Paleopolyploidy

Question 1

Paleopolyploidy

Answer 1

ancient polyploidy events

- ~10 mya

Question 2

paleopolyploidy in vertebrates

Answer 2

2 rounds of polyploidy, one before emergence of jawless fish and one after

Question 3

Fish specific genome duplication

Answer 3

many genes present in 2 copies in teleost fish but one copy in other vertebrates
- pairs in teleost seem to have originated at the same time

Question 4

How is paleopolyploidy detected?

Answer 4

1. find duplicated gene blocks
2. estimate ages using synonymous substitutions (Ks)
3. analyze degree of overlap between adjacent blocks
   - if overlap were generated by segmental duplications NOT polyploidy

Question 5

evidence for paleopolyloidy

Answer 5

large duplicated, non-overlapping regions, with genes of similar ages

Question 6

evolution after paleopolyploidy

Answer 6

• organisms return to a diploid state by chromosomal structural changes, including rearrangements and fusions
• many duplicated genes are lost
• duplicated genes that are retained often diverge in expression patterns
• one copy may experience relaxation of purifying selection or positive selection
• retained duplicates can undergo subcellular relocalization
• neo or sub functionalization can occur

Question 7

hypotheses for single copy status after paleopolyploidy

Answer 7

dosage balance and dominant negative effect

Question 8

dosage balance

Answer 8

for small segmental duplications only

• predicts that stoichiometric imbalance among protein complex subunits is harmful
• WGD ensures that relative ratios among subunits are maintained, whereas this is not necessarily the case for small-scale duplications (SSDs)

Question 9

dominant- negative effect

Answer 9

• Explains single copy status for both WGDs and SSDs
• Gene duplication can result in an extra mutational target, in which mutations can occur that interfere with WT function
• E.g. duplicate gets mutation that abolishes function but still allows it to form a complex → inactive complex created → selected against

Question 10

Which genes are likely to return to single copy after WGD

Answer 10

overrepresented: DNA repair, replication, recombination, photosynthesis , etc
underrepresented: regulation of transcription, regulation of gene expression and phosphorylation

Question 11

short term consequences of polyploidy

Answer 11

gene silencing + loss of redundant genes/sequences

• chromosome exchanges resulting in loss or doubling in sequences + genome wide rewiring
• subfunctionalization or neofunctionalization

Question 12

what genes are retained/ lost after polyploidy

Answer 12

retained: transcription factors
lost: genes involved in organellar processes + meiosis

Question 13

Biased fractionalization

Answer 13

the non-random or biased loss of ancestral genes following allopolyploidy
- more loss from one sister genome compared to other

Question 14

genome dominance in context of polyploidy

Answer 14

genome wide homology expression bias

- 2 subgroups - more genes from one group expressed than other = genome dominance of expressed subgroup

Question 15

Transposable elements multiply rate in plant genomes

Answer 15

repeated bouts of proliferation followed by silencing and decay of most newly inserted TEs

Question 16

how can small RNAs and TEs affect expression levels of homeologs and result in one homeolog having lower expression

Answer 16

can silence one homeolog as they are silenced by epigenetic modifications, when insert next to a gene can silence that gene