Altklausur

20-61

transposon wird eingesetzt

has many pseudogenes in nuclear DNA, derived from mitochondrial genes (NUMTs)

Drosophila

Of 289 human disease genes:

• 230 (80%) were found in the fly

• 212 (73%) were found in the worm

• 120 (42%) were found in yeast

256

hyperthermophile

RNA-seq, microarrays

580Kb

480 gene

Lepra mehr pseudogenes

M. tuberculosis: 4000 genes, 6 pseudogenes

M.leprae: 1600 genes, 1100 pseudogenes

Molecular Function, Cellular component, biological process, genomic location

Cytochrom P450, Cyp6gl

Olfactory Receptor (OR) genes

Y

Homolog - similar sequence, derived from same common ancestral

Ortholog - homologs derived through speciation

Paralog - homologs derived through gene duplication

Basic Local Alignment Search Tool

—> find subsequences with best possible alignment

scored with E-value

BLAST-like alignment tool

faster algorithm based on 11-mers or 4-mers to find matches

previously encoding genes —> Mutations —> non-functional

Carsonella (160 Kb, 182 genes)

Arabidopsis thaliana

25.000 genes, more than

• fly (14.000)

• worm (19.000)

• Human (21.000)

BUT: rice —> 40.000-50.000

98% homologs

M. genitalium, M. pneumoniae

results of studies: loci responsible for hybrid incompatibilites (hybrid male sterility) disproportinally found in X-chromosome

expectation: rate of adaptive evolution faster on X-chromosome

in males with 1 X-chromosome —> beneficial mutations

• less selective constraint

• more positive (sexual) selection

compare ratio of divergence and polymorphism at non-synonymous and synonymous sites.

For Drosophila

• MBG Dn/Ds)/(Pn/Ps) ≈ 2

• FBG ≈ 1.2

• UBG ≈ 0.9

• For X-linked MBG, (Dn/Ds)/(Pn/Ps) ≈ 3.4

16% of the genes in the genome:

• 11% of MBG are on the X

• 21% of FBG are on the X

• 16% of UBG are on the X

long stretches (100s of kb) of DNA with uniform %GC

High %GC = heavy isochores (H)

Low %GC = light isochores (L)

codons not used equally, some preferred. e.g:

• E.col CTG = 90%

• yeast TTG = 90%

measure: ENC, Fop

Effective Number of Codons

avg number of codons (20-61) to encode 20 amino acids

Low ENC = high codon bias

• can be applied to any species

• without prior knowledge

Frequency of Optimal Codons

optimal codons = highest frequency

High Fop = high codon bias

• species-specific

• requires that optimal codons are known

FOXP2 – humans with mutations in this gene have impaired speech and language skills.

also:

microcephalin – humans with mutations in this gene have primary microcephaly (small brain of ≈400 cm3). A normal human brain has a volume of ≈1,400 cm3.

ASPM – mutations in this gene also cause primary microcephaly in humans.

Ka = the number of nonsynonymous differences per nonsynonymous site

Ks = the number of synonymous differences per synonymous site

• Ka/Ks < 1: negative (purifying) selection

• Ka/Ks = 1: no selection; completely neutral evolution

• Ka/Ks > 1: positive selection

X-chromosome

bis zu etwa 50%

Deletion rate: Dros > Lau > Pod

Deletion size: Dros > Lau > Pod

Genome size: Pod > Lau > Dros

20 Gb

verly low rate of DNA loss

1-2% unterschied —> 20.000-25.000

5%

Afrika

TE insertion increases gene expression

cis-regulatorische sequenzdivergenz in upstream region

2-3 times higher expression in european than african

Yeast, 15 Mb total, 6,000 genes

Human, 3,000 Mb (3 Gb) total, 25,000 genes

For DNA, the C ratio (human to yeast) = 3,000/15 = 200

For genes, the G ratio = 25,000/6,000 = 4.2

C-Vlaue = size of genome

paradox —> not strong correlation btw organism complexity and genome size.

bands of DNA heavier/lighter

repeated sequences (1000) and short (2-2000bp)

• Minisatellites —> seq of 9-100 bp repeated 10-100 times

• Microsatellites —> seq of 1-5 bp repeated 10-100 times

2.500-7.000 bp

• genetic code is different between mitochondria and nucleus

• no promoter

• no signal sequence to target them to mitochondria

—> “Dead-on-arrival”