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

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

DevelopmentalTemporalSpatial

DNA ……….………. mRNA……….……….Protein

Transcription

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