturalist contributors (2025). Scarabaeinae observations. iNaturalist.org. https://www.inaturalist.org/taxa/125819
| Name | Role | Affiliation |
|---|---|---|
| Dr. Philip L. Davidson | Principal Investigator | Mississippi State University |
| Adi Singh | Bioinformatics Full Stack Developer / Research Software Engineer | Mississippi State University |
Collaborating Principal Investigators:
| Name | Institution |
|---|---|
| Dr. Sofía Casasa | Boston University |
| Dr. Yonggang Hu | Southwest University |
| Dr. Armin Moczek | Indiana University |
| Dr. Patrick Rohner | University of California San Diego |
- Lab website: davidsonlab-msu.github.io
- GitHub Issues: researchingadi/db2-platform/issues
- Department: Biological Sciences, Mississippi State University
MIT License — see LICENSE for details.
Genomic data is sourced from NCBI and subject to NCBI data use policies. Biodiversity occurrence data is sourced from iNaturalist and subject to iNaturalist terms of use. Literature data is sourced from Europe PMC and subject to Europe PMC terms of use.