Eduard Kejnovský and Roman Hobza:Evolutionary genomics

Semestral course (2/0, spring semester) for students of the Faculty of Science, the Masaryk University

1. Origin of life

Cosmological introduction. Atributes of life. Origins of life. First genetic systems based on proteins or nucleic acids. Ribozymes. Origin of genetic code and proteosynthesis. Clay theory. Takeover of genetic information by DNA.  Panspermia and extremophiles. Silicon based life, other solvents than water.

2. Relics of RNA world and first genomes

Evidence for RNA world. Origin of RNA world. Evolutionary destiny of first RNA replicators. Relict of RNA world: tRNA (from replication to proteosynthesis), ribosome, spliceosome, snorposome, telomerase, srpRNA, gRNA, vaultRNA, RNaseP. Viruses and viroides – functional relics of RNA world. 

3. Evolution of genes

First genes. Anatomy of genes. Origin of new genes. Mechanisms of evolution of new genes. Introns –first or late.

4. Evolution of genomes

Genome size and C value paradox. Gene families, pseudogenes, orphans and number of genes. Gene organization in genomes. Numbers of chromosomes. Syntheny. The role of multiplications in genome evolution. RNA based regulation. Genome dynamics.

5. Selfish DNA

Proportion of repetitive DNA in genomes. Retroelements and DNA transposons.  Tandem repeats. Microsatellites.

6. Genomes of organelles and promiscuous DNA

Genomes of organelles as the remnants of prokaryotic organisms. Discovery of promiscuous DNA. Migration of genes to nucleus. Mechanisms of gene transfer. Genomes of organelles and intracellular parasites.

7. Interaction of genomes

Parasitic DNA. Restriction-modification systems as parasites. Viruses. Intracellular parasites (Mycoplasma, Rickettsia) and their genomes. Defense mechanism of trypanosoma. Sex reversal induced by Wolbachia. Molecular parasites of animals and plants. Arm races, red queen and the speed of evolution. Positive influence of the parasites on the host.

8. Evolution of sexuality: (A) Causes of sexuality: recombination and sexuality, degeneration in nonrecombining DNA – Mullers ratchet, genetic hitchhiking, background selection. Haploidy and diploidy.

9. Evolution of sexuality. (B) Consequences of sexuality:mechanisms of sex determination, origin and evolution of sex chromosomes – palindromes on the Y chromosome, evolutionary strata on the Y chromosome. Papaya – incipient sex chromosome.

10. The role of meiosis and recombination in genome evolution

What is a cause and what is a consequence.

11. Structure and evolution  of human genome

Basic characteristics. Gene families in human genome. Repetitive DNA. Comparison of human genome with mouse and chimpanzee genomes. Human evolution.

12. Genomics – strategies and methods

Mapping of genomes. Genomic libraries, sequencing and sequence analysis. Genome projects.