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Gene Duplication Clades & Ka/Ks Analysis using TBtools

Bioinformatics Lecture Series | Evolutionary Genomics | 🧬

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Introduction to Gene Duplication

  • • Gene duplication is a major force in evolution.
  • • Leads to gene family expansion and functional diversification.
  • • Common in plant genomes due to polyploidy events.
  • • Useful for evolutionary and functional genomics studies.

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Types of Gene Duplication

  • • Tandem Duplication – adjacent copies in the genome
  • • Segmental Duplication – duplication of large genomic regions
  • • Whole Genome Duplication – polyploidy events
  • • Retrotransposition – duplication via mRNA intermediate

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Gene Duplication Clades

  • • Clades represent evolutionary relationships among duplicated genes.
  • • Derived from phylogenetic trees.
  • • Help classify gene family members.
  • • Useful in identifying functional divergence.

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Understanding Ka/Ks Analysis

  • • Ka = Non-synonymous substitution rate
  • • Ks = Synonymous substitution rate
  • • Ka/Ks < 1 → Purifying selection
  • • Ka/Ks = 1 → Neutral evolution
  • • Ka/Ks > 1 → Positive selection

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Why Ka/Ks Analysis Matters

  • • Detects selection pressure on genes.
  • • Identifies adaptive evolution events.
  • • Useful for comparative genomics.
  • • Provides insight into gene function diversification.

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TBtools Software Overview

  • • A powerful toolkit for biological data analysis.
  • • GUI-based—no programming required.
  • • Supports gene duplication, Ka/Ks, and FASTA processing.
  • • Free and widely used in plant genomics.

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Steps for Ka/Ks Analysis in TBtools

  • 1. Prepare CDS and protein FASTA files.
  • 2. Load gene pair file or detect duplication pairs.
  • 3. Run Ka/Ks calculator tool in TBtools.
  • 4. Export Ka/Ks result table.
  • 5. Interpret selection patterns.

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Interpreting Ka/Ks Results

  • • Ka/Ks < 1 → Functional constraint, conserved genes.
  • • Ka/Ks = 1 → Neutral drift, no selection.
  • • Ka/Ks > 1 → Adaptive evolution, functional divergence.
  • • Useful to annotate candidate genes.

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Visualization and Export

  • • TBtools allows easy visualization of gene duplication pairs.
  • • Export Ka/Ks results in table or chart form.
  • • Results can be integrated with phylogenetic trees and gene structure.
  • • Publication-ready outputs.

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Applications of Ka/Ks & Gene Duplication Analysis

  • • Understanding gene family evolution
  • • Detecting adaptive evolution
  • • Identifying key regulatory genes
  • • Supporting molecular breeding strategies
  • • Plant stress response and trait improvement

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References & Resources

  • • TBtools: https://github.com/CJ-Chen/TBtools
  • • Yang Z. (2007) PAML: Phylogenetic Analysis by Maximum Likelihood
  • • Li et al. (2020) TBtools: An Integrative Toolkit for Biological Data Analysis
  • • Genomics databases: Phytozome, NCBI, Ensembl Plants

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