Genome evolution

Question 1

Transposons move around the genome. True or false?

Answer 1

True

Question 2

Transposons are rare in the human genome. True or false?

Answer 2

False

Question 3

Define a retrotransposon.

Answer 3

Transposons that replicate via an RNA intermediate using reverse transcriptase.

Question 4

What is an LTR?

Answer 4

A long terminal repeat.

Question 5

What produce LTRs?

Answer 5

Retroviruses with reverse transcriptase.

Question 6

What is a LINR?

Answer 6

Long interspersed nuclear repeat.

Question 7

What is used to transcribe LINRs?

Answer 7

Reverse transcriptase.

Question 8

What is a SINR?

Answer 8

Short interspersed nuclear repeat.

Question 9

Do SINRs use reverse transcriptase?

Answer 9

No.

Question 10

Define a DNA transposon.

Answer 10

DNA is ‘cut and paste’ using transposase.

Question 11

Selection tries to remove transposons. If there is no selection what happens?

Answer 11

Transposons accumulate.

Question 12

Give 2 deleterious effects of transposons.

Answer 12

1. Disrupt coding regions of DNA or regulatory sequences

2. Cause ectopic recombination, resulting in one chromosome with a deletion and one with a duplication.

Question 13

There tend to be more insertions of transposons if…?

Answer 13

The rate of recombination is low.

Question 14

Give 2 host mechanisms that control transposons.

Answer 14

1. Transcriptional silencing

2. Post-transcriptional silencing

Question 15

Explain transcriptional silencing.

Answer 15

Transcription is prevented via DNA methylation and chromatin modification.

Question 16

Explain post-transcriptional silencing.

Answer 16

There is RNAi (interference) by Argonaute proteins and the enzyme Dicer, preventing translation of the RNA.

Question 17

A stable transposon rate in the genome is possible under what condition?

Answer 17

Rate of insertion is balanced by the rate of excision.

Question 18

Transposons are not the only cause of genome evolution. Give another.

Answer 18

WGD, thus leading to neo/subfunctionalisation etc.

Question 19

The loss of gene duplicates can be deleterious. How?

Answer 19

It causes less gene product to be produced, causing an imbalance. This is particularly true in protein networks.

Question 20

Duplicates are often retained. Why?

Answer 20

Genes that are highly expressed are preferentially selected for.

Question 21

What does CNV stand for?

Answer 21

Copy Number Variation.

Question 22

CNV is often implicated in disease. Why?

Answer 22

The amount of gene product is important to fitness.

Question 23

Genomes can evolve endosymbiosis. Give an example of this?

Answer 23

The mitochondria of eukaryotes used to be free-living alpha-proteobacteria.

Question 24

Why was endosymbiosis favourable for the mitochondria? Give 2 reasons.

Answer 24

1. They are able to avoid Muller’s ratchet.

2. They can streamline their own genomes, making replication more energy efficient.

Question 25

Define CMS in plants.

Answer 25

Cytoplasmic male sterility: plants are hermaphrodite, but the mitochondria suppress male function, leading to pure females.

Question 26

Why does CMS exist?

Answer 26

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.

Question 27

What is a gynodioecious population?

Answer 27

A sexually dimorphic breeding population created by CMS whereby pure females and hermaphrodites coexist.

Question 28

Why does CMS harm nuclear gene transmission?

Answer 28

They are only passed on by the female and not the male parts.

Question 29

Define a nuclear restorer mutation.

Answer 29

One that has evolved to restore the hermaphrodite condition and thus male function in CMS.

Question 30

There has been co-evolution of the mitochondria and the nuclear genome. Why?

Answer 30

The mitochondria keep trying to dominate the nuclear genes, and the nuclear genes have to keep compensating.