1. Genome architecture and evolution
Key considerations:
Genes
Chromosomes
C value paradox
Gene regulation
Epigenetics
Transposable elements

2. Genes Other RNAs? DNA ……..……..mRNA……….…….Protein Plant
Transcription
tRNA
rRNA
Translation
Plant
Estimated # genes
Arabidposis thaliana
27,000
Fragaria vesca
35,000
Theobroma cacao
29,000
Zea mays
40,000
Other RNAs?

3. Genes (classically..) DNA specifying a protein 200 – 2,000,000 nt (bp)
promoter
Coding region
Exon
Intron
Exon
Intron
Exon
Start
codon
Stop
codon
5’UTR
3’UTR
Basal
promoter +1
Termination
signal
ORF
mRNA
CDS

4. Chromosomes
Plant
2n = _X = _
Arabidposis thaliana
2n = 2x = 10
Fragaria vesca
2n = 2x = 14
Theobroma cacao
2n = 2x = 20
Zea mays
F. vesca: 35,000 genes/7 chromosomes = 5,000 genes/chromosome?

5. Genes, chromosomes, and genomes
F. vesca: 2n = 2x = 14
genome = 240 Mb
average gene ~ 3kb
79,333 genes? 11,333 genes/chromosome?
35,000 genes….. ~ 5,000 genes/chromosome
What’s the rest of the genome???????

6. C-value paradox “Organisms of similar evolutionary complexity
differ vastly in DNA content”
Federoff, N Science. 338:
1 pg = 978 Mb

7. The C-value paradox
Fig. 1.The C-value paradox. The range of haploid genome sizes is shown in kilobases for the groups of organisms listed on the left. [Adapted from an image by Steven M. Carr, Memorial University of Newfoundland]
Fedoroff Science 2012;338:

8. 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 ??

9. C-value paradox Junk??????? Shining a Light on the
Genome’s ‘Dark Matter’

10. 40% of all human disease-related SNPs are OUTSIDE of genes
Gene regulation
Pennisi, E 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:
RNAi
lncRNA

11. Epigenetics
Observe changes in phenotype without changes in genotype - due
to alternative regulation ( 0 – 100%) of the gene
Methylation expression
Acetylation expression

12. Epigenetics Facultative heterochromatin:
Holoch and Moazed Nature Genetics

13. 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

14. Transposable elements
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 help to explain the C value paradox

15. Transposable elements
Transposition events lead to genome expansion and help to explain the C value paradox:
TEs nested within TEs nested within TEs

16. Transposable elements
The arrangement of retrotransposons in the maize adh1-F region
Fig. 6.The arrangement of retrotransposons in the maize adh1-F region. The short lines represent retrotransposons, with the internal domains represented in orange and the LTRs in yellow. Younger insertions within older insertions are represented by the successive rows from the bottom to the top of the diagram. Small arrows show the direction of transcription of the genes shown under the long blue line that represents the sequence in the vicinity of the adh1 gene. [Adapted with permission from (102)]
N V Fedoroff Science 2012;338:
Published by AAAS

17. Transposable elements
Sequence adjacent to the bronze (bz) gene in different lines of maize
Fig. 7.The organization of the sequence adjacent to the bronze (bz) gene in eight different lines (haplotypes) of maize. The genes in this region are shown in the top diagram: bz, stc1, rpl35A, tac6058, hypro1, znf, tac7077, and uce2. The orientation of the gene is indicated by the direction of the green pentagon, pointing in the direction of transcription; exons are represented in dark green and introns in light green. Each haplotype is identified by its name and the size of the cloned NotI fragment. The same symbols are used for gene fragments carried by Helitrons (Hels), which are represented as bidirectional arrows below the line for each haplotype. Vacant sites for HelA and HelB are provided as reference points and marked by short vertical red bars. Dashed lines represent deletions. Retrotransposons are represented by yellow bars. DNA transposons and TAFTs (TA-flanked transposons), which are probably also DNA transposons, are represented by red triangles; small insertions are represented by light blue triangles. [Redrawn with permission from (113)]
N V Fedoroff Science 2012;338:
Published by AAAS

18. 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

19. 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”

20. Transposable elements
Reid and Ross. Mendel’s genes….An Ac/Ds-like 0.8 kb insertion: round vs. wrinkled peas
Transposon tagging – find genes by mutation due to TE
Holoch and Moazed. RNAi….Transposons held in check by epigenetic mechanisms

21. 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
2,300 Mb
Pinus taeda
50,000
2n = 2x =24
23,200Mb
Paris japonica ??
2n = 8x = 40
148,852Mb
Wessler on TEs