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Lecture 9

BIOC 4403 Lecture Notes - Lecture 9: Saccharomyces Cerevisiae, Comparative Genomics, Fot


Department
Biochem & Molecular Biology
Course Code
BIOC 4403
Professor
Archibald John
Lecture
9

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Lecture 9
Comparative Genomics
- the study of the differences and similarities in genome structure and organization in
different organisms
- by recording and analyzing differences in genomes in the light of a phylogenetic
framework, we can study how genomes changed over time, and hosw those changes
related to the observed biological diversity
Why do genomes evolve?
- A mutation is acted on by natural selection and drift/sorting/luck which leads to
evolution
- In this case, mutation = anything that generates variation at the genome level
- Process → Change/Effect
o Polyploidy → whole genome duplication
o Segmental/chromosomal duplications → other large scale duplications
o Chromosomal rearrangements → ‘gene shuffling’, gene order alterations
o Retroviral insertions → mutagenesis, gene shuffling
o Transposition → changes in genome seize, shuffling
There are factors that are not generators of variation per se but create conditions that are
conductive to genome evolution
- Radical lifestyle/environmental changes
o ↑ exposure to radiation, ↑ metabolic rate; other stresses can lead to ↑ rates of
mutation and rearrangements
o Changes in population structure and/or population size affect probability of
fixation of rate chromosomal changes (including large duplications)
o Shift to living in high temperature → ↑ GC content favoured
- Exposure to pathogens → also affect population structure, favour fixation of low-
frequency genomic changes
- Becoming a parasite → massive gene loss due to pressure for small genome and
redundancy of gene function, increased mutation → genome reduction and overall
sequence divergence
- Acquiring endosymbionts → induce massive acquisition and replacement of genes,
affects gene seize and gene complement
What traits can we look at?
- Genomes are multi-dimensional entities we can use comparative genomics to
analyze a myriad of characteristics
- Genome architecture - # of chromosomes, non-coding DNA distribution, order of
genes
- Base composition usuall as %AT or %GC
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