Genomes and evolution

Prokaryotic gene and genome structure
1. Genome size is related to complexity
  1. More genes corresponds to bigger genomes
  2. Selection for small genomes seems to occur. This is because rapid growth and short generation times leads to a selective advantage
Eukaryotic gene and genome structure
1. No relationship between gene number, genome size and complexity
2. Functions of complex transcription units
  1. The different proteins encoded may have slight functional differences allowing them to be specialized for particular functions, eg different regulatory protein domains could be included in different tissues
  2. More specialisation and greater complexity is due to more combinations, not more genes
3. Exons
  1. Exons often correspond to protein domains
    1. A protein domain is a region of a protein with a specific structure or function. This region often folds independently of the rest of the protein
  2. Exon shuffling
    1. New genes evolve by joining together new combinations of exons
    2. Occurs over evolutionary time
4. Multigene Families
  1. A multigene family consists of a set of genes that arose by duplication of ancestral gene and subsequent divergence due to small changes to the nucleotide sequence
    1. May contain pseudogenes that are homologous but do not produce a functional protein
    2. Within a gene family, particular members may show specialized functions, eg for tissue or developmental stage specificity
  2. The globin gene family
    1. Haemoglobin carries oxygen in our blood and consists of four globin proteins, two copies each of α and β and the cofactor haem
      1. Foetuses require haemoglobin with a higher affinity for oxygen and express the γ globin gene
Mechanisms of genome evolution
1. Point mutations
2. Replication strand slippage
  1. Replication strand slippage can lead to misalignment of the template and newly synthesised strand and results in unequal daughter strands
    1. Replication slippage also causes insertions or deletions of several nucleotides
      1. Generation of simple sequence repeat
      2. Trinucleotide expansion
3. Transposition (Transposons)
  1. Moderately-repeated, mobile DNA sequences are interspersed throughout the genomes of prokaryotes, plants and animals
  2. These sequences appear to serve no useful function: selfish DNA General
  3. DNA transposons (Class 2)
    1. Move via a 'Cut and Paste' mechanism
    2. Short terminal inverted repeats, short flanking direct repeats at target site
    3. Transposase gene (and sometimes others)
    4. Transposition through DNA replicative or non replicative
  4. RNA transposons (Class 1)
    1. Move via a 'Copy and Paste' mechanism
    2. Reverse Transcriptase
      1. Reverse transcriptase produces a DNA/RNA hybrid
        This is converted to double stranded DNA by degradation of the RNA and synthesis of a new DNA strand
    3. Transposition by an RNA intermediate
    4. Long terminal direct repeats, short flanking direct repeats at target site
4. Recombination
  1. Repeated sequences allow misalignment and then recombination
    1. Gene duplication
    2. Deletion
    3. Inversion
The human genome
1. Copy Number Variation (CNV)
  1. Difference among individual organisms in the number of copies of any large DNA sequence (larger than 1000 bp)
    1. Individuals vary in the number of copies of particular DNA sequences (genes, repeated sequences, any chunk of DNA)
      1. Repeated DNA
        Simple sequence repeats (highly repeated) accounts for 3% of the human genome
        Tandem repeats spanning 20-100 kb
        Repeat length 1-500 bp
        Concentrated in particular regions of chromosomes, especially centromeres and telomeres
        Most has no known function, but can be used as the basis of DNA fingerprinting as the number of SSRs varies between individuals
        Different types of mobile DNA elements (moderately repeated) accounts for 45% of the human genome

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Genomes and evolution

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