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Whole Genome Duplications (Polyploidy) us by S. Ohno, who suggested WGD can be a route to tionary innovation (focusing on neofunctionalization) osed in the 1970s that vertebrate lineage underwent two r confirmed with whole-genome sequence data. most common in plants but observed in vertebrates, fish ramecium, among other species

Whole Genome Duplications (Polyploidy)

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Whole Genome Duplications (Polyploidy). Made famous by S. Ohno, who suggested WGD can be a route to evolutionary innovation (focusing on neofunctionalization ) Ohno proposed in the 1970s that vertebrate lineage underwent two WGDs … later confirmed with whole-genome sequence data. - PowerPoint PPT Presentation

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Page 1: Whole Genome Duplications (Polyploidy)

Whole Genome Duplications (Polyploidy)

Made famous by S. Ohno, who suggested WGD can be a route to evolutionary innovation (focusing on neofunctionalization)

Ohno proposed in the 1970s that vertebrate lineage underwent two WGDs … later confirmed with whole-genome sequence data.

WGDs are most common in plants but observed in vertebrates, fishes, yeast,and Paramecium, among other species

Page 2: Whole Genome Duplications (Polyploidy)

Major mechanisms of polyploidy

1. Gametic nonreduction - production of unreduced gametes caused by an error in meiosis

2. Somatic doubling - production of a cell with twice the normal chromosome number caused by an error in mitosis

3. Polyspermy – fertilization of multiple gametes

Errors in meiosis/mitosis can be caused by genetic or environmental factors

Page 3: Whole Genome Duplications (Polyploidy)

Spindle error or failure

Abnormal chromosome pairing

Abnormal or absent cytokinesis

Pre-meiotic doubling

Produced at an average rate of 0.5% per gamete

Bretagnolle and Thompson New Phytol. (1995) 129: 1-22

Production of 2n gametes

Page 4: Whole Genome Duplications (Polyploidy)

Types of Polyploidy

Allopolyploidy – chromosomal duplications derived from different species

… produce homeologs

Autopolyploidy – chromosomal duplications derived from the same

species … produce ohnologs

Page 5: Whole Genome Duplications (Polyploidy)

Timeline after WGD

1. Initial duplication of entire genomeautopolyploid = identical genome

2. Gene loss is likely frequent immediately after (although some papersfind no evidence of this)which copy is lost is initially random

3. As sequences diverge, loss may not be randomsub/neofunctionalization may favor retention of specific ohnologs

4. Chromosomal rearrangements reduces 2X chromosome number

5. Reciprocal Gene Loss (RGL) in different individuals can promote speciation

Page 6: Whole Genome Duplications (Polyploidy)

From Kellis & Lander. Nature 2004

Page 7: Whole Genome Duplications (Polyploidy)
Page 8: Whole Genome Duplications (Polyploidy)

Reciprocal Gene Loss (RGL): differential loss of ohnologs can lead to speciation (due to problems pairing chromosomes)

WGDevent

RGL inindividuals

Mating

Difficulties during subsequent meiosis (F2s)

Ancient WGD’s correlate with increased species diversity and even radiations

WGD-driven speciation (via RGL) may be more likely to occur soon after WGD:rate of gene loss is highest soon after WGD and the copy lost is more likely to be random

Page 9: Whole Genome Duplications (Polyploidy)

The costs & benefits of WGD

Costs:Doubles the DNA content and chromosome number

More DNA = larger cells, larger volume, more proteins required

Benefits:Doubles whole pathways of functionally related genes

Maintains balanced expression across the genome

Page 10: Whole Genome Duplications (Polyploidy)

The Balance Hypothesis

Single-gene duplication can = stoichiometric imbalance

WGD maintains stoichiometry (at least initially)

The Balance Hypothesis predictsthat proteins in multi-subunit complexes

and proteins that require precise stoichiometry are more likely to be influenced

by WGD vs single-gene duplications

Page 11: Whole Genome Duplications (Polyploidy)

The fate of duplicate genes after WGD

1. ‘Classical’ sub- or neo-functionalization (“6 – 36% of ohno. pairs have one with higher rate of divergence

note this evolution can occur at the level of function OR expression

Page 12: Whole Genome Duplications (Polyploidy)

The fate of duplicate genes after WGD

note this evolution can occur at the level of function OR expression

2. Buffering (?)

1. ‘Classical’ sub- or neo-functionalization

Observation: yeast genes with retained ohnologs have less phenotypic consequenceof deletion … probably due to redundancy

? But is the driving force for their retention?( seems weird that buffering could drive their retention )

Page 13: Whole Genome Duplications (Polyploidy)

2. Buffering (?)

note this evolution can occur at the level of function OR expression1. ‘Classical’ sub- or neo-functionalization

The fate of duplicate genes after WGD

3. Benefit of copy number increase (maintaining stoichiometry across pathways)

e.g. Most glycolytic enzymes & most ribosomal proteins in S. cerevisiaeare retained Ohnologs

Page 14: Whole Genome Duplications (Polyploidy)

2. Buffering (?)

note this evolution can occur at the level of function OR expression1. ‘Classical’ sub- or neo-functionalization

The fate of duplicate genes after WGD

3. Benefit of copy number increase (maintaining stoichiometry across pathways)

Page 15: Whole Genome Duplications (Polyploidy)

2. Buffering (?)

note this evolution can occur at the level of function OR expression1. ‘Classical’ sub- or neo-functionalization

The fate of duplicate genes after WGD

3. Benefit of copy number increase (maintaining stoichiometry across pathways)

4. Need to maintain stoichiometry across pathways

Page 16: Whole Genome Duplications (Polyploidy)

2. Buffering (?)

note this evolution can occur at the level of function OR expression1. ‘Classical’ sub- or neo-functionalization

The fate of duplicate genes after WGD

3. Benefit of copy number increase (maintaining stoichiometry across pathways)

4. Need to maintain stoichiometry across pathways

5. Evolution of new regulatory circuits (‘rewiring’)

Page 17: Whole Genome Duplications (Polyploidy)

Veron et al. Mol Biol Evol 2007

Page 18: Whole Genome Duplications (Polyploidy)

unicellular ciliate (eukaryote): evidence of three ancient and successive WGDs

- find no evidence for rapid gene loss shortly after WGD- the latest WGD correlates with expansion of sister species- 10-16% of ohnologs show asymetric evolutionary rates (i.e. one copy faster)- Gene retention driven by stiochiometric requirements (complexes) and expression

abundance (higher expression = more likely to be retained)