Reading - Genomic plasticity and the diversity of polyploid plants

Question 1

Polyploidy

Answer 1

a change whereby the entire chromosome set is duplicated

• arises through meiosis and mitosis
• frequently involves unreduced gametes and interspecific hybridization

Question 2

Success of newly formed angiosperm polyploids is partly attributable to

Answer 2

their highly plastic genome structure, as manifested by:

• tolerance to changing chromosome numbers
  
  • anueploidy and polyploidy
• genome size
• (retro)transposable element mobility
• insertions, deletions
• epigenome restructuring

Question 3

The ability to withstand large-scale changes is associated with

Answer 3

a restructuring of the transcriptome, metabolome, and proteome

results in an altered phenotype and ecology

→ polyploid-induced changes can generate individuals that are able to exploit new niches or to outcompete progenitor species

Question 4

…. % of extant angiosperms show 1 or more ancient genomewide duplications

Answer 4

>90%

(shown by molecular analyses)

Question 5

Allopolyploidy

Answer 5

polyploidy in association with interspecific hybridization

• can result in the generation of new species

Question 6

Polyploidy occurrence in gymnosperms

Answer 6

5%

Question 7

Polyploids commonly arise from

Answer 7

unreduced gametes by nondisjunction of chromosomes in the germline

humans

• diploid gametes occur 0.2 - 0.3% of the time
• rarely lead to triploid young
• don’t survive to adulthood

angiosperms

• unreduced gametes ~0.56% of the time
• triploid angiosperms frequently survive, establish higher ploidy levels
• newly formed allopolyploids may be particularly common in angiosperms due to the abundance of unreduced gametes and lack of targeting in pollen delivery (insects, wind)
• few successfully establish
  
  • York groundsel - arose naturall in the 1970s through allopolyploidy (native and introduced species), weed of the industrial wasteland, will go extinct unless it can disperse elsewhere (less than 50 years from birth)

Question 8

Genomic plasticity

Answer 8

angiosperms tolerate the considerable impact of polyploidy arising from:

• the accommodation of divergent genomes in the same nucleus
• intraspecific chromosome numbers
• unbalanced parental chromain contributions
• chromosomal rearrangements

Question 9

Genomic plasticity is evident from

Answer 9

the diverse genetic and epigenetic changes associated with polyploidy

• retrotransposon mobility
• sequence rearrangements and losses
• gene silencing
• DNA methylation changes
• chromatin remodelling

Question 10

Abnormalitites

Answer 10

such as multivalent formation and aberranat segregation of chromosomes at meiosis inn early generations

→ reduced fertility

→ sexual selection willf avor the most fertile and viable individuals, remove those that are maladapted

Question 11

Meiosis may impact the evolution of m any newly formed polyploids by

Answer 11

• enabling sexual propagation
• generating - through meiotic errors - large-scale chromosomal variation upon which genetic drift and selection can act

Question 12

High frequencies of unreduced gametes

Answer 12

• provide evolutionary pressure toward polyploid
• genomic plasticity relaxes the genetic and developmental constraints against polyploid formation

Question 13

Changes in the epigenetic profile

Answer 13

can lead to partitioning of the expression of duplicated ancestrala genes to specialized tissue-specific activity or function (subfunctionalization)

• duplicate genes can be lost → genome diploidization
  
  • returns the genome to a diploid-like form

Question 14

Further diploidization through

Answer 14

the erosion of differences between parental genomes in the polyploid

• over 5-10 million years retroelement turnover and tandem repeat replacement

→ loss ofmany genome-specific sequences

• contrasts with mammalian genomes
  
  • single chromosome losses or gains are usually detrimental
  • polyploidy is rare/absent

Question 15

Polyploidy

→

Answer 15

instantaneous multiplication in DNA content

after which divergence accompanied by

• genome sizes increases and decreases
  
  • expand genome by retroelement insertion
  • shrink genome by deletions

Question 16

… is often in limiting supply

Answer 16

phosphorus

Question 17

Plants in areas where nutrient levels are limiting

Answer 17

selection against polyploids or for those that can eliminate excess DNA

• support: after polyploidy, genome downsizing in angiosperms is the most common response

Question 18

Transcriptome level

Answer 18

• genome-wide nonadditive, nonrandom changes in gene regulation
  
  • eg silencing, up-regulation, down-regulation
• tissue/species specific
• triggered predominantly by interspecific hybridization rather than by chromosome multiplication

Question 19

Changes in the transcriptome aren’t necessarily reflected in the proteome

Answer 19

Brassica allopolyploids

• 25-38% (depending on tissue) of proteins vary from an expected additive pattern of proteins found in the 2 parents
• stimulated by interspecific hybridization

Question 20

Metabolome

Answer 20

secondary metabolites manufactured in defense of herbivory differ substantially in time, duration, and strength between 2 Nicotiana allopolyploids

• such physiological differences may affect allopolyploidy evolution and survival

Question 21

Homoploid species

Answer 21

• derived from interspecific hybrids without an accompanying genome duplication
• exploit niches unavailable to the parents
• may diverge throughs patial isolation or rapid genome divergence
• success attributed to the acquisition of transgressive characters - those characters that fall outside the range found in the parents

Question 22

Interspecific hybridization typically causes

Answer 22

gene flow between populations

→ breaking down species isolation barriers and doesn’t usually lead to speciation

• in contrast - choromosome multiplication can create instant barriers with diploid parents

Question 23

Both components of allopolyploidy contribute to their widespread occurrence

Answer 23

• interspecific hybridization to trigger changes at all levels from gene to ecology
• chromosome multiplicatoin to establish these changes