10-11 Genome Evolution Flashcards
Give four factors that create conditions that are conducive to genome evolution
- Radical lifestyle/environmental changes (eg. shift to higher GC content if living in high temp)
- Exposure to pathogens (bottlenecks)
- Becoming a parasite (genome reduction)
- Acquiring endosymbionts (acquisition and replacement of genes)
What traits can we look at the study genome evolution?
- Base composition
- Genes
- Genome size (and interactions with genes)
- Genome evolution and gene order
Describe how nucleotide composition can give us clues for genome evolution.
Base composition
- Composition can become biased
- Intracellular parasites exhibit strong AT biases, prob because they have poor DNA repair efficiency resulting in high rates of certain mutations, especially those that turn C to A.
- Tightly related with other compositional parameters: codon usage and amino acid content are highly interdependent with nucleotide comp.
This interdependence makes it hard to determine at what level the bias is occuring (nucleotide, codon or amino acids)
What can we look at in genes to study genome evolution?
Homology (duh), but also:
- Fundamental genes (eg. rRNA, polymerases etc.). Aka the minimal gene set or ‘core’ genes.
- Genes involved in central metabolism and other cellular activities that are more or less ubiquitous.
- Genes involved in specific pathways and restricted to a particular group of organisms with shared phenotype. Eg. photosynthesis, specific nutrient metabolism etc.
- We can look at functions of shared genes to find proporiton of genes that have a common function within a specific category
How is the number of core genes related to phylogeny?
The more closely related organisms are phylogenetically, the more core genes they share!
We can use a phylogenetic framework to infer rates of expansion and contractions of genes and gene families that occurred on individual lineages.
How can we look at genes and genome size to make inferences about genome evolution?
- Gene number and genome size are not correlated in eukaryotes except for those with small genomes.
Eg. pufferfishes have about the same number of genes as humans, but their genome is much much much smaller (transposable elements are rare)
By mapping genomes by genes on top of the total size of their genome and comparing, you can sometimes see things like inversion events.
How can we make inferences about genome evolution based on reduced eukaryotic genomes?
Important to also look at gene density.
S. cerevisiae (yeast) have genomes that are about as small and compact as genomes from free living eukaryotes can get (along with green algae).
Microsporidia are a group of fungi that are obligate intracellular parasites, they also exhibit extremely compacted genomes.
How does the importance of gene order differ between eukaryotes and prokaryotes?
How can this be used to study genome evolution in eukaryotes?
Prokaryotes have operons and the order of genes on the operon is strongly influenced by the functional nature of the genes (and is therefore NOT random).
But in eukaryotes, genes are regulated and transcribed individually, and thus gene order is not expected to be important.
Genes from closely related species are arranged in the same order, but over time they will differentiate from each other because of many events of chromosomal rearrangements (large and small) occurring independently. Over long evolutionary distances, most of the genes end up completely shuffled!
Give an exception to the shuffling of gene order normally seen among evolutionarily distant species.
Why does this occur?
HOX genes in animals are organized in clusters and these genes have maintained their order for over 500 million years.
Some genes stay together because shuffling would disrupt tightly organized regulatory networks. At the primary (sequence), secondary (nucleosome), tertiary (chromatin hub) and chromosome territory level.
It may also be because there are little spaces between some genes, giving few opportunities for chromosomal breaks and rearrangements
Why are hemiascomycete fungi (yeast) excellent models for studying eukaryotic genome evolution?
Yeast illustrate the molecular mechanisms of eukaryotic genome evolution well.
They have the greatest number of sequenced species for a single phylum and show dynamic interplay between formation and lols of genes and the mechanisms that are involved.
Yeast genomes show extensive loss of introns and a reduced role of transposable elements, and so probably have a more limited potential to form novel genes and functions than multicellular organisms, possibly explaining their conserved biological and morphological properties, despite their considerable evolutionary range.
