04 — Mini Project
DNA Barcoding & Phylogenetics
COI gene analysis of prawn & shrimp species
From the wet lab to the tree — COI barcoding and phylogenetic analysis of prawns and shrimp.
01 — Problem
What this project set out to solve
DNA barcoding and phylogenetic analysis of prawn and shrimp species using the COI gene span the whole molecular pipeline — from wet-lab extraction through sequencing to the trees that reveal species relationships.
A reproducible barcode pipeline needs each link in the chain: extraction, amplification, sequencing, identification, alignment and phylogenetics.
02 — Approach
How it was approached
Performed DNA extraction, PCR amplification of the mitochondrial COI gene, agarose gel electrophoresis and Sanger sequencing for species identification.
Conducted NCBI BLAST-based species identification and Multiple Sequence Alignment (MSA) using Clustal Omega.
Generated DNA barcodes and constructed phylogenetic trees to evaluate genetic relationships among the identified species.
03 — Workflow
Workflow & architecture
Barcoding pipeline
- DNA extractionWet lab
DNA extraction was performed for prawn and shrimp species identification.
- COI PCRMitochondrial COI
PCR amplification of the mitochondrial COI gene was carried out.
- Gel & SangerSequencing
Agarose gel electrophoresis and Sanger sequencing were performed.
- Species IDNCBI BLAST
NCBI BLAST-based species identification was conducted.
- AlignmentClustal Omega
Multiple Sequence Alignment (MSA) was performed using Clustal Omega.
- PhylogeneticsMEGA
Phylogenetic analysis was carried out using MEGA.
- Barcodes & treeBOLD Systems
DNA barcodes were generated and phylogenetic trees constructed to evaluate genetic relationships among identified prawn and shrimp species.
Stage 01 / 07
DNA extraction
Wet lab
DNA extraction was performed for prawn and shrimp species identification.
- Molecular lab — DNA extraction, COI PCR, agarose gel electrophoresis, Sanger sequencing.
- Identification — NCBI BLAST-based species identification, with BOLD Systems as reference.
- Alignment — Multiple Sequence Alignment (MSA) with Clustal Omega.
- Phylogenetics — tree construction and analysis with MEGA.
04 — Technologies
What it was built with
Wet lab
Identification
Alignment
Phylogenetics
05 — Implementation
What was built
- DNA extraction followed by PCR amplification of the mitochondrial COI gene, agarose gel electrophoresis and Sanger sequencing.
- NCBI BLAST-based species identification and Multiple Sequence Alignment (MSA) using Clustal Omega.
- Phylogenetic analysis using MEGA, with DNA barcodes generated and trees constructed for the identified species.
06 — Results
Results & output
Results and detailed analysis available in the project repository.
07 — Learnings
What it taught me
- A species barcode project is a complete pipeline — wet-lab work, sequencing and analysis each matter for a trustworthy identification.
- Standard, reproducible links — BLAST, Clustal Omega, MEGA — connect molecular data to phylogenetic inference.
- The COI marker ties molecular taxonomy to evolutionary relationships in a single workflow.