Lecture 11 Synteny

Question 1

What is Synteny?

Answer 1

Synteny refers to the relative order of genes on chromosomes that share a common evolutionary history.

Question 2

When are two regions considered syntenic?

Answer 2

when multiple consecutive genes are found in a conserved order between the two genomes under consideration

Question 3

What can cause synteny to break down?

Answer 3

genome rearrangements.

Question 4

What have comparative fungal genomic analysis shown in respect to synteny?

Answer 4

• syntenic structures are generally conserved between very closely related fungal species but reduces as species become more distantly related
• conservation of gene order between closely related species correlates with phylogenetic analyses.

Question 5

homologous chromosomes between the Saccharomyces species

Answer 5

are almost collinear, differing only by a small number of translocations and large inversions (segment of DNA is reversed).

Question 6

Where do the largest syntenic blocks occur?

Answer 6

regions with low meiotic recombination rates

Question 7

what do the largest syntenic blocks not contain?

Answer 7

transposable elements (cause translocations).

Question 8

What is CGOB?

Answer 8

Tool for visualising, assessing and scoring genomic data, within and between closely related yeast genomes.

Question 9

what does CGOB allow for?

Answer 9

Allows analysis of gene order (synteny)

Question 10

CGOB Allows analysis of gene order (synteny)

Answer 10

• Perl driven web interface
• Cross genome ‘pillar’ data structure representing homology
• Synteny assigned by CGOB’s algorithms

Question 11

CGOB synopsis (look as slides for more detail)

Answer 11

• Have completed manual inspection of homology pillars.
• Have curated and improved gene sets.
• Have mapped Tandem duplications.
• Have located loci with rapid/unusual evolution.
• Have mapped known biological pathways and located metabolic clusters.