Bi6589 Methods of plant taxonomy

Faculty of Science
Spring 2017
Extent and Intensity
0/2/0. 2 credit(s). Type of Completion: z (credit).
Teacher(s)
Mgr. Petr Šmarda, Ph.D. (seminar tutor)
Guaranteed by
Mgr. Petr Šmarda, Ph.D.
Department of Botany and Zoology – Biology Section – Faculty of Science
Contact Person: Mgr. Petr Šmarda, Ph.D.
Supplier department: Department of Botany and Zoology – Biology Section – Faculty of Science
Prerequisites (in Czech)
! B6589 Methods of plant taxonomy
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
Theoretical and practical introduction to basic laboratory, molecular biological and bioinformatic methods of plant biosystematics.
Learning outcomes
Students will acquire the theoretical knowledge of basic laboratory, molecular biological and bioinformatic methods of plant biosystematics.
Students will acquire basic practice in the molecular biological, cytometric and karyological laboratories.
Students will be able to process raw sequence data or data from fragmentation analyzes and to choose and use a suitable bioinformatics tool to analyze them (e.g. to construct phylogeny, to perform selection analysis or analysis of genetic diversity of species and populations).
Syllabus
  • 1) Introductory lesson
    - Syllabus, training of students for work in the laboratory
    2) Isolation of nucleic acids
    - Basic principles of DNA / RNA isolation; CTAB isolation, isolation using a commercial kit
    - Practical exercises
    3) PCR
    - Principle of the polymerase chain reaction (PCR) method and its modifications
    - Practical exercises
    4) Electrophoresis
    - Principles, variants, evaluation of electrophoretic gels
    - Practical exercises
    5) Flow cytometry
    - Principles of flow cytometry and its application in determining the genome size, AT/GC base ratio in the genome, degree of ploidy, endopolyploidy and the reproductive system (sexual vs. apomixis)
    - Practical exercises
    6) Stomata and karyology
    - Nucleotypic effect
    - Methods of cell size measurement (stomata)
    - Counting of chromosomes
    - Practical exercises
    7) Basics of working with sequences
    - Principles of sequencing techniques: Sanger sequencing, New Generation Sequencing (NGS)
    - Sequence databases (GenBank, Blast), sequence file formats
    - Fundamentals of work with sequences in the MEGA program (coding and non-coding sequences, nucleotide and amino acid sequences, translation, genetic code)
    - Practical exercises
    8) Sequence Alignment
    - Basic principles of alignment methods
    - Alignment of nucleotides, amino acids, codons
    - Aligning software and web interfaces (MEGA, PRANK, GUIDANCE, BAli-Phy)
    - Practical exercises
    9) Construction of phylogenetic trees, analysis of selection modes
    - Principles of the main methods (Neighbor-joining, maximum parsimony, maximum likelihood, Bayesian methods)
    - Dating phylogenetic trees using fossils
    - Analysis of selection modes acting on coding genes
    - Practical exercises
    10) Molecular markers for population analysis
    - Types of molecular markers; dominant x codominant markers
    - Example studies
    - Working with fragmentation analysis data
    - Software
    - Binary matrix creation
    11) Fundamentals of Population Analysis I
    - PCoA, tree methods
    - Genetic diversity x divergence
    - Spatial structure of populations (AMOVA, spatial autocorrelation)
    12) Fundamentals of Population Analysis II
    - Work in STRUCTURE software, data interpretation
    13) METACENTRUM
    - Utilization of METACENTRUM computational capacities in cases of large data files and computational time-consuming tasks. Scripts for selected software
    - turning in semestral works/protocols
Literature
  • HEYWOOD, V. H. Modern methods in plant taxonomy. 1st ed. London & New York: Academic Press, 1968, 312 pp. ISBN 68-9103. info
Teaching methods
Teaching takes the form of theoretical lectures and practical exercises. Practical methods are explored by students in the laboratory and by working with selected software. Students will regularly prepare homeworks, the fulfillment of which is a prerequisite for entering the next lesson, as homework often involves preparing the data needed for the next lesson.
Assessment methods
To get the credit for the course, students have to elaborate two protocols from processing of raw data (e.g., from sequences to a dated phylogenetic tree or from rough AFLP data to the genetic structure of the population visualized in the STRUCTURE program) and interpret these analyzes. To pass the course attendance is required in classes. Two absences are possible. However, in the case absences, the obligation to prepare a homework for the next lesson remains.
Language of instruction
Czech
Further Comments
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2003, Spring 2004, Spring 2005, Spring 2006, Spring 2007, Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, spring 2018, Spring 2019, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.
  • Enrolment Statistics (Spring 2017, recent)
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