Transcript Genic contribution to expansion in genome size

EVOLUTION OF GENOMES
C-value paradox:
- in certain cases, lack of correlation
between morphological complexity and genome size
“[For] some commonly cited extreme values for amoebae... considerable
uncertainty about the accuracy of these measurements and the ploidy level of
the species...” Gregory Nature Rev. Genet. 6:699, 2005
Table 8.3 &
Alberts Fig.1.38
Genic fraction vs. genome size
Function of non-genic DNA in eukaryotes?
Composition of human genome
Gregory Nature Rev. Genet. 6:699, 2005
Fig. 8.15
Genic contribution to expansion in genome size
Hartwell Fig. 21.11
Scenario showing possible events following whole genome duplication
26 genes on 2 chromosomes
36 genes on 4 chromosomes
Figure 8.7
Evidence for whole genome duplication in ancestor of yeast
~ 100 million years ago?
Kellis Nature 428:617, 2004
see also Fig.8.7
Duplication of entire genome much more common in plant
evolution than in animal evolutionary history
For chromosome number
>12, even numbers much
more common than odd
numbers
Frequency distribution of haploid chromosome numbers in dicot plants
Griffiths 7th ed, Fig. 26-12
Evolution of tandem arrays of eukaryotic genes
Over evolutionary time
expect independent mutations
to accumulate
… but often observe all copies
identical (or nearly so)
- evolve “in concert”
Fig. 6.25
Concerted evolution
- maintenance of homogeneous nt sequences among
multi-gene family members (especially when in tandem arrays)
- exchange of sequence info so members kept very similar
- eg. eukaryotic ribosomal RNA gene copies
Fig. 6.26
Possible evolutionary scenarios resulting in “homogenized” tandem array
1. Beneficial mutations fixed by positive selection
-but spacers with no known function show concerted evolution
2. Recent amplification
3. Mutation in one repeat “spreads” to others
Fig. 6.27
Unequal crossing over
- homologous recombination between misaligned arrays
- change in number of repeats
Fig. 6.31
Example of unequal crossing over in human b-globin array
“Lepore” b - thalassemia
misalignment (of sister chromatids
during mitosis in germ cell or
homologous chromosomes during
meiosis…)
Page & Holmes Fig. 3.15
Gene conversion
- non-reciprocal recombination
- no change in gene copy number
- can occur in dispersed as well as tandem repeats
- example of yeast mating-type
switching
Fig. 6.29
Watson Fig. 10-21
Example of concerted evolution in primate b -globin gene cluster
Exon 3
Exons 1 & 2
How do you interpret these data?
... and panel 3 of Fig.6.33 ?
Fig. 6.33
Resurrection of ribonuclease pseudogene by gene conversion
PR pancreative ribonuclease
SR seminal ribonuclease
… in some bovine species, gene conversion
of y SR with PR gene, so functional again
What is predicted status of SR gene in giraffe? or sheep?
Fig. 6.33
Factors affecting rate of concerted evolution (p. 317-320)
1. Number, arrangement, structure of repeats
- non-coding regions evolve more rapidly, and if
divergent enough may “escape” homogenization
2. Functional requirement
- selective advantage of high amount of same gene
product vs. diversity
3. Population size
- time for variant to be fixed or eliminated
Evolutionary implications of concerted evolution (p.320-322)
“molecular drive”
1. Spread of advantageous mutations (or removal of deleterious ones)
2. Retards paralogous gene divergence (preventing redundant copy
from becoming non-functional)
3. Generates increased genetic variation at a particular locus within a
population
Methodological implications
- degree of sequence divergence of paralogous genes undergoing
concerted evolution is not correlated with evolutionary time
so gene duplications can appear younger than they really are…