Reading - Evolution of rDNA in Nicotiana allopolyploids Flashcards
Active rDNA units are vulnerable to homogenization
acts to reduce mutational load across the active array
rDNA units that are epigenetically silenced
less vulnerable to homogenization
- selection can’t act on these silenced genes
- accumulate mutations and eliminated from the genome
rDNA unit
- each large rDNA unit with
- 18s
- 5.8s
- 26s
- ITS
- IGS
- genes highly conseved
- ITS divergence = resolve species relationships
- IGS with transcription start site and genetic/epigenetic fetures diverges more rapidly
The pattern of divergence of the whole rDNA array is often influenced by
sqeuence homogenization
which functions to replace existing genic units with variants of that unit over time
in a process called concerted evolution
Concerted evolution is important to
maintain sufficient numbers of active rDNA units
Ohta
from computer models
- homogenization acts to reduce mutational load
- favored by selection
Patterns of rRNA gene expression are influenced by
epigenetic events
- cytosine methylaiton
- histone acetylation
- initiated by siRNAs
In hybrid organisms and allopolyploid species
(interspecific hybrids with chromosome number duplication)
silencing of entire loci is common, leading to…
one parental rDNA array being expressed in preference to another
= nucleolar dominance
Allopolyploids of Nicotiana
presumed relationships between diploids and polyploids have been confirmed using
- molecular cytogenetics
- mapping of repetitive DNA probes
To determine the influence of time on
the divergence or rDNA and distribution of loci carrying rDNA (nucleolus organizer regions)
it’s necessary to
estimate the time elapsed since the allopolyploids were formed
- dated nodes of phylogenetic tree
- determined likely maximum ages of all nodes
estimates of ages of the allopolypoloids enable to examine trends in evolution of rDNA over time
Synthetic hybrids and allopolyploids enable us to
follow genetic changes occurring in response to de novo allopolyploidy
- any deviation from genetic additivity considered to be induced by allopolyploidy
De novo allopolyploidy is thought to induce a “genomic shock” responsible for the activation of
- transposons
- retrotransposons
- genomic translocations
- insertions/deletions
- epigenetic reprogramming
In synthetic allopolyploids of N. tabacum,
observed losses of repetitive sequences
(incuding tandem and dispersed repeats and retroelements)
predominanly from the paternal genome in early generations
Synthetic tobacco line Th37
N. tomentosiformis x N. sylvestris
- only 3/20 plants showed additive pattern of rDNA RLFPs (method used to follow a particular sequence of DNA as it is passed on to other cells) observed in the parents
- in 75% of plants the IGS from N. tomentosiformis replaced by a novel hybrid-specific rDNA cluster
- all novel rDNA variants were of N. tomentosiformis orign but longer
- amplified SRII and SRVI reptitive subregionsof the IGS
- all novel rDNA variants were of N. tomentosiformis orign but longer
Synthetic tobacco line Th37
Plant 37.9
- RFLP bands additive for those observed in the parents
- additive number of 35s rDNA loci
- 3 from N. sylvestris on chrom S10, S11, S12
- 1 from N. tomentosiformis on chrom T3
Synthetic tobacco line Th37
Plant 37.1
- had a hybrid-specific cluster of rDNA units
- new rDNA locus on 1 of the 2 homologues of T4 from tomentosiformis
Synthetic tobacco line Th37
Plant 37.8
- lost the N. tomentosiformis-derived rDNA units
- rDNA sites on both T3 homolgues were still present
- the units at tehse sites had been replaced by the new hybrid-sepcific cluster of rDNA units
- both homologues of chromosome T4 now carried the new site
Th47 N. tabacum revealed
- rapid amplification of 35s rDNA units (in 4 generations)
- first occurred at a new chromosomal locus (on chromosome T4)
- new 35s rDNA units in most plants transferred to chromosome T3, by
-
sequnece homogenization involving:
- recombination machinery
- unequal recombination
- saltatory replication
- rDNA unit amplification
-
reciprocal traslocations between the rDNA loci on chromosomes T3 and T4
- followed by random segregation of chromosomes at meiosis that could lead to the loss of all chromosome T3-derived rDNA units in subsequent generations
-
sequnece homogenization involving:
GISH
- labels whole genome
- shows ploidy level - by representing each parental genome
RFLP analysis of structure of 35s rDNA units in N. tabacum reveal
the pattern of bands doesn’t correspond to that in parents
→ N. tabacum ahs evolved its own distinct gene family
- sequence analysis showed tobacco-specific units from reorganizatoin of parental N. tomenot units, then amplification and homogenization
- IGS subrepeats may have a role in homogenization by promoting/facilitating recombination between units
Reorganization of rDNA units and their amplificatoin within and between rDNA loci are
more rapid genetic events than changes in numbers of rDNA loci
- over millions of years of allopolyploid divergence observe a reduction in rDNA locus number
- locus number changes aren’t necessarily associated with the early evolution of allopolyploids
Activity at any particular rDNA locus → nucleolar dominance
influenced by
- the action of homogenization
- epigeneticallly - cytosine methylation and histone acetylation
Homogenization of rDNA arrays to
maintain a high proportion of functional rDNA units (Ohta)
- also leads to divergence of the IGS (and proteins that bind to it) bc it’s not under such strong selective constraints
Epigenetic silencing and sequence homogenization
-
nucleolar dominance - epigenetic silencing of rDNA genes
- leads to one parental gene family being transciptionally silenced
- eg in N. tabacum - silenced N. sylvestris
- Dadejova - used RT-PCR to investigate exprsesion of rRNA genes in N. rustica and N. tabacum
- observed that units that weren’t replaced by gene conversion were transcriptionally silenced
Epigenetic silencing of rDNA loci makes them
less vulnerable to homogenization and more likely to be lost
Info from Nicotiana → link betwen epigenetic (nucleolar dominance) factors and genetic outcome (homogenization)
- rDNA units that are unconverted and inherited little change from diploid progenitor are epigenetically silenced
- inverse correlation betwen the degree of epigenetic silencing of parental rDNA units in F1 and the proportion of parental units that have been homogenized in natural allopolyploids
In early polyploids there may be
- over-expression of genes
- imbalanced gene-product dosages
from genome duplication
if this applies to rDNA, can be tuend to meet physiology
- physical elimination of genes
- epigenetic inactivation of units (epigenetic rDNA dominance)
- overwriting of one rDNA variant with another, perhaps a version that will be silenced (genetic rDNA dominance)
- combination of these
Active rRNA genes organized as
decondensed chromatin
- vulnerable to recombination to promote homogenization and altered copy numbers
Epigenetic inactivation
- increasres levels of chromatin condensation and heterochromatin
- protect rDNA from genetic recombination
- inactive, non-homogenized rDNA parental units transmitted over many generations
Homogenization is a powerful process that
keeps the tandem arrays uniform,
acting to remove non-functional units from the cluster
(Ohta, 1989)
Silenced rDNA units that aren’t homogenized
acquire changes leading to:
- loss of function
- could be lost over evolutionary time
Consequences of silencing of rDNA loci
- reduced/eliminated interlocus homogenization
- divergence of units in silenced loci → loss of function
- deletion of silenced genes
