Evolutionary genomics
Eduard Kejnovský & Roman Hobza

1. Origin of life

Cosmological introduction. Atributes of life. Origins of life. Classical and modern abiogenesis. Urey-Miller experiment. 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 – old or young, functional relics of RNA world, are viruses alive? 

3. Small RNAs, RNA interference (RNAi)

History of RNAi research. The role of RNAi in evolution. The role of small RNAs in cell (siRNA, miRNA, piRNA), dicer and RISC complexes. Plants and animals: what is a difference in RNAi mechanism. The use of RNAi in genetic engineering.    

4. Evolution of genomes

Genome size and C value paradox. Minimal genome. Mechanisms of genome size increase, genome obesity in plants. Genome topography - gene organization in genomes, syntheny. Numbers of chromosomes in different species, the role of multiplication, chromosomal rearrangements, B chromosomes. Isochores.

 5. Polyploidization

Genome interactions in polyploids (genetic and epigenetic consequences), hybrid sterility. Polyploidy and speciation. Polyploidy in animals and plants. Polyploidy and ecology of species. Evolutionary consequences of polyploidization.

 6. Evolution of genes

First genes. Anatomy of genes. Origin of new genes. Mechanisms of evolution of new genes. Introns –first or late. Alternative splicing. Gene families, pseudogenes, orphans and numbers of genes. Horizontal transfer. Recently formed genes. Gene sizes. Interesting genes.

 7. Genome dynamics I.

Repetitive DNA as a dominant component of genome. Paradigm shift in genetics – genome is dynamic. Mobile genetic elements (transposable elements). Retroelements – retroviruses, retrotransposons, bacterial retrons. DNA transposones. Origin and evolution of transposones.

 8. Genome dynamics II.

Function of transposable elements. Coevolution of  transposable elements and their host: conflict-compromise-cooperation. Host defense – transposone silencing. Transposable elements useful for host – domestication of transposable elements. Explosive amplification of transposable elements in evolution of mammals. Tandem repeats. Microsatellites. Genomes of organelles as relics of prokaryotic organisms. Discovery of promiscuous DNA. Gene migration from organelles to nucleus. Mechanisms of gene transfer. Genomes of organelles and intracellular parasites.

9. Evolution of sexual reproduction

Recombination and sexuality. „Negative“ effects of lost of recombination  – Mullers ratchet, genetic hitchhiking, background selection. Haploidy versus diploidy. Advantages and disadvantages of sexual reproduction.

10. Consequences of sexual reproduction

Sex determination, origin and evolution of sex chromosomes in plants and animals. History of understanding of processes leading to sexual reproduction and evolution of sex chromosomes. Human sex chromosomes – puzzling DNA palindromes on sex chromosomes, gene rescue as a defense against degeneration, evolutionary strata on Y chromosome. Papaya – sex chromosomes at the beginning of evolution. Alternative pathways of sex determination.

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 – methods and strategies

Genome mapping. Microdissection of cells and chromosomes.  Genome libraries, sequencing. Integration of genetic and physical maps. Current methods in genome sequencing. Eco-tilling.

13. History of genomics

Avery versus Watson and Crick. Watson versus Venter. Rise and fall of model organisms. Genome projects, main databases.