The 3 genomic paradoxes

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The 3 genomic paradoxes
3c
K
C
N
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K-value paradox Complexity does not correlate
with chromosome number.
Ophioglossum reticulatum
Homo sapiens
Lysandra atlantica
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250
1260
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C-value paradox Complexity does not correlate
with genome size.
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N-value paradox Complexity does not correlate
with gene number.

21,000 genes
25,000 genes
60,000 genes
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Possible solutions
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What is complexity?
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Solution 1 to the N-value paradox Many
protein-encoding genes produce more than one
protein product (e.g., by alternative splicing or
by RNA editing).
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RNA editing
Alternative splicing
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The combinatorial use of RNA editing and
alternative splicing probably causes the human
proteome to be 5-10 times larger than that of
Drosophila or Caenorhabditis.
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108 cells
19,000 genes
13,600 genes
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Solution 2 to the N-value paradox We are
counting the wrong things, we should count other
genetic elements (e.g., small RNAs).
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Solution 3 to the N-value paradox We should
look at connectivity rather than at nodes.
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L. Mendoza and E. R. Alvarez-Buylla. 1998.
Dynamics of the genetic regulatory network for
Arabidopsis thaliana flower morphogenesis. J.
Theor. Biol. 193307-319.
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Solution 4 to the N-value paradox The numbers
provided by the various genome annotations are
wrong!
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Comparison of three databses
Hogenesch JB, Ching KA, Batalov S, Su AI, Walker
JR, Zhou Y, Kay SA, Schultz PG, Cooke MP. 2001.
A comparison of the Celera and Ensembl predicted
gene sets reveals little overlap in novel genes.
Cell 106413-415.
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Range of C-values in various eukaryotic
taxa _____________________________________________
__________________ Taxon Genome size range
Ratio (Kb) (highest/lowest)
_________________________________________________
______________ Eukaryotes 2,300 -
686,000,000 298,261 Amoebae 35,300
- 686,000,000 19,433 Fungi
8,800 - 1,470,000 167 Animals
49,000 - 139,000,000 2,837 Sponges
49,000 - 53,900 1 Molluscs
421,000 - 5,290,000
13 Crustaceans 686,000 - 22,100,000
32 Insects 98,000 - 7,350,000
75 Bony fishes 340,000 - 139,000,000
409 Amphibians 931,000 - 84,300,000
91 Reptiles 1,230,000 - 5,340,000
4 Birds 1,670,000 - 2,250,000
1 Mammals 1,700,000 -
6,700,000 4 Plants 50,000 -
307,000,000 6,140 ______________________
_________________________________________
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If the variation in C-values is attributed to
genes, it can be due to interspecific differences
in (1) the number of protein-coding
genes (2) the size of proteins (3) the size
of protein-coding genes (4) the number and sizes
of genes other than protein-coding ones.
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The number of protein-coding genes in eukaryotes
is thought to vary over a 50-fold range. This
variation is insufficient to explain the
300,000-fold variation in nuclear-DNA content.
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The bigger the genome, the smaller the genic
fraction
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Nongenic DNA is the sole culprit for the C-value
paradox!
99.998
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Genome increase (1) global increases, i.e., the
entire genome or a major part of it is
duplicated (2) regional increases, i.e., a
particular sequence is multiplied to generate
repetitive DNA.
MECHANISMS FOR GLOBAL INCREASES IN GENOME SIZE
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Polyploidization the addition of one or more
complete sets of chromosomes to the original set.
An organism with an odd number of autosomes
cannot undergo meiosis or reproduce sexually.
Musa acuminata
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allopolyploidy
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Triticum urartu (AA) ? Aegilops speltoides (BB)
T. turgidum (AABB) ?
T. tauschii (DD)
T. aestivum (AABBDD)
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autopolyploidy
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Following polyploidization, a very rapid process
of duplicate-gene loss ensues.
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Allohexaploid Triticum aestivum originated about
10,000 years ago. In this very short time, many
of its triplicated loci have been silenced. The
proportion of enzymes produced by triplicate,
duplicate, and single loci is 57, 25, and 18,
respectively.
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During evolution autopolyploidy allopolyploidy
becomes cryptopolyploidy.
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Genome sizes in 80 grass species (Poaceae).
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It has been suggested that the emergence of
vertebrates was made possible by two rounds of
tetraploidization.
Two cryptooctoploids?
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Does chromosome number increase due to polyploidy
affect the phenotype?
Chrysanthemum species have 9 to 90 chromosomes in
haploid cells.
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54 duplicated regions.
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2 possible explanations (1) the duplicated
regions were formed independently by regional
duplications occurring at different times. (2)
the duplicated regions have been produced
simultaneously by a single tetraploidization
event, followed by genome rearrangement and loss
of many redundant duplicates.
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50/54 duplicated regions have maintained the same
orientation with respect to the centromere. 54
independent regional duplications are expected to
result in 7 triplicated regions (i.e.,
duplicates of duplicates), but none was observed.
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Loss of 92 of the duplicate genes. Occurrence
of 70-100 map disruptions.
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Arabidopsis thaliana regional duplications
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What about polysomy?
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trisomy 21
Polysomy is usually deleterious.
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An exception?
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MAINTENANCE OF NONGENIC DNA HYPOTHESES (1) The
selectionist hypothesis. (2) The neutralist
hypothesis (junk DNA). (3) The intragenomic
selectionist hypothesis (selfish DNA). (4) The
nucleotypic hypothesis.
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3.5
3
log nuclear volume (mm3)
2.5
2
1
1.5
2
log DNA per cell ()
Correlation between nuclear volume and nuclear
DNA content in apical meristem cells of 30
herbaceous species. Regression slope 0.826
fitted by least squares.
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MAINTENANCE OF NONGENIC DNA EVIDENCE (1) The
selectionist hypothesis. (2) The neutralist
hypothesis (junk DNA). (3) The intragenomic
selectionist hypothesis (selfish DNA). (4) The
nucleotypic hypothesis.
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Even whole chromosomes may be junk.
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with apologies to Irina Dunn, Australian feminist
(1970).
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Nature (2004) 431988-993.