Key considerations Genes Chromosomes C value paradox Gene regulation Epigenetics Transposable elements DNA mRNAProtein Plant Estimated genes Arabidposis ID: 755604
Download Presentation The PPT/PDF document "Genome architecture and evolution" is the property of its rightful owner. Permission is granted to download and print the materials on this web site for personal, non-commercial use only, and to display it on your personal computer provided you do not modify the materials and that you retain all copyright notices contained in the materials. By downloading content from our website, you accept the terms of this agreement.
Slide1
Genome architecture and evolution
Key considerations:Genes ChromosomesC value paradoxGene regulationEpigeneticsTransposable elementsSlide2
DNA ……..……..mRNA……….…….Protein
Plant Estimated # genesArabidposis thaliana 27,000Fragaria vesca 35,000
Theobroma
cacao
29,000Zea mays40,000
Transcription
tRNArRNATranslation
Other RNAs?
Genes Slide3
DNA specifying a protein
200 – 2,000,000 nt (bp)
Coding region
promoter
Exon
Exon
Intron
Intron
Start
codon
Stop
codon
+1
Basal
promoter
5’UTR
Termination
signal
3’UTR
ORF
mRNA
CDS
Exon
Genes (classically..) Slide4
Chromosomes
Plant 2n = _X = _Arabidposis thaliana 2n = 2x = 10Fragaria vesca 2n = 2x = 14Theobroma
cacao
2n
= 2x = 20Zea mays2n = 2x = 20
F. vesca: 35,000 genes/7 chromosomes = 5,000 genes/chromosome? Slide5
Genes, chromosomes, and genomes
F. vesca: 2n = 2x = 14genome = 240 Mbaverage gene ~ 3kb 79,333 genes? 11,333 genes/chromosome?
35,000 genes….. ~ 5,000 genes/chromosome
What’s the rest of the genome???????
Slide6
C-value
paradox“Organisms of similar evolutionary complexity differ vastly in DNA content”Federoff, N. 2012. Science. 338:758-767.1 pg
= 978 MbSlide7
The
C-value
paradox
Fedoroff
Science 2012;338:758-767Slide8
C-value
paradoxPlant Genome size # GenesArabidposis thaliana 135 Mb27,000Fragaria
vesca
240 Mb35,000Theobroma cacao 415 Mb
29,000Zea mays2,300 Mb40,000
Pinus taeda23,200Mb50,000Paris japonica148,852Mb??Slide9
C-value
paradoxJunk???????
Shining a Light on the
Genome’s
‘Dark Matter’Slide10
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: RNAilncRNA
40% of all human disease-related SNPs are OUTSIDE of genes
Pennisi
, E. 2010. Science 330:1614. Slide11
Observe changes in phenotype without changes in genotype - due to alternative regulation ( 0 – 100%) of the gene
Epigenetics
Methylation expression
Acetylation expression Slide12
Epigenetics
Facultative heterochromatin: Holoch and Moazed. 2015. Nature Genetics Slide13
Transposable elements
DNA sequences that can move to new sites in the genomeMore than half the DNA in many eukaryotesTwo major classes:Transposons: Move via a DNA cut-and-paste mechanismRetrotransposons: Move via an RNA intermediatePotentially disruptive – can eliminate gene function. Therefore,
usually
epigenetically silencedSlide14
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 genesModify genesProgram and re-program genes Transposition events lead to genome expansion and help to explain the C value paradox Slide15
Transposition events lead to genome expansion and help to explain the C value paradox: TEs nested within TEs nested within TEs
Transposable elementsSlide16
The
arrangement of
retrotransposons
in the maize adh1-F
region
N V Fedoroff Science 2012;338:758-767
Published by AAAS
Transposable elementsSlide17
Sequence
adjacent to the bronze (
bz
) gene in
different
lines
of maize
N V Fedoroff Science 2012;338:758-767
Published by AAAS
Transposable elementsSlide18
85% of the maize genome consists of transposons
Transposition events are in real time: differences between maize inbredsTransposons can move large bocks of intervening DNATransposases are the products of the most abundant genes on earthTransposable elementsSlide19
~ 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 elementsSlide20
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 TEHoloch and Moazed. RNAi….Transposons held in check by epigenetic mechanisms Transposable elementsSlide21
Genome architecture and evolution
Plant #genes (est)2n = _x = _Genome size Arabidposis thaliana 27,000
2n = 2x = 10
135 Mb
Fragaria vesca 35,0002n = 2x = 14
240 MbTheobroma cacao 29,0002n
= 2x = 20415 MbZea mays40,0002n = 2x = 202,300 MbPinus taeda50,000
2n = 2x =2423,200MbParis japonica
??
2n = 8x = 40
148,852Mb
Wessler
on TEs