Genome architecture and evolution Key considerations: DNA…RNA…Protein Chromosomes C value paradox Gene regulation Epigenetics Transposable elements

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

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

DNA …………mRNA………….Protein Autopolyploid AAAA Allopolyploid AABB Polyploidy Formula Genome Haploid # genes 2n = 2x =14 AA A 30,000 2n = 4x = 28 AAAA 60,000 2n = 2x = 14 BB B AABB AB

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. 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 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

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] 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’

DNA ……….………. mRNA……….……….Protein Gene regulation DNA ……….………. mRNA……….……….Protein Transcription Developmental Temporal Spatial

40% of all human disease-related SNPs are OUTSIDE of genes 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: RNAi 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

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;338:758-767 Published by AAAS

The organization of the sequence adjacent to the bronze (bz) gene in eight different lines (haplotypes) 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;338:758-767 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 2,300 Mb Pinus taeda 50,000 2n = 2x =24 23,200Mb Paris japonica ?? 2n = 8x = 40 148,852Mb