Course: Evolutionary genomics

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Course title Evolutionary genomics
Course code KMB/777
Organizational form of instruction Lecture
Level of course Master
Year of study not specified
Frequency of the course In academic years starting with an odd year (e.g. 2017/2018), in the winter semester.
Semester Winter
Number of ECTS credits 3
Language of instruction Czech
Status of course Compulsory-optional
Form of instruction Face-to-face
Work placements This is not an internship
Recommended optional programme components None
Lecturer(s)
  • Hobza Roman, RNDr. CSc.
  • Zrzavá Magda, RNDr. Ph.D.
Course content
1. Origin of life (Cosmological introduction. Atributes of life. Origins of life. Classical and modern abiogenesis. 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 (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.

Learning activities and teaching methods
Monologic (reading, lecture, briefing)
  • Preparation for classes - 30 hours per semester
  • Preparation for exam - 30 hours per semester
  • Class attendance - 30 hours per semester
Learning outcomes
The goal of the course is to provide an overview concerning opinions about origin of life, formation of first replicators on RNA basis, about origin and evolution of genetic code. Students will get familiar with present state of knowledge of genome structure and evolution, main mechanisms of genome formation, where especially genome dynamics will be stressed. Evolution of sexuality will be presented as well. Students will get a complex picture of strategies and methods of current genomics as well as its history.
The student will understand principles of genome evolution and its impact on the phenotype.
Prerequisites
basic understanding of genetics

Assessment methods and criteria
Written examination

To pass the exam, the student must score at least 60% of points from the final examination text.
Recommended literature
  • E. Kejnovský a R. Hobza: Evoluční genomika [Evolutionary genomics ] (textbook)..
  • Ryan Gregory: The Evolution of the Genome (2005). Elsevier..


Study plans that include the course
Faculty Study plan (Version) Category of Branch/Specialization Recommended year of study Recommended semester
Faculty: Faculty of Science Study plan (Version): Zoology (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Winter
Faculty: Faculty of Science Study plan (Version): Experimental Biology (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Winter