8c C-Value Paradox

3c
The 3 genomic paradoxes
C
1
K-value paradox: Complexity does not correlate with chromosome Homo sapiens Lysandra atlantica Ophioglossum reticulatum number.
46
250
~1260 2
C-value paradox: Complexity does not correlate with genome size.
3.4 109 bp Homo sapiens
1.5 1010 bp Allium cepa
6.8 1011 bp Amoeba dubia 3
N-value paradox: Complexity does not correlate with gene number.
~21,000 genes~25,000 genes 60,000 genes ~

4
Possible solutions:
What is complexity?
Solution 1 to the Nvalue 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
~108 cells
19,000 genes
13,600 genes
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We are counting the wrong things, we should count other genetic elements (e.g., small RNAs).
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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. 193:307-319. 13

The numbers provided by the various genome annotations are wrong!
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Comparison of three databses
15 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
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 16 ___________________________________________________________
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
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The number of proteincoding 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 Musa acuminata meiosis or
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allopolyploidy
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Triticum urartu (AA) Aegilops speltoides (BB)
T. turgidum (AABB) T. tauschii
(DD)
`
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autopolyploidy
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Following polyploidization, a very rapid process of duplicate-gene loss ensues.

27
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?

34
Chrysanthemum species have 9 to chromosomes in haploid cells.
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),
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Loss of 92% of the duplicate genes.

Occurrence of 70-100 map
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Arabidopsis thaliana: regional duplication
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What about polysomy?
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trisomy 21
Polysomy is usually deleteriou

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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).
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3.5
log nuclear volume (mm3)

2.5
1.5
log DNA per cell ()
Correlation between nuclear volume and nuclear DNA content in apical meristem cells of 30 48 herbaceous species. Regression slope = 0.826
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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).
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Even whole chromosomes may be junk.

A person needs an Y, like a fish needs bicycles.
51
with apologies to Irina Dunn, Australian feminist52 (1970).
Nature (2004) 431:988-993.
53

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3c

The 3 genomic paradoxes

C-value paradox: Complexity does not correlate with genome size.

3.4 109 bp Homo sapiens

1.5 1010 bp Allium cepa

6.8 1011 bp Amoeba dubia 3

N-value paradox: Complexity does not correlate with gene number.

~21,000 genes~25,000 genes 60,000 genes ~

Solution 1 to the Nvalue paradox:

959 cells 1,031 cells

Solution 2 to the Nvalue paradox:

Solution 3 to the Nvalue paradox:

Solution 4 to the Nvalue paradox:

Comparison of three databses

Range of C-values in various eukaryotic taxa

If the variation in C-values is attributed to genes, it can be due to interspecific differences in

The bigger the genome, the smaller the genic fraction

Nongenic DNA is the sole culprit for the C-value paradox!

MECHANISMS FOR GLOBAL INCREASES IN GENOME SIZE

Triticum urartu (AA) Aegilops speltoides (BB)

T. turgidum (AABB) T. tauschii

Following polyploidization, a very rapid process of duplicate-gene loss ensues.

During evolution autopolyploidy & allopolyploidy becomes cryptopolyploidy.

Genome sizes in 80 grass species (Poaceae).

Does chromosome number increase due to polyploidy affect the phenotype?

Chrysanthemum species have 9 to chromosomes in haploid cells.

Loss of 92% of the duplicate genes.

Arabidopsis thaliana: regional duplication

What about polysomy?

Polysomy is usually deleteriou

MAINTENANCE OF NONGENIC DNA: HYPOTHESES

log nuclear volume (mm3)

log DNA per cell ()

MAINTENANCE OF NONGENIC DNA: EVIDENCE

Even whole chromosomes may be junk.

with apologies to Irina Dunn, Australian feminist52 (1970).

Nature (2004) 431:988-993.

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