Bioinformatics 5: Eukaryotic genomes to comparitive genomes

Question 1

How are eukaryotic genomes organised? Variation within? Exceptions?

Answer 1

Organised into chromosomes (usually linear)

Most variation is in number (1-630)
and size (90kb - 245Mb)

Exceptions
Minichromosomes: in birds e.g. chickens have 33 with 75% of genes
Supernumerary chromosomes - polymorphic chromosome fragments
Holocentric chromosomes (many centromeres)

Question 2

What is meant by the C value paradox?

Answer 2

Some animals have significantly larger/smaller genomes than expected e.g. amphibian range 1000Mbp-100Gbp (small/average - Large)

Question 3

What is a cot analysis? What can it show?

Answer 3

C0t analysis = technique based on the principles of Genome hybridisation kinetics

Biochemical technique that measures how much repetitive DNA is in a DNA sample such as a genome

• indicates 3 major classes of complexity:
  highly repetitive, moderately, unique.

Question 4

2 approaches to genome sequencing?

Answer 4

Top down

Bottom up

Question 5

What is top down sequencing? What is it dependant on?

Answer 5

Known as Hierarchical shotgun (HS)

Break large sequences into smaller pieces that overlap and cover the whole genome, fragment pieces, sequence and assemble

Dependant on a physical and/or genetic map

Question 6

What is bottom up sequencing?

Answer 6

Known as Whole Genome Shotgun (WGS)

Fragment whole genome into smaller pieces, sequence and assemble

Question 7

What is meant by ‘shotgun’ sequencing?

Answer 7

Shotgun -> random fragmentation of a large piece of DNA into overlapping fragments

Question 8

needs more

Answer 8

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