Whole Genome Duplications (Polyploidy)
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Transcript of 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
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
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
Types of Polyploidy
Allopolyploidy – chromosomal duplications derived from different species
… produce homeologs
Autopolyploidy – chromosomal duplications derived from the same
species … produce ohnologs
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
From Kellis & Lander. Nature 2004
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
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
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
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
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 )
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
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)
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
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’)
Veron et al. Mol Biol Evol 2007
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)