8c c-value paradox

1

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

3

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

4

N-value paradox:

Complexity does not

correlate with gene number.

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

5

Possible

solutions:

6

What is

complexity?

7

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).

8

RNA editing

Alternative

splicing

9

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.

10

959 cells 1,031 cells

19,000 genes 13,600 genes

~108 cells

11

Solution 2 to the N-

value paradox:

We are counting the wrong

things, we should count

other genetic elements

(e.g., small RNAs).

12

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!

15

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.

16

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

_______________________________________________________________

17

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-

18

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

20

The bigger the genome, the smaller the genic fraction

21

Nongenic DNA

is the sole

culprit for the

C-value

paradox!

99.998%

22

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.

23

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

24

allopolyploidy

25

Triticum urartu (AA) Aegilops speltoides

(BB)

T. turgidum (AABB) T. tauschii

(DD)

`

T. aestivum

(AABBDD)

26

autopolyploidy

27

Following

polyploidization, a

very rapid process

of duplicate-gene

loss ensues.

28

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.

29

During evolution

autopolyploidy

&

allopolyploidy

becomes

cryptopolyploidy.

30Genome sizes in 80 grass species

(Poaceae).

31

32

33

It has been suggested that the

emergence of vertebrates was

made possible by two rounds of

tetraploidization.

Two cryptooctoploids?

34

Does chromosome

number increase due

to polyploidy affect

the phenotype?

Chrysanthemum species have 9 to 90

chromosomes in haploid cells.

35

54 duplicated regions.

36

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.

37

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.

39

Arabidopsis thaliana: regional duplications

40

What about polysomy?

41

Polysomy is usually deleterious.

trisomy 21

42

An exception?

43

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

44

45

46

47

48

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

50

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.