🧬 Tracking the Evolution of the Hemoglobin Beta (HBB) Gene Across Species 🧑‍🦰🐟🐄🐒🐔🐁

📝 Project Description

This project investigates the evolutionary conservation of the Hemoglobin Beta (HBB) gene across vertebrate species. The HBB gene encodes a critical subunit of hemoglobin, the protein responsible for oxygen transport in vertebrates. The study includes:

• 🧩 Sequence retrieval
• 🔍 Pairwise and multiple sequence alignments
• 🌳 Phylogenetic analysis
• 📊 Visualization of conserved motifs

🔑 Key Findings

• 🧬 Sequence Conservation: HBB shows high conservation in functional domains (e.g., heme-binding regions), with decreasing identity as evolutionary distance increases.
• ✨ Conserved Motifs: Identified critical motifs (e.g., YPWTQR, HCDKLHVDPENFR) for heme binding and structural stability.
• 🌍 Phylogenetic Analysis: Tree aligns with vertebrate relationships, highlighting strong purifying selection.
• 🏥 Clinical Relevance: Pathogenic mutations (e.g., sickle cell disease) often occur at conserved residues.

📂 Files Included

1. HBB_MiniProject_TomilolaAkingbade.pdf: Full project report.
2. Figures/:
   • 🖼️ Pairwise alignments (Human vs. Chimpanzee, Human vs. Zebrafish).
   • 🧬 Multiple sequence alignment (MSA) of HBB proteins.
   • 📊 Sequence logo showing conservation patterns.
   • 🌳 Phylogenetic tree of HBB sequences.

🛠️ Tools and Methods

• 🔎 Sequence Retrieval: NCBI BLAST (blastp) using human HBB (NP_000509.1).
• 📏 Alignments: NCBI BLAST Pairwise Alignment, CLUSTAL O for MSA.
• 🎨 Visualization: Skylign for sequence logos.
• 🌳 Phylogenetics: MEGA X (Neighbor-Joining, JTT model, 1000 bootstraps).

🐾 Species Analyzed

Species	Common Name	Accession Number
Homo sapiens	Human	NP_000509.1
Pan troglodytes	Chimpanzee	XP_508242.1
Bos taurus	Cow	NP_776342.1
Mus musculus	Mouse	NP_001265090.1
Gallus gallus	Chicken	NP_990820.1
Danio rerio	Zebrafish	NP_001003431.2

🔄 How to Reproduce

1. Download sequences from NCBI using the provided accession numbers.
2. Align: Use BLAST or Clustal Omega for pairwise/MSA.
3. Visualize: Upload MSA to Skylign for logos.
4. Build Tree: Run MEGA X (Settings: Neighbor-Joining, JTT model, 1000 bootstraps).

🚀 Future Directions

• 🌐 Expand taxonomic sampling (e.g., reptiles, amphibians).
• 🔄 Analyze the entire globin gene family for duplication events.
• 🏜️ Investigate lineage-specific adaptations (e.g., high-altitude species).

📬 Contact

Tomilola Akingbade
📧 victomilola@gmail.com

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📜 License: Open-source under MIT License.
🏷️ Keywords: HBB | hemoglobin | evolution | phylogenetics | sequence conservation