Evolution of Genome Size

There is not a strong correlation between organism complexity and genome size (C-value)

Large genomes may not necessarily gain DNA faster; they may simply lose unnecessary DNA much more slowly

inverse correlation:

large genome ~ 1/spontanious deletion rate

• bacteria genomes: 580 Kb to 13 Mb,

  -> 20–30-fold size variation within prokaryotes

• A few eukaryotic genomes fall in the size range of bacteria (e.g. yeast), but most are much larger.

• eukaryotic genomes: 8.8 Mb to ≈700 Gb

  -> 80,000-fold size

• in bacteria correlated

• in eukaryotes not really, but a bit more than for genome size and complexity:

• variation in eukaryotic gene number is estimated to be <50 fold

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

In general, there is a steep decline in the fraction of genic DNA (coding DNA) as genomes become larger.

large regions of the genome with no (or very few) genes. It is difficult to clone and usually not sequenced in genome projects

Satellite DNA (2-2000bp, 1000’s x rep)

Minisatellites (9-100bp, 10-100 x rep)

Microsatellites (1-5bp, 10-100 x rep)

• These are repeated sequences that have either

  high GC (heavy) or high AT (light) content

• 2–2000 repeated 1000’s of times in a row

• in heterochromatic regions and around centromeres

FIRST IDENTIFIED with density centrifugation:

-> distinct bands of DNA that are heavier or lighter than the majority of genomic DNA

• 9–100 bp repeated 10–100 times.

• In subtelomeric regions and (rarely) dispersed throughout chromosomes

= SRS “short repetitive sequences”

= STR “short tandem repeats”

= SSR “simple sequence repeats”

• 1-5 bp repeated 10–100 times

• dispersed throughout chromosomes, often in and around genes

• very high mutation rates (changing the repeat number, polymerase “slips“) -> useful in pop. genetics and DNA fingerprinting

• eg: dinucleotide short tandem repeat CA is very common in the human genome (≈50,000 copies)

inherited diseases. Some examples include:

• Fragile-X syndrome (CCG)

• Huntington’s disease (CAG)

• Schizophrenia? (CAG)

• Myotonic Dystrophy (CTG)

… plus many other neuro-muscular disorders

= interspersed repetitive elements

= jumping genes

• pieces of DNA that can move within the genome and increase in number

• About 50% of the human genome is made up of TEs and remnants of TEs

transposons

2,500-7,000 bp long, DNA -> DNA

can be autonomous or non-outonomous (need helper element)

• Conservative transposition – cut-and-paste”

  • does not necessarily lead to an increase in copy number/ Copy number can be increased through recombination between elements at different chromosomal locations.

    -> equal number of gains and losses.

• Replicative transposition – “copy-and-paste”

  • original element remains at donor site, while a new copy inserts into a new site

    -> copy number is increased

  
  

retrotransposons

active or dead

• Retrotransposition – “copy-and-paste”

  • the TE is transcribed into RNA, then reverse transcribed into cDNA, then inserts into new chromosomal location. The copy number increases.

  • typically the most abundant in a genome

autonomous

• have terminal repeats at the ends, encode a single gene (transposase)

  -> can move by themselves.

  
  

non-autonomous

• have terminal repeats at ends, but no transposase gene. -> -> Cannot move by themselves,

  -> but can move if there is another element in the genome producing transposase: Helper element

  
  

“Helper element”

• does not have inverted repeats, but does have transposase gene. Cannot move, but can cause non-autonomous elements to move.

-> These are very useful for experiments in organisms like Drosophila.

• transposase gene of a TE can be replaced with any gene

• a helper element can be used to make transposase and insert this gene into the Drosophila genome

• then the helper element is removed so the new gene becomes a stable part of the genome

Active

• have intact promoter, are transcribed, and can retrotranspose

“Dead” or “Dead On Arrival (DOA)”

• retroelements are often truncated at the 5’ end when inserting into DNA.

  -> they lose their promoter and no longer can be transcribed or retrotransposed.

  = “junk DNA” that is under no selective constraint

  -> accumulate mutations at random

• Previously functional genes

• Most cases: gene duplication

• have lost their function due to mutation

  eg:

  • mutation that introduces a stop codon into the ORF

  • InDel that disrupts the reading frame

  • In rare cases: LoF due to parasitic or symbiotic relationship with their host

    -> genes are not needed and can be lost through mutations (ex. pathogenic bacteria, M. tuberculosis).

unprocessed

• through tandem duplication: an entire section of DNA is duplicated during replication

  -> two copies of a gene (adjacent in the genome)

• If only one copy is required, the other copy may accumulate mutations and become a non-functional pseudogene

processed = or retrotransposed genes

• through reverse transcription of mRNA of a nuclear gene into cDNA,

• then re-inserts into the genome

• Most likely this uses the reverse transcriptase and integrase enzymes encoded by a retroelement.

• Does not have introns present in the “parental” gene

• If recent, may have a poly(A) sequence at 3’ end

• lacks promoter sequences

  (thus “Dead on arrival” = not expressed)

some more, depends on:

• Expression level – highly-expressed genes have more mRNA and thus have a greater chance of being reverse transcribed.

• Gene size – short mRNAs may retrotranspose better than long mRNAs.

• Sequence specific – the primary sequence of some genes may be better for retrotransposition.

2 ideas

• adaptive – the non-coding DNA is functionally important to the organism

• junk DNA – most of the non-coding DNA serves no purpose. It may even be parasitic or “selfish DNA”.

inverse correlation:

large genome ~ low deletion rate

genome size: Pod (20Gbp) > Lau (1.9Gbp) > Dro (168Mbp)

deletion rate: Dro > Lau (1.9Gbp) > Pod

deletion size: Dro > Lau (1.9Gbp) > Pod

Nuclear copies of mitochondrial genes

= pseudogenes in the nuclear DNA that are derived from mitochondrial genes

grasshopper has many of them (Podisma)