Post on 19-Dec-2015
Genome architecture and evolution
Key considerations:• DNA…RNA…Protein • Chromosomes• C value paradox• Gene regulation• Epigenetics• Transposable elements
DNA ……….………. mRNA……….……….Protein
Plant Estimated # genes
Arabidposis thaliana 27,000
Fragaria vesca 35,000
Theobroma cacao 29,000
Zea mays 40,000
TranscriptiontRNArRNA
Translation
DNA …………mRNA………….Protein
Polyploidy Autopolyploid AAAAAllopolyploid AABB
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
ChromosomesPlant 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 ??
ChromosomesF. 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 2 3 4 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
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? Dark matter…
Shining a Light on the Genome’s ‘Dark Matter’
Gene regulation
The dark matter is conserved and therefore must have a functionDNA 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. RNAi2. lincRNA
Epigenetic factors
40% of all human disease-related SNPs are OUTSIDE of genes
Pennisi, E. 2010. Science 330:1614.
EpigeneticsEpi = “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: VernalizationIf a specific allele is present, the plant will not transition from a vegetative to a reproductive state until sufficient cold units are received
Observe changes in phenotype without changes in genotype - due to alternative regulation ( 0 – 100%) of the gene
Epigenetics
Methylation expression
Acetylation expression
Observe changes in phenotype without changes in genotype - due to alternative regulation ( 0 – 100%) of the gene
RNA interference - RNAi: targeted degradation of specific mRNALong non-coding RNA - lncRNA: X chromosome inactivation
Epigenetics
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
Transposition events lead to genome expansion and explain the C value paradox
TEs nested within TEs nested within TEs
Transposable elements
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
• 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”
Transposable elements
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
Paris japonica ?? 2n = 8x = 40 148,852Mb