W4L3 polyploidy

Question 1

C value paradox

Answer 1

The paradox is that the amount of DNA does not correlate with perceived complexity or position on the phylogenetic tree
* Complexity =
* number of cell types,
* metabolic complexity,
* behavioral complexity

Question 2

What explains genome size variation

Answer 2

• Gene duplication
• Blocks of duplication
• Satellites (repetitive regions)
• Relative rate of insertions and deletions
• Transposable elements
• Polyploidy

Question 3

Definition of polyploidy, euploidy and aneuploid

Answer 3

Polyploid: having more than two complete sets of chromosomes
*Euploid: having a complete complement of chromosomes
*Aneuploid: having an incomplete complement of chromosomes

Question 4

Polyploidy in plant

Answer 4

• Selective breeding of plants
• Five of fifty cotton species tetraploid 95% cotton cultivation
• Some major crops, e.g. sugarcane and wheat, are polyploid (though others, e.g. corn and rice, are diploid)
• Deliberate induction of polyploidy, e.g. by colchicine, long-standing in agriculture
• Larger fruit and (sometimes) seedlessness are desirable crop traits

Question 5

What is autopolyploidy and allopolyploidy

Answer 5

Autopolyploidy is duplication of the genome within a species
Allopolyploidy is genome duplication from hybridization of two parental species

Question 6

Mechanisms of allopolyploidy

Answer 6

• Allopolyploidy - involves interspecies hybridisation
• In plants, hybridisation possible up to about 10 million years’ divergence
• May develop from diploid hybrids in which gametes are not reduced - non-reduction more frequent in hybrids
  -chromosome doubleing of haploid, fusion of unreduced gamete’s and direct hybridization

Question 7

Mechanic of polyploidy

Answer 7

Gametic non-reduction: failure of cell division during meiosis producing 2n gametes
– Unreduced sperm is uncommon in animals
– Common step in pathway to allopolyploidy in plants
*Somatic doubling: mitotic doubling then failure of cell division
– vegetative propagation in plants
*Polyspermy: multiple sperm fertilising an egg
– 1-3% of human conceptions (not viable)

Question 8

How common is polyploidy

Answer 8

Very common in plants
– Polyploidization has occurred in the lineages of 70% of angiosperms !
–&raquo_space; 15% of angiosperm speciation events
-also common in fish, amphibian and insect
-rare in mammals

Question 9

Wheat varieties

Answer 9

Progenitors diverged~4mya 14chr
AAxBB hybridization~0.5mya 28chr
AABB x DD hybridization~0.01mya 42chr

Question 10

How is polyploidy viable

Answer 10

Hexaploid history is backed up by genome-wide sequencing
* An obvious rearrangement after hybridization
* ‘Diploidization’: most loci now behaving/segregating like diploids
* In wheat, high diversity remains after domestication

Question 11

Chromosome Pairing In ploidy

Answer 11

Meiosis requires pairing of sister chromosomes -complicated when more than two are present
* Multivalent pairing increases likelihood of aneuploid offspring
* Bivalent pairing more common in allopolyploids -some divergence between homeologs
* Bivalent pairing can occur without homeolog differentiation - random pairing within chromosome sets

Question 12

Polyploidy in Animals

Answer 12

• Polyploidy relatively frequent in reptiles, amphibians, fish, insects, crustaceans
• Interspecific hybridisation rarer than in plants (both hybridisation and polyploidy common in fish)
• Mechanisms of polyploidy - unreduced sperm rare (poorer performance?), though unreduced eggs less so; polyspermy most common
• Extremely rare in birds and mammals -

Question 13

Mammalian Mysteries - The Plains Viscacha Rat

Answer 13

Described as tetraploid based on high chromosome number (102), genome size, large sperm (‘gigas effect’ - from initial description of polyploidy in evening primrose as ‘gigas mutant’)

Question 14

The Red Viscacha Rat - The Evidence

Answer 14

Y chromosome only acrocentric
chromosome in Tympanoctomys barrerae -evidence against chromosome fission
* Similar number of transcripts to diploid relatives and no increase in pseudogenes -polyploidy appears unlikely
* Increased copy number of repetitive elements in T. barrerae - possible explanation for increased genome size (~50% of genome vs. ~20% in diploid relative)

Question 15

Yeast - a paleo-polyploid

Answer 15

• ~5,800 genes
• 450 pairs in ~30 duplicated blocks
  -after a duplication event, some gene can be loss
  -alternatively : sub-genomic duplication event
  -if there is sub-genomic, some gene might be triplicated or quadruplicated

Question 16

Factor to determine sub-genomic dup and whole genome dup

Answer 16

No evidence that duplicated gene blocks are duplicated again
All blocks have the same centromere-telomere orientation
-Synonymous site divergence is about the same for all pairs of block (suggest at the same time)

Question 17

Vertebrate ‘2R’ hypothesis

Answer 17

Susumu Ohno (1970) proposed that there had been two rounds of polyploidy in the vertebrate lineage
* C-value (amount of nuclear DNA)
* Isozymes
* identified two pairs of duplicated genes on chromosome 11 and 12 delineating duplicated chromosomal segment

Question 18

2R hyphothesis confirm

Answer 18

-mammal have 4 conserved homes-boxes region where as lamprey only have one
Duplication events that were close together are hard to distinguish (saturation of the clock)Need:
*enough species to cover before/after putative duplication events
*enough genes to give statistical power
-looking at multiple whole genome would be ideal

Question 19

Evidence to showed that ancient polyploidy event took place

Answer 19

-jump in C values
-jumps in chromosome number
-gene number
-chromosomal pairing (quadrivalents)
-gene arrangement
-ages of gene duplication event (molecular clock)
-gene topology in phylogenetic tree

Question 20

Possible cost of polyploidy

Answer 20

• Chromosomal (segregation error and pairing, sex determination)
• Developmental (gene expression level, timing of DNA replication, disruption in dosage compensation mechanism)
• Physiological (higher phosphorus need)
• Population
  – Initially rare - loss due to drift
  – Competition with locally adapted progenitor species
  – ‘2n’ gametes in a sea of ‘n’ can lead to inviable 3n zygotes

Question 21

Polyploidy and asexual reproduction

Answer 21

• Polyploidy in plants suggested to promote asexual reproduction by disrupting genetic self-incompatibility systems and reducing inbreeding costs
• Some evidence for partial breakdown, but no elevation in polyploidy in self-compatible species
• Asexual reproduction in some animals is a precursor to polyploidy -polyploids arising in asexual species encounter fewer obstacles to establishment

Question 22

Possible selective advantage for polyploidy

Answer 22

-increase DNA content (maintain genetic diversity, more DNA for subfuctionalization and different expression)
-increased nucleus, cell size ,bigger plant organs
-slower developmental/ division rate
-increase in heterozygosity ( initially, all alloploids are heterozygous, possible gene flow between ploidy and progenitor)

Question 23

The overall big picture of polyploidy

Answer 23

Recently-formed polyploids have
- Higher extinction rate than diploids
- Lower speciation rate
- Lower diversification rate
Yet major evolution diversification are associated with polyploidy envent