Lecture Summary February 14 2001: Genome Evolution

Genome size

Prokaryotes

Eukaryotes

What increases genome size

Polyploidization

Autopolyploid: During meiosis the genome doubles and then segregates into haploid genome sets (in the gametes). When this process goes wrong (e.g. stopping of the segregation through some chemicals or genetic defects) we can end up instead of having 4 haploid gametes with diploid gametes, these often endreduplicate and form a tetraploid organism.

Allopolyploid: By hybridizing two species A, B and endoreduplication one can form a tetraploid that contains 2 sets from species A and two sets from species B.

Polyploidisation is a common tool in plant breeding and almost all our crop plants are polyploid. The wheat we use for bread flower was created by a hybrid crossing between two diploid species with 14 pairs (2n=14) of chromosomes and an endoreduplication (2n=28), this allotetraploid hybrid (which is used for semolina flower (pasta)) then was crossed another diploid species with 2n=14. The resulting hybrid is hexaploid (2n=42).

Tetraploids (and other even-ploids) are normally fertile and produce viable offspring. Triploids (diploid gamete joined by a haploid gamete) normally are healthy individuals, but because in meiosis the chromsome pairing gets messed up, triploids are often sterile. This is used in production of seedless crop, such as bananas, water melons, grapes.

Gene duplications, Transposons

How much of the genome is used?

• single copy DNA (scDNA): these genes exist only as single copies and code for essential proteins.
• repetitive DNA: in many groups of species we can find sequences that are duplicated or exist in several copies, these can be found throughout the genome.
• highly repetitive DNA: small sequences pieces that exist in many hundreds to thousands copies. These or often found around the centromer or the telomers (the ends of the chromosomes).

The repetitive DNA is most non-coding.

Birds have a rather small genome that is remarkable similar in size among all birds. It is believed that because of their high metabolic rate (much higher than in many mammals and amphibians) copying large unused chunks of DNA would cause a fitness reduction. An alternative to this view would be that the small genome size in birds is just a historical accident, their closest living relative crocodiles have a genome that is not much larger than the birds.

Maintenance of genome size

Genome sizes vary widely among species, and even among closely related species, so one can wonder what maintains the genome size. Several hypotheses were put forward, and the case is still not decided, some of them most likely apply, at least partly

• Noncoding DNA performs essential function (Zuckerkandl 1976), deletions and additions will have a deleterious effect on fitness. it has been shown that this hypothesis is most likely wrong, because one can excise some parts of non-coding genomes and the organism still functions.
• Noncoding DNA is just junk (Ohno 1972), excess does not affect fitness.
• Nongenic DNA is a functionless "parasite" or "selfish" (e.g Doolittle and Sapienza 1980)
• DNA has a structural or nucleoskeletal function (Cavalier-Smith 1978).

GC-content

The contents of Guanine and Cytosine in DNA in many species has some typical frequency, it is often higher than what we would expect when all the mutations between the different nucleotides were equal. For example in bacteria, E. coli it is 50%, in Mycobacterium tuberculosis 67%, but in some it is very low (e.g. Clostridium 26%). Similar striking differences are seen also in eukaryotes: Gardia has about 80% GC content whereas Plasmodium falciparum <20% (Malaria causing organism). Several hypotheses were put forward and it seems that GC contents may be related to selection for thermal stability: codons with more GC code for more thermostable aminoacids. UV and radiation also produces dimers between T - T that produces a DNA defect. An alternative hypothesis is the one that the bias is caused by differences of the mutation rate from A and T to G and C.

We can explore these hypotheses using the genetic code. The expectation is that changes at the 3rd position are neutral because any change does not change the protein, but differences at the first, the second position will change the protein and may not be neutral. If the GC content is neutral we would expect the same ratio on all nucleotides in the codon. This ratio should be dependent on the overall GC content. The observation is that the third position follows a neutral expectation whereas the first and, even stronger, the second nucleotide show that the ratio in high GC content species is lower than we would expect.