1

Junk DNAJunk DNA

domestic importeddomestic imported(e.g., dead genes) (e.g., retroviruses)(e.g., dead genes) (e.g., retroviruses)

2

Intergenicregions

(junkjunk)

Introns (junkjunk)Exons

1.5%1.5%

The genome is empty.The genome is empty.

3

Junk DNA =

98.5%

4

5

Why do similar species have different genome sizes?

Creation of Junk

Disposal of Junk

6

Hawaiian cricketDrosophila 165 MBLaupala 2,000 MB

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Segments of DNA Segments of DNA that do not repeat that do not repeat themselves are themselves are referred to asreferred to as single-single-copy copy or or uniqueunique DNADNA..

9

The proportion of the genome taken up by repetitive sequences varies widely among taxa:

Yeast ~20%Midge (Chironomus tetans) ~5%Newt (Necturus masculosus) ~90%Humans ~50%

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Localized repeated sequences

Most eukaryotic genomes contain tandemly arrayed, highly repetitive DNA sequences. These localized repetitive sequences can account for major portions of the genome.

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Kangaroo Rat (Dipodomys ordii)

50% of the genome consists of:

AAG 2.4 timesTTAGGG 2.2 times ACACAGCGGG 1.2 times

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40% of the Drosophila virilis genome consists of:

ACAAACT 1.1 timesATAAACT 3.6 timesACAAATT 3.6 times

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35% of the genome of Absidia glauca, which is only 9 times larger than that of E. coli, is made of repetitive DNA.

14

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Satellite DNA may be Satellite DNA may be extremely GC-rich or extremely GC-rich or extremely AT-richextremely AT-rich

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Low GC content in satellites: 1% in Cancer gracilis and C. antennarius.

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High GC content in satellites: 73% in Leishmania infantum and Chironomus plumosus

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Satellite DNA as fraction of Satellite DNA as fraction of total genometotal genome

Mammals Mammals 5-30% 5-30% Plants Plants 5-40%5-40%

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60% of the genome of60% of the genome of Drosophila Drosophila nasutoides consists of satellite DNA.nasutoides consists of satellite DNA.

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15% of the genome.

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Simple-tandem repetitive sequences_______________________________________________________Class Repeat size Array size (bp) (number of units)_______________________________________________________Satellites 2-2,000 >1,000

Minisatellites 9-100 10-100

Microsatellites 1-6 10-150_______________________________________________________

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Minisatellites & microsatellites are used in DNA fingerprinting(Variable Number Tandem Repeats, VNTR)

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24

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Dispersed repeatsDispersed repeats(1) (1) SINESINEss(2) (2) LINELINEss(3) retrovirus-like and (3) retrovirus-like and retrotransposon-like elementsretrotransposon-like elements(4) DNA-mediated transposable (4) DNA-mediated transposable

fossilsfossils

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Mobile elements Mobile elements or ex-mobile or ex-mobile elements in the elements in the human genome.human genome.

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Dispersed repetitive sequences in the human genome

LINE1 600,000 15%LINE2 271,000 5%Alu 1,300,000 10%MIR 400,000 3%Retroelements 5% DNA-transposable elements 2% unclassified 60,000 1%

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>1/3 of the human genome >1/3 of the human genome is derived from mobile is derived from mobile elements. elements.

The vast majority of these The vast majority of these sequences no longer sequences no longer possess the ability to move. possess the ability to move.

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Feature Name Number (base pairs) (%)

AluAlu Repeats Repeats 20,18820,188 562199816.3CpG Islands 536 575970 1.7HERV Repeats 255 160697 0.5Line1 Repeats 804332569139.4Line2 Repeats 638112735713.7LTR Repeats 848 256412 0.7MER Repeats 3757763390 2.2MIR Repeats 842610634193.1MLT Repeats 2483605813 1.8Other Repeats 2313625562 1.8Other Tandem Repeats 305 102245 0.3Dinucleotide Repeats 1775133765 0.4Trinucleotide Repeats 166 18410 0.1Quadranucleotide Repeats 404 47691 0.1Pentanucleotide Repeats 16 1612 0.0THE Repeats 304 93159 0.3

42.4%42.4%Chromosome 22Chromosome 22

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98%98% of the variation in genome size in apes is explained by the variation in repetitive sequences (heterochromatin).

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A summaryA summary

1.5%1.5%