1 Junk DNA domestic imported domestic imported (e.g., dead genes) (e.g., retroviruses)

2 Intergenic regions junk ( junk ) junk Introns ( junk ) Exons1.5% 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 cricket Drosophila 165 MB Laupala 2,000 MB

7

8 Segments of DNA that do not repeat themselves are referred to as single- copy or unique DNA.

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%

10 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.

11 Kangaroo Rat (Dipodomys ordii) 50% of the genome consists of: AAG2.4   times TTAGGG2.2   times ACACAGCGGG1.2   times

12 40% of the Drosophila virilis genome consists of: ACAAACT1.1   times ATAAACT3.6   times ACAAATT3.6   times

13 35% of the genome of Absidia glauca, which is only 9 times larger than that of E. coli, is made of repetitive DNA.

14

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

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

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

18 Satellite DNA as fraction of total genome Mammals 5-30% Plants 5-40%

19 60% of the genome of Drosophila nasutoides consists of satellite DNA.

20 15% of the genome.

21 Simple-tandem repetitive sequences _______________________________________________________ ClassRepeat size Array size (bp) (number of units) _______________________________________________________ Satellites2-2,000>1,000 Minisatellites Microsatellites _________________________________________________ ______

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

23

24

25 Dispersed repeats (1) SINEs (2) LINEs (3) retrovirus-like and retrotransposon-like elements (4) DNA-mediated transposable fossils

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

27 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%

28

29 >1/3 of the human genome is derived from mobile elements. The vast majority of these sequences no longer possess the ability to move.

30 Feature Name Number(base pairs) (%) Alu Repeats20,188 Alu Repeats 20, CpG Islands HERV Repeats Line1 Repeats Line2 Repeats LTR Repeats MER Repeats MIR Repeats MLT Repeats Other Repeats Other Tandem Repeats Dinucleotide Repeats Trinucleotide Repeats Quadranucleotide Repeats Pentanucleotide Repeats THE Repeats % Chromosome 22

31 98% 98% of the variation in genome size in apes is explained by the variation in repetitive sequences (heterochromatin).

32 A summary 1.5%