Genome evolution Flashcards
Transposons move around the genome. True or false?
True
Transposons are rare in the human genome. True or false?
False
Define a retrotransposon.
Transposons that replicate via an RNA intermediate using reverse transcriptase.
What is an LTR?
A long terminal repeat.
What produce LTRs?
Retroviruses with reverse transcriptase.
What is a LINR?
Long interspersed nuclear repeat.
What is used to transcribe LINRs?
Reverse transcriptase.
What is a SINR?
Short interspersed nuclear repeat.
Do SINRs use reverse transcriptase?
No.
Define a DNA transposon.
DNA is ‘cut and paste’ using transposase.
Selection tries to remove transposons. If there is no selection what happens?
Transposons accumulate.
Give 2 deleterious effects of transposons.
- Disrupt coding regions of DNA or regulatory sequences
2. Cause ectopic recombination, resulting in one chromosome with a deletion and one with a duplication.
There tend to be more insertions of transposons if…?
The rate of recombination is low.
Give 2 host mechanisms that control transposons.
- Transcriptional silencing
2. Post-transcriptional silencing
Explain transcriptional silencing.
Transcription is prevented via DNA methylation and chromatin modification.
Explain post-transcriptional silencing.
There is RNAi (interference) by Argonaute proteins and the enzyme Dicer, preventing translation of the RNA.
A stable transposon rate in the genome is possible under what condition?
Rate of insertion is balanced by the rate of excision.
Transposons are not the only cause of genome evolution. Give another.
WGD, thus leading to neo/subfunctionalisation etc.
The loss of gene duplicates can be deleterious. How?
It causes less gene product to be produced, causing an imbalance. This is particularly true in protein networks.
Duplicates are often retained. Why?
Genes that are highly expressed are preferentially selected for.
What does CNV stand for?
Copy Number Variation.
CNV is often implicated in disease. Why?
The amount of gene product is important to fitness.
Genomes can evolve endosymbiosis. Give an example of this?
The mitochondria of eukaryotes used to be free-living alpha-proteobacteria.
Why was endosymbiosis favourable for the mitochondria? Give 2 reasons.
- They are able to avoid Muller’s ratchet.
2. They can streamline their own genomes, making replication more energy efficient.
Define CMS in plants.
Cytoplasmic male sterility: plants are hermaphrodite, but the mitochondria suppress male function, leading to pure females.
Why does CMS exist?
The mitochondria and nuclear DNA have a conflict of interest. Mitochondria follow matrilineal inheritance and want to ensure they will be passed on to all the offspring. Nuclear DNA is inherited regardless of sex.
What is a gynodioecious population?
A sexually dimorphic breeding population created by CMS whereby pure females and hermaphrodites coexist.
Why does CMS harm nuclear gene transmission?
They are only passed on by the female and not the male parts.
Define a nuclear restorer mutation.
One that has evolved to restore the hermaphrodite condition and thus male function in CMS.
There has been co-evolution of the mitochondria and the nuclear genome. Why?
The mitochondria keep trying to dominate the nuclear genes, and the nuclear genes have to keep compensating.
