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The 3 genomic
paradoxes
3c
KN
C
2
K-value paradox:
Complexity does not
correlate with chromosome
number.
46 250
Ophioglossum reticulatumHomo sapiens Lysandra atlantica
~1260
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C-value paradox:
Complexity does not
correlate with genome size.
3.4 109 bp
Homo sapiens
6.8 1011 bp
Amoeba dubia1.5 1010 bp
Allium cepa
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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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959 cells 1,031 cells
19,000 genes 13,600 genes
~108 cells
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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.
13
L. Mendoza and E. R. Alvarez-Buylla. 1998. Dynamics of the genetic
regulatory network for Arabidopsis thaliana flower morphogenesis. J. Theor.
Biol. 193:307-319.
14
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
106:413-415.
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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-
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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.
19
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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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MECHANISMS FOR
GLOBAL INCREASES
IN GENOME SIZE
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.
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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.
30Genome sizes in 80 grass species
(Poaceae).
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32
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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.
38
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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Polysomy is usually deleterious.
trisomy 21
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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
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3.5
3
2.5
2
log nuclear volume (mm3)
log DNA per cell ()1 1.5 2
Correlation between nuclear volume and nuclear
DNA content in apical meristem cells of 30
herbaceous species. Regression slope = 0.826
fitted by least squares.
49
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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
51
Even whole chromosomes
may be junk.
A person
needs an Y,
like a fish
needs
bicycles.
52with apologies to Irina Dunn, Australian feminist
(1970).
53
Nature (2004) 431:988-993.
