Genome Evolution Notes

Overview of Genome Size Variation

• Diversity in genome sizes:

  • Ranges from small viruses to larger eukaryotes (e.g., flowering plants, mammals).

  • Genome size is measured in Megabases (Mb).

• Species and their Genome Size:

  • Examples include:

    • Viruses (e.g., Bacteriophage) with small genomes.

    • Bacteria like E. coli have compact genomes.

    • Eukaryotes (e.g., mammals, plants) exhibit larger genome sizes owing to different factors.

Status of Genome Sequencing

• Historical Costs:

  • First human genome sequence cost approximately $3 billion.

  • As of today, costs have reduced to below $5,000.

• Completed Species Genomes:

  • As of 2014, over 500 eukaryotic and 17,000 prokaryotic genomes were sequenced.

Factors Influencing Genome Size

• Differences arise primarily due to:

  • Non-coding DNA: Much of the genome may not code for proteins.

  • Cell volume: Larger nuclei may facilitate larger genomes.

  • Transposons: Movements of genetic material within genomes contribute to size variations.

Key Genetic Concepts

• Gene Complexity:

  • Number of genes is not the sole determinant of phenotype complexity.

  • Gene regulatory networks vary among organisms and affect phenotypes.

  • Non-coding regions can play significant regulatory roles.

  • Alternative splicing allows one gene to code for multiple proteins.

Examples of Genomes

• Viruses:

  • SARS Coronavirus RNA: Approximately 21,485 bp with key proteins (Spike (S), Nucleocapsid (N), etc.).

  • Hepatitis B DNA: Contains multiple surface proteins and a polymerase gene.

• Bacterial Genome (E. coli):

  • Contains various features influencing pathogenicity such as virulence factors and toxin production.

Horizontal Gene Transfer in Prokaryotes

• Methods:

  • Transduction: Transfer of DNA via bacteriophages.

  • Transformation: Uptake of environmental DNA.

  • Conjugation: Transfer of plasmid DNA from one bacterium to another.

• Implications: Enables rapid genetic variations and adaptations.

Eukaryotic Genome Characteristics

• Human Genome Composition:

  • Protein-coding genes: ~1.5%.

  • Non-coding regions including introns and transposable elements (50% of human genome).

• Mitochondrial Genome:

  • Significant as it reflects a separate lineage due to endosymbiosis.

Evolutionary Gene Function Development

• Mechanisms include:

  1. Descent with Modification: Changes in genomes over time.

  2. Duplication Events: Lead to gene families and functional variability.

  3. Retrotransportation: mRNA converted back to DNA, creating duplicates without introns.

• Pseudogenes: Non-functional duplicates resulting from mutations.

Genetic Exchange and Evolution

• Introgression: Mixing of alleles between species; significant in evolutionary history (e.g., Neanderthal genes in Homo sapiens).

• Incomplete Lineage Sorting: Can lead to incorrect phylogenetic inferences if based on single genes.

Phylogenetics and Genome Analysis

• Using whole genomes can clarify evolutionary relationships better than single genes.

• Out-of-Africa Model: Supported by phylogenetic data reflecting human development and migration patterns.

Key Terms to Remember

• Exons: Coding regions of DNA.

• Introns: Non-coding segments spliced out before protein synthesis.

• Transposable Elements: Mobile genetic elements influencing genome structure and evolution.