Reading - Contrasting evolutionary dynamics between angiosperm and mammalian genomes

Question 1

Angiosperms have less highly compartmentalized and more diverse genomes than mammals

4 causes

Answer 1

• polyploidy
• recombination
• retrotransposition
• genome silencing

Question 2

Angiosperm genomes vs mammalian genomes

(general)

Answer 2

angiosperms

• evolutionary more dynamic and labile

mammals

• more stable at both the sequence and chromosome level

different life strategies and devleopment feed back on genome

Question 3

Global genomic architecture

Answer 3

mammals

• R- and G- bands (stain condense chromosomes) are highly conserved, enabling karyotypes to be compared
• occurrence of bands = sequences of chromosomes are organized into compartments and relatively stable
• evolutionary stability reflected in widespread occurrence of conserved noncoding sequences (CNS)

angiosperms

• failed to reveal compartmentalization and genome stability
• R- and G- bands not edetected
• CNS are fewer in number, smaller in size, degrade more rapidly
• genome is more fluid and less compartmentalized organization of DNA

Question 4

Chromosome painting

(identifies individual chromosomes)

Answer 4

mammals

• stability in chromosome structure over millions of eyars of mammalian divergence
• allows predictions of ancestral mammalian karyotype
• suggest that mammalian chromosome divergence had relatively few rearrangements of large genomic segments

angiosperms

• painting fails
• labels much of the genome
• more dispersed, genome-wide distribution of repeats in agiosperms

Question 5

To determine the frequency of chromsomal rearrangements in angiosperm evolution, use comparative linkage maps

Answer 5

• reveals more chromosomal translocations and local reshuffling of short DNA segments in angiosperms than in mammals

Question 6

Genome size

Answer 6

DNA c-values = genome size

angiosperms

• 2000-fold range
• 2n=4 to 2n=640

mammals

• 5-fold range
• 2n=6 to 2n=134
• fewer constraints on genome size and chromosome number in angiosperms compared with mammals

Question 7

Polyploidy and interspecific hybridization are more important in the divergence of angiosperms than mammals

Answer 7

angiosperms

• most species have at least one round of polyploidy
• at least 25% show evidence of interspecific hybridization
• hybridization easier because gametes released with only limited targeting systems

mammals

• polyploidy has not played a role in the divergence of mammals
• 2 rounds of polyploidy early in vertebrate evolution
• hybridization is lower because of internal fertilization and complex mating behavior

Question 8

Polyploidy leads to

Answer 8

• increases in genome size
• gene and allele diversity

Question 9

Together with local duplications, polyploidy results in

Answer 9

large multigene families in angiosperms

Question 10

Gene duplication might release functional constraints on copies, allowing them to

Answer 10

• evolve new or tissue-specific functions
• form pseudogenes
• be deleted

Question 11

Many duplicate copies are retained to

Answer 11

generate balanced amounts of gene products in relation to other duplicated genes

• eg 30% duplicated genes retained in A. thaliana

Question 12

Polyploidy and interspecific hybridization trigger

Answer 12

genetic and epigenetic changes to the genome

Question 13

One consequence of recurrent polyploidy and hybridization in angiosperms is

Answer 13

ongoing genome restructing

inhibiting the establishment of a highly compartmentalized genome

Question 14

Recombination

shuffling, incorporation, and elimination of DNA occurs more rapidly in angiosperms than mammals

Answer 14

• recombination rates are higher and activity more variable in angiosperms than in mammals

→ differences in genome structure and long-term stability

higher recombination frequencies reflected in

• the greater number of translocations that can occur during species divergence
• frequencies of illegitimate DNA insertions
  
  • supplies a constant supply of DNA from a variety of sources
    
    • transposable elements
    • mitochondrial DNA - incorporation of mitochondrial DNA higher in agiosperms, generation a higher proportion of nuclear mitochondrial sequences (NUMTS)
    • plasmid DNA
      *

Question 15

Insertion of DNA is associated with DNA repair processes

Answer 15

experiments in which protoplasts of tobacco and human HeLa cells were transfected with linear DNA sequences

→ DNA repair was less precisely regulatd and error-prone in tobacco

Question 16

DNA deletion

Answer 16

angiosperms

• rates of DNA loss astonishingly high
• half-life of a range of retroelements of rice is less than a few million years
• 80% of nuclear insertions of plastid genes might disappear within 1 million years

mammals

• chromosome paints remain effective between species despite 93million years of divergence
  
