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Course, academic year 2022/2023
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Target enrichment for plant systematics - methodological workshop - MB120C117
Title: Target enrichment for plant systematics - methodological workshop
Czech title: Target enrichment v rostlinné systematice - praktické cvičení
Guaranteed by: Department of Botany (31-120)
Faculty: Faculty of Science
Actual: from 2021
Semester: summer
E-Credits: 5
Examination process: summer s.:
Hours per week, examination: summer s.:0/8, C [DS]
Capacity: 15
Min. number of students: unlimited
Virtual mobility / capacity: no
State of the course: taught
Language: English
Note: enabled for web enrollment
Guarantor: Roswitha Elisabeth Schmickl, Ph.D.
Mgr. Tomáš Fér, Ph.D.
Class: Ultrapřesný sonikátor pro štěpení DNA/RNA pro příp
Původní předmět
Annotation -
Last update: Mgr. Tomáš Fér, Ph.D. (01.03.2021)
Practical course of phylogenomic methods focused on Hyb-Seq NGS method. The Hyb-Seq method combines
target enrichment and genome skimming of the genome. The course covers the theory, discussion of the newest
papers from the field, probe design, laboratory and computer part. Several methodological approaches to data
analysis, from raw data to species tree analysis, are demonstrated within the course. The lab part includes NGS
library preparation (using sonicator) and enrichment.

The course is established within the project CZ.02.2.69/0.0/0.0/18_056/0013322 with the name ‘ESF pro VŠ II na UK‘.
Literature -
Last update: Roswitha Elisabeth Schmickl, Ph.D. (01.03.2021)

Bleidorn C. (2017): Phylogenomics. An Introduction. Springer
Bromham L. (2016): An introduction to molecular evolution and phylogenetics. 2nd edition. Oxford University Press
Weitemier K .et al. (2014): Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics. Applications in Plant Sciences 2(9): apps.1400042

Requirements to the exam -
Last update: Roswitha Elisabeth Schmickl, Ph.D. (01.03.2021)

Short protocol about training dataset analysis.

Syllabus -
Last update: Roswitha Elisabeth Schmickl, Ph.D. (01.03.2021)

1. Theoretical part A: target enrichment
- full background, (diss)advantages of the method
- most important papers - discussion
- wetlab theory
- phylogenomics, gene trees/species tree

2. Theoretical part B: probe development
- probe design
- universal vs group specific probes
- software for probe development

3. Laboratory part
- library preparation including sonication
- size selection, quantification and pooling
- library enrichment

4. Computer practical - working with Hyb-Seq data using MetaCentrum
- HybPhyloMaker
- HybPiper

 

The course is established within the project CZ.02.2.69/0.0/0.0/18_056/0013322 with the name ‘ESF pro VŠ II na UK‘.

 
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