Lecture 4 - Plant Genome Structure

Question 1

What happens to genes over evolutionary timescales?

Answer 1

Genes can duplicate within a genome over time

Question 2

What happens once a gene is duplicated?

Answer 2

each gene copy is under reduced evolutionary constraint

there is another ‘back-up copy’ if a gene becomes damaged or mutated

Question 3

What is a pseudogene?

Answer 3

-when individual gene copes become inactivated , dead

DNA sequences that resemble protein-coding genes but they are not transcribed to a messenger RNA (mRNA) in a way that could then be translated into some functional protein.

these are dead genes - which are common in plants.

Question 4

When pseudogenes are produced - what happens?

Answer 4

divergence of each member of the growing gene family,
with regard to both sequence and function

if there is a selective advantage to the host

this is driven by selection

Question 5

what are examples of gene duplication?

Answer 5

• Tandemly repeated gene clusters
• gene divergence , new gene function and pseudogenes
• gene deletion

Question 6

How do genes become tandemly duplicated ?

Answer 6

1. Normal genetic recombination between sister chromatids during the first meiotic division, relies upon the two chromatids lining up together -
2. recombination occurs at a ( more or less) random position on both chromatids
3. this normally has no effect on gene order or number because the 2 recombination sites are identical on each chromatid.
4. But the genes on REAL chromosomes are embedded in “junk” repeated tranposable element-derived sequences
5. These repeats can confuse the recombination machinery
   - leading to cross-overs between different positions on the two chromatids
6. resulting in gene duplication and gene deletion

example ( slide 6 - Red strand will recombine with the blue one… the chromosomes line up with each other , and then there is a break in the strand , leading to one strand invading the other – for that to happen there has to be identical sequence – so double stranded homologue can be formed. )
They will recombine at purple part
Then you will see there is this junction ( where red and blue recombine chromosomes together)
So here the bottom strand has shifted along abit , so they recombine differently – everything has moved – so there may be a gene duplication or gene deletion on the other chromosome
Duplcation and deletion go together
These arrangements can go by selection – so if duplciation advantage it will persist or if deletion is an advantage it will persist

Question 7

WHY do genes become tandemly duplicated?

Answer 7

it gives rise to gene duplication and gene divergence

Gene duplication produces 2 identical copies of a gene - these copies can then diverge by mutation over evolutionary timescales

The point is that two genes may diverge – to create a new charachteristic as such – that was not previously noticed in the organism

Gene divergence can result in the ‘death’ of a gene, producing a non-functional pseudogene

This occurs agin and again

This shows how a gene accumulates mutations and creates a psudeo gene – which is a dead gene

Question 8

Examples of tandem gene duplication?

Answer 8

Aluminium tolerance and duplication of transporter genes in rye