Plant Comparitive Genome Analysis

Question 1

Similarities between animals and higher plant genomes

Answer 1

Diploid (for plants at least most of their life)
DNA in chromosomes
Nuclear and mitochondrial DNA

Question 2

Differences between animal and higher plant genomes

Answer 2

Variation in genome size and chromosome number
Genome duplications and polyploidy more common (can also happen in fish and amphibians)
Chloroplast DNA

Question 3

Why not just nuclear DNA?

Answer 3

Nuclear, mitochondrial and plastid genomes interdependent.
Plastid = ~100 genes for translation and photosynthesis
Mito = ~ 60 for translation and respiration
Some proteins combined e.g. Rubisco = 8 large sun units form chloroplast and 8 small subunits from nuclear

Question 4

How to know genome size

Answer 4

Flow cytometry

• lysis buffer
• leaf discs (standard and unknown)
• extract nuclei
• remove debris
• stain nuclei
• flow cytometry
• compare peak size between standard and control to determine

Question 5

The C value paradox

Answer 5

C value = characteristic/ constant size of the haploid genome
Measured in pg = picograms
the paradox:
- Similar species have different genome sizes
- C value/ genome size doesnt relate to the number of genes coded

Question 6

Crop genomes

Answer 6

Most are intermediate = 30,000-100,000

Known by sequencing/cytometry

Question 7

Types of repetitive DNA

Answer 7

Tandem repeats

Dispersed repeats

Question 8

Tandem repeats

Answer 8

2-10 bases forming repetitive blacks

Often associated with telomeres or centromeres

Question 9

Dispersed repeats

Answer 9

Scattered throughout the genome

Often derived from transposable elements = self replicating, mobile and classed in families

Question 10

Transposable elements

Answer 10

Discovered in maize by Barbara McClintock
- patches of colour on maize kernels
Divide into class 1 or 2 transposons
Cause mutations during transposition but most are inactive

Question 11

Class 1 transposons

Answer 11

Retro transposons (require reverse transcription) 
Transcribe RNA into DNA in order to transpose

Question 12

Class 2 transposons

Answer 12

Move via DNA

Question 13

Describe telomeres

Answer 13

• Protect the end of chromosomes to avoid shortening
• ‘non sticky’ = unfragmented
• attach chromosomes to nuclear envelope
• sequence mostly multiple repeats of TTTAGGG, ranging form 2-150kb
• can be the same sequences as humans? E..g in onions

Question 14

Are telomeres linked to ageing?

Answer 14

Telomerase = stops shortening
Expressed in most meristems
Plant telomeres dont shorten during development
No close link between telomere length and plant age

But have seen telomere shortening link to apoptosis and shorter telomeres associated with higher diseases

Question 15

Describe centromeres

Answer 15

• for spindle attachment
• no always in centre of chromosome
• composed of tandem arrays and repeated seqeunce
• can contain retro transposon repeats
• difficult to sequence

Question 16

Where are genes located on chromosomes?

Answer 16

Chromosome arms
Density lower in plants with larger genomes
Gene density also greater away from the centromere

Question 17

What happens after polyploidy?

Answer 17

Genome down sizing (lose repetitive DNA)
Aneuploidy
Fractionation
Chromsome rearrangements e.g. trans location
Changes in gene expression e.g. methylation changes

Question 18

Aneuploidy

Answer 18

Loss of whole chromosomes

Question 19

Fractionation

Answer 19

Loss of whole pair of chromosomes

Question 20

Polyploidy

Answer 20

When a diploid cell acquires one or more sets of chromosomes
= 3+ x the haploid number

Question 21

What is synteny?

Answer 21

• conservation of blocks of genes order along chromosomes
  in different related species
• can apply to whole genomes and see how chromsomes map onto eachother
• aids understanding in evolution
• informs plant breeding

Question 22

The arabidposis genome

Answer 22

• The first sequenced in 2000
• 5 chromosomes and 5 known polyploidy events
• includes 2 episodes of duplication during evolution (one recents polyploidy in last 20-40MY)
• recent changes make older ones harder to detect

Question 23

Gene expression after polyploidy

Answer 23

Not all genes from all chromosomes present will be expressed 
Which one shown varies with 
- cell type
- gene function 
- development