Target enrichment for plant/animal systematics - methodological workshop
9^th - 17^th June 2025

Roswitha Schmickl, Tomáš Fér, Vojta Zeisek, Soňa Píšová

Department of Botany, Charles University, Prague
Contact, registration: roswitha.schmickl@natur.cuni.cz

Course schedule (detailed) is here.

Day 1
General introduction to the course
Introduction to target enrichment & phylogenomics - presentation
Theory - Library preparation and target enrichment principle & discussion - presentation

Wet lab work demonstration (DNA sonication...) - basic protocol, full & detailed protocol
Independent/group work - preparing presentation of Ufimov et al. (2021) paper - create shared presentation here

Day 2
Wet lab work demonstration (library prep) - NEBNext Ultra II protocol, video, SPRI beads size selection protocol

Paper discussion - Ufimov et al. 2021

Day 3
Theory - Approaches for data analysis - presentation
Computer work with the data - HybPiper - presentation

Theory - Gene trees vs. species tree - presentation

Day 4
Theory - Gene trees vs. species tree - presentation (continue)

Computer work with the data - R code

Day 5
Computer work with the data - HybPhyloMaker - presentation, rapid instruction (PDF or txt)

Computer work with the data - HybPhyloMaker (continue)

Day 6
Student presentations - papers of their choice - put your presentation here

Theory & discussion - Assessment of phylogenetic conflict - presentation (partially based on Joyce et al. 2025 paper)

Day 7
Theory - Plastome assembly - presentation, HybPhyloMaker with chloroplast data (instructions), how to run FastPlast on MetaCentrum (txt)

Wrap up - presentation, varia, hands-on session with own data

Practical stuff

- bring your own laptop
- bring your own labcoat (if you have any) for the first two days. However, few labcoats are available in the lab as well.
- contact us immediatelly in case you do not have working access to eduroam wifi (we need to arrange another wifi for you)
- we expect you have already established access to MetaCentrum Grid Computing, if not go here for application. Let us know in case of troubles.
- the course might be easier for you if you look a bit at HybPiper and HybPhyloMaker documentation before entering the course
- essential paper about Hyb-Seq technique (Weitemier et al. 2014)

Thank you for participating ...