Genome architecture and evolution
Key considerations:
• DNA…RNA…Protein
• Chromosomes
• C value paradox
• Gene regulation
• Epigenetics
• Transposable elements
DNA ……….………. mRNA……….……….Protein
Transcription
Plant
tRNA
rRNA
Translation
Estimated # genes
Arabidposis thaliana
27,000
Fragaria vesca
35,000
Theobroma cacao
29,000
Zea mays
40,000
DNA …………mRNA………….Protein
Autopolyploid AAAA
Allopolyploid AABB
Polyploidy
Formula
Genome
Haploid
# genes
2n = 2x =14
AA
A
30,000
2n = 4x = 28
AAAA
AA
60,000
2n = 2x = 14
BB
B
30,000
2n = 4x = 28
AABB
AB
60,000
Chromosomes
Plant
2n = _X = _
Arabidposis thaliana
2n = 2x = 10
Fragaria vesca
2n = 2x = 14
Theobroma cacao
2n = 2x = 20
Zea mays
2n = 2x = 20
F. vesca: 35,000 genes/7 chromosomes = 5,000 genes/chromosome.
1 2 3 4 ………………………2500
2501 2502 2503 ……………..5000
??
Chromosomes
F. vesca: 2n = 2x = 14; genome = 240 Mb; average gene = 3kb
79,333 genes? 11,333 genes/chromosome?
No….. 35,000 genes….. = 5,000 genes/chromosome
1
234
5
4995 4996
4997
5000
C-value paradox
“Organisms of similar evolutionary complexity
differ vastly in DNA content”
Federoff, N. 2012. Science. 338:758-767.
1 pg = 978 Mb
Fig. 1.The C-value paradox.
N V Fedoroff Science 2012;338:758-767
Published by AAAS
C-value paradox
Plant
Genome size
# Genes
Arabidposis thaliana
135 Mb
27,000
Fragaria vesca
240 Mb
35,000
Theobroma cacao
415 Mb
29,000
Zea mays
2,300 Mb
40,000
Pinus taeda
23,200Mb
50,000
Paris japonica
148,852Mb
??
C-value paradox
If not genes, what is it? Junk???????
C-value paradox
If not genes, what is it? Dark matter…
Shining a Light on the Genome’s ‘Dark Matter’
Gene regulation
DNA ……….………. mRNA……….……….Protein
Transcription
Developmental
Temporal
Spatial
Gene regulation
Pennisi, E. 2010. Science 330:1614.
40% of all human disease-related SNPs are OUTSIDE of genes
The dark matter is conserved and therefore must have a function
DNA sequences in the dark matter are involved in gene regulation
~80% of the genome is transcribed but genes account for ~2%
RNAs of all shapes and sizes:
1. RNAi
2. lincRNA
Epigenetic factors
Epigenetics
Epi = “above”
Phenotype “above and beyond” what the genotype would predict
Observe changes in phenotype without changes in genotype - due
to alternative regulation ( 0 – 100%) of the gene
Example: Vernalization
If a specific allele is present, the plant will not transition from a
vegetative to a reproductive state until sufficient cold units are
received
Epigenetics
Observe changes in phenotype without changes in genotype - due
to alternative regulation ( 0 – 100%) of the gene
Methylation
expression
Acetylation
expression
Epigenetics
Observe changes in phenotype without changes in genotype - due
to alternative regulation ( 0 – 100%) of the gene
RNA interference - RNAi:
targeted degradation of specific mRNA
Long non-coding RNA - lncRNA: X chromosome inactivation
Transposable elements
• DNA sequences that can move to new sites in the genome
• More than half the DNA in many eukaryotes
• Two major classes:
 Transposons: Move via a DNA cut and paste mechanism
 Retrotransposons: Move via an RNA intermediate
• Potentially disruptive – can eliminate gene function. Therefore, usually
epigenetically silenced
• Federoff (2012) argues that TE’s, via altering gene regulation, account for the
“evolvability” of the “massive and messy genomes” characteristic of higher plants
 Create new genes
 Modify genes
 Program and re-program genes
• Transposition events lead to genome expansion and explain the C value paradox
Transposable elements
Transposition events lead to genome expansion and
explain the C value paradox
TEs nested within TEs nested within TEs
Fig. 6.The arrangement of retrotransposons in the maize
adh1-F region.
N V Fedoroff Science 2012;338:758-767
Published by AAAS
Fig. 7.The organization of the sequence adjacent to the
bronze (bz) gene in eight different lines (haplotypes) of
maize.
N V Fedoroff Science 2012;338:758-767
Published by AAAS
Transposable elements
• 85% of the maize genome consists of transposons
• Transposition events are in real time: differences
between maize inbreds
• Transposons can move large bocks of intervening DNA
• Transposases are the products of the most abundant
genes on earth
Transposable elements
~ 24% of the cacao genome
~ 21% of the Fragaria genome
~68,000 TE-related sequences in cacao
“Gaucho” is a retrotransposon ~ 11Kb in length and
present ~1,000 times
“The lack of highly abundant LTR transposons is likely to
be the reason F. vesca has a relatively small-size genome”
Genome architecture and evolution
Plant
#genes (est)
2n = _x = _
Genome size
Arabidposis thaliana
27,000
2n = 2x = 10
135 Mb
Fragaria vesca
35,000
2n = 2x = 14
240 Mb
Theobroma cacao
29,000
2n = 2x = 20
415 Mb
Zea mays
40,000
2n = 2x = 20
2,300 Mb
Pinus taeda
50,000
2n = 2x =24
23,200Mb
??
2n = 8x = 40
148,852Mb
Paris japonica