  • conservation of non-coding DNA sequences

Question 17

Higher recombination rates in angiosperms than mammals results in

Answer 17

• more translocations
• enhanced integration of sequences
• faster DNA deletion
• more error-prone DNA repair

Question 18

Recombination will blur genome substructure in angisperms

Answer 18

contribute to a more dynamic and fliud genome structure

Question 19

Cause of difference in recombination rates

Answer 19

• higher proportion of repetitive DNA and number of multigene families in angiosperms

→ multiple substrates for homologous recombination

• size of genes
  
  • average total exon length similar
  • gene larger in mammals because of greater intron lengths
  • intron length up = recombination down

Question 20

Retroelements

Answer 20

retrotransposons are the major determinants of genome structure and evolution

angiosperms

• retroelements more mobile and diverse
• contain predominantly LTR retrotranposons
  
  • massive diversity
  • up to 80% of the genome
• higher background levels of retrotransposition
• retroelement turnover frequent

→ loss of genome substructure and higher rates of genome divergence compared with mammals

mammals

• LTR retrotransposons are less abundant, diverse, and active
• LINES and non-autonomous SINES

Question 21

Recombination and retrotransposition lead to

Answer 21

homogenization of sequences between and within chromosomes

• rates higher within chromosomes (intrachromosomal homogenization)

mammals

• contribute tot he divergence of chromomsomes and the formation of a compartmentalized structure

angiosperms

• rate of intrachromosomal and interchromosomal homogenization are similar

Question 22

Angiosperms have 3 devlopmental features that are absent in mammals

Answer 22

1. alternation of generations resulting in 2 distinct life phasess
   
   • haploid gametophyte
   • diploid sporophyte
2. double fertilization in most species
   
   • forms zygote and a triploid endosperm that nourishes the zygote
3. the absence of a sequestered germline

Question 23

Consequence of alternation of generations and double fertilization is that

Answer 23

many genes have 3 different dosages

• single dosage
• double dosage
• tirploid dosage

Question 24

Sequestration of germline

Answer 24

mammals

• sequestration early in development means relatively few cell divisions leading to gamete formation
• germline largely protected from the environment

angiosperms

• no sequestratio of germline
• gametes formed from somatic cells in the apical meristem
• many hundreds of divisions between the seeds of one generation and those of the next
  
  • the number of mutations and cell divisions are positively correlated → many more opportunities for mutations
• germline vulnerable to environmental streses, stimulates mutations and retrotransposition

Question 25

Development

Answer 25

angiosperms

• plasticity in their genome → high degree of phenotype variability
• morphology influenced by environmental conditions

mammals

• highly constrained development controlled by coordinated developmental pathways

Question 26

Genome structure and life strategy

Answer 26

different life strategies drive genomic differences

mammals

• high levels of mobility to find food and mates, escape disease, predation, and adverse conditions
• genome constrained because genomic reorganization can be detrimental to a finely tuned, complex system
  
  • selected against

angiosperms

• sessile, so survival depends on being able to respond to adverse conditions through biochemical complexity and developmental plasticity
• reflected in the large number of genes involved in the production of secondary metabolites
• sessile life strategy against evolution of development complexity
• genomic restructuring advantageous to generate biochemical complexity

in angiosperms, lack of a sequestered germline and large number of offspring typical of many angiosperms → many opportunities for generating variation upon which selection can act

Question 27

The effects of genetic drift vs selection in fixing variation

Answer 27

influenced by the effective population size

• small Ne values for angiosperms → explain some of the variety
  
  • favoring effects of drift

Question 28

Genome size limitations

Answer 28

angiosperms

• nucleic acids are an expensive resource for plants becdause nitrates and phosphates must be harvested from the environment, often in limiting supply
• time taken to replicate DNA in the cell cycle increases with genome size

→ angiosperms with larger genomes are restricted in type of life history strategies and habitats they can adopt

→ less able to adapt to changing environments

• why the genome size distribution is skewed

mammals

• synthesis of DNA isn’t limiting because food source has plentiful DNA and RNA
• narrow range of small genome sizes to maximize enrgy flows for an active, dynamic life strategy
  
  • eg bats small genome to maximize energetics for flight