Evolution Genomesize

C-value (=size of genome) depends on organism

—> constant within a species

—> varies widely among species

Paradox: no strong correlation between complexity and genome size

bacterial smaller than eukaryotes

bacteria: 580 Kb to 13 Mb (20-30 fold size variation in prokaryotes)

eukaryotes: 8.8 Mb to 700 Gb (80.000 fold size variation)

In bacteria —> Yes!

In eukaryotes —> No

(some correlation e.g yeast<Drosophila<human, but range of variation <50 fold)

for DNA C ratio (human to yeast) —> 3.000/15 = 200

for genes G ratio (human to yeast) —> 25.000/6.000 = 4.2

—> most of C-value variation is due to amount of non-coding DNA

large regions of genome with no/very few genes

—> difficult to clone and usually not sequenced in genome projects

2%

distinct bands of DNA —> heavier / lighter than majority of genomic DNA.

Repeated (1.000 times a row) short sequences (2-2.000 bp) that have:

• high GC (heavier) content

• high AT (lighter) content

found in heterochromatic regions and around centromers

• Minisatellites: sequences of 9-100bp repeated 10-100 times

  —> in subtelomeric regions

• Microsatellites: very short sequences of 1.5 bp repeated 10-100 times

  • SRS = short repetitive sequences

  • STR = short tandem repeats

  • SSR = simple sequence repeats

  —> dispersed throughout chromosomes (in and around genes)

dinucleotide repated CA (50.000 copies)

DNA fingerprinting

• Fragile X-syndrome (CCG)

• Huntington’s disease (CAG)

• Schizophrenia (CAG)

• Myotonic Dystrophy (CTG)

many other neuromuscular disorders

pieces of DNA that can move within the genome and increase in number (jumping genes)

50% of human genome

Transposons, Retrotransposons

classified by their mechanism of transposition

• Conservative transposition -> Transposon (involve only DNA)

• Replicative transposition -> Transposon (involve only DNA)

• Retrotransposition -> Retrotransposon (requires RNA intermediate)

Retrotransposons

• Conservative transposition

  TE move from one place to another

  recombination between elements at different chromosomal locations (‘cut-and-paste)

  —> no increase

• Replicative transposition

  original element remains at donor site, while new copy inserted in new site (‘copy-and-paste’)

  —> copy number increases

• Retrotransposition

  TE transcribed to RNA —> reverse transcribed to cDNA —> inserts in new chromosomal loc (‘copy-and-paste’)

  —> copy number increases

2.500 - 7.000 bp long

autonomous

• terminal repeats at ends

• encode single gene (transposase)

• can move by themselves

non-autonomous

• terminal repeats at ends

• no transposase gene

• cannot move by themselves

• can move if another element in genome producing transposase

• no inserted repeats

• has transposase gene

• cannot move, but can cause non-autonomous elements to move

useful for experiments in organisms like Drosophila, e.g.:

transposase gene of a TE replaced with any gene

—> helper-element make transposase

—> insert gene into Drosophila genome

—> helper element removed

—> new gene becomes stable part of genome

• Active - have intact promoter

• transcribed

• can retrotranspose

‘Dead’ or ‘Dead On Arrival (DOA)’ - retroelements

• often shortened at 5’, when inserted in DNA

  —> remove promoter

  —> can not longer be transcribed / retrotransposed

—> under no selective constraint and accumulate mutations at random —> ‘junk-DNA’

previously functional genes, lost function due to mutation:

• stop codon into ORF

• insertion / deletion that disrupts reading frame

rare cases: lost function, due parasitic / symbiotic relationship with their host —> genes not needed —> lost due mutation (M. tuberculosis)

often arise through tandem duplication

—> entire section of DNA duplicated during replication

—> producing 2 copies of gene

if only 1 copy required: other copy accumulate mutations —> non-functional psuedogene

(or retrotransposed genes)

mRNA of nuclear gene is reverse transcibed into cDNA —> re-inserts into genome

uses reverse transcriptase + integrase enzymes encoded by retroelement

Key features:

• no introns present in ‘parental’ gene

• if recent, evtl poly-A sequence at 3’ end

• usually lacks promotor sequences (—> Dead-on-Arrival)

• expression level:

  highly-expressed genes have more mRNA —> greater chance of being reverse transcribed

• gene size:

  short mRNAs may retrotranspose better than long

• sequence-specific:

  primary sequence of some genes may be better for retrotransposition

mutational and selective forces affect genome size

major classes of explanation:

• adaptive

  non-coding DNA is functionally important to organism

• junk DNA

  most of non-coding DNA serves no purpose

  may event be parasitic/’selfish-DNA’

approach:

• Laupala sp. (Hawaiian crickets) have genome 11 times larger than Drosophila (genome small, almost no psuedogenes)

• Rates of DNA deletion estimated in both by comparing sequences of DOA transpoasble elements (similar to pseudogenes)

result:

• spontaneous DNA loss faster in Drosophila

  —> may explain why Dros. genome small and almost no pseudogenes (lost rapidly by deletion mutations)

• Grasshoppers (Podisma)

  • over 10X greater than Laupala

  • over 100X greater than Drosophila

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

—> Podisma very low rate of DNA loss

—> inverse correlation between genome size and rate of spontaneous DNA deletion holds for 3 insect groups with greatly diff genome sizees

Nuclear copies of mitochondrial genes = ‘new mites’

non-functional, bc:

• genetic code different between mitochondria and nucleus

• often lack promoter

• dont have signal seq to target to mitochondria

• Deletion rate: Dros > Lau > Pod

• Deletion size: Dros > Lau > Pod

• Genome size: Pod > Lau > Dros