Chp 7 Lec 5

Question 1

1. Large-scale duplications, genomes of many species contain duplications of ___,with the(affected) length ___from species to species.
2. Why are large-scale segmental duplications an important component of the difference between human and chimpanzee genomes, affecting about 2.7% of the genome.
3. Explain why in humans duplications contributes to the frequency of the disease , by presenting sites for homologous recombination during meiosis.

Answer 1

1. Multigene regions, varying
2. (1) some duplications are found in chimpanzees, but not humans, vice versa, and some in both.
   (2) some duplications appearing in humans,but not chimpanzees genome involve segments associated with developmental disorders, including a region on human chr 15 (Prader Willi and Angelman syndrome), arising from microdeletions.
3. Show up in some of the gametes as deletions.
   It is therefore likely that Prader-Willi and Angelman syndromes are less common in chimpanzees than in human.

Question 2

1. When does whole-genome duplications (WHDs) occur?

2. Why is it that the mere appearance of two copies of many genes do not prove WGD?

Answer 2

1. When Chr’s replicate but don’t segregate properly into separate progeny cells upon mitosis.
2. It is because one copy must provide with evidence that (1) the genome-wide occurrence of pairs of homologous genes appearing in the same order(synteny) (2) ‘molecular clock’ evidence showing equal divergence times in many pairs of homologues.

Question 3

1. When did yeast genome undergo a WGD ?
2. The yeast WHD effects are obscured by? How do we know that they’ve been obscured?
3. The yeast genome contains ___, on average ___,together covering ___of the genome and including ___.

Answer 3

1. About 10^8 yes ago
2. (1) by subsequent chr arrangements (2) massive loss of duplicated material.
   By the traces left after duplication in multiple homologues that retain their genomic order.
3. 55 duplicated regions, 55kb long, ~50% ,376 pairs of homologues genes.

Question 4

1. What did S. Ohno in the book ‘Evolution by gene duplication’ propose and where has this proposal also occured?
2. In the lineage leading to vertebrates, the genomes of the cephalochordate Amphioxus ( Branchiostoma floridae) and urochordate(Ciona intestinalis) showed evidence for 2 rounds of WGD:
3. State the more recent duplication (3rd one):

Answer 4

1.That the vertebrate genome is the product of one or more WGDs, confirmed by genome seq. It occurred in plant lineages too.

2. (1) individual genes in these relatives corresponded to multiple genes in vertebrates, with enough synteny preserved to show that the process happened in parallel on a large scale.
   (2) WGD occured in vertebrates lineage after the split between the primitive chordate relatives (urochordates and cephalochordates) from vertebrates, about 400-600 MYA
3. Occured in the lineage leading to ray-finned fishes, such as zebrafish and medaka.

Question 5

1. What happens to all the extra genes after WGD is followed by massive gene loss?
2. To see which genes were duplicated, a comparison of the genome of the primitive chordate Branchiostoma floridae with genomes of vertebrates was done, what were the results?

Answer 5

1. -Most metazoa have roughly the same no.of proteinprotein-coding genes, in the range 20 000 - 25 000.
   - some genes do form paralogous groups, and can even duplicate further, individually, creating gene and protein families of various sizes, e.g. globins, G-protein coupled receptors (GPCRs), etc.
2. It showed that duplicates retained after WGD were enriched for signal transduction transcriptional regulation neuronal activity and development.

Question 6

1. Give a reason why plant genomes are very susceptible to duplication?
2. What does it mean when we say most plants are polyploids?
3. Give two types of polypoids.
4. Examples of polypoids.
5. Useful property of polypoidy in agriculture?

Answer 6

1. Because Arabidopsis genome reveals at least 3 and probably 5 successive duplication events.
2. Meaning they contain multiple sets of the entire chr’s.
3. (1) autopolypoids - contain multiple copies of genomes from the same parent (e.g. highbush blueberry)
   (2) allopolyploids - contain multiple copies of genomes from different parents (e.g. Triticum aestivum)
4. Crops, wild species (wheat, alfalfa, oats,coffee, potatoes, sugarcane, cotton, peanuts and bananas)
5. Increases fruit or grain size