Bi8350 Evolutionary genomics

Faculty of Science
Spring 2016
Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Teacher(s)
doc. RNDr. Eduard Kejnovský, CSc. (lecturer)
RNDr. Roman Hobza, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Jiřina Relichová, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. RNDr. Eduard Kejnovský, CSc.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Tue 10:00–11:50 BFU
Prerequisites
Bi4020 Molecular biology
Basics of genetics and molecular biology
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
The course is focused on origin and evolution of genomes. The lectures have broad scope, first covering origin of life and first genomes, replicators based on RNA molecules (RNA world) and relics from RNA world. In this context we deal with the phenomenon of RNA interference and describe various types of small RNA (smRNA) molecules and mechanisms of their functioning in present genomes. Then, the lectures cover structure and mechanisms of evolution of viral, prokaryotic and eukaryotic genomes with a special focus on the role of polyploidization in evolution of plants and animals. Structure and mechanisms of formation of new genes will be presented. The special attention will be given to genome dynamics and the role of various repetitive DNA sequences like mobile genetic elements (transposones) and tandem repeats. We describe origin, evolution and consequences of sexuality and structure and evolution of sex chromosomes. The structure of human genome will be presented in the light of future trends of its research and student will be faced with ethical implications of the knowledge of human genome. Presented findings will be presented in context of the history of their discoveries as well as methods used. Special lesson will be focused on modern methods and strategies in genomics.
Syllabus
  • 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.

Literature
  • J. Maynard Smith and E. Szathmary: The major transitions in evolution (1995) Oxford University PressRyan Gregory: The evolution of the genome (2005) Elsevier T.A. Brown: Genomes (1999) BIOS Scientific Publishers, Oxford
  • KEJNOVSKÝ, Eduard and Roman HOBZA. Evoluční genomika. Elportál. Brno: Masarykova univerzita, 2006. ISSN 1802-128X. URL info
Teaching methods
Lectures in Czech language.
Assessment methods
Written test and oral exam.
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
Teacher's information
http://www.evolucnigenomika.cz
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.
  • Enrolment Statistics (Spring 2016, recent)
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