Target enrichment for plant/animal systematics -
methodological workshop
9th - 17th 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
This schedule is preliminary only and might slightly change as we are preparing the course...
Day 1
General introduction
Theory - library preparation - presentation
Theory - target enrichment principle & discussion -
presentation
Wet lab work demonstration (DNA sonication...) - basic 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
Independent work on paper of choice about target enrichment in plant/animal
systematics - create shared presentation
here
Day 3
Theory - approaches for data analysis - presentation
Computer work with the data (HybPiper etc.) -
presentation
Gene trees vs. species tree -
presentation
Day 4
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)
Theory - discordance, networks, hybridization - presentation
Day 6
Student presentations - papers of their choice - put your presentation
here
Group work/discussion - discussion of tools & approaches based on
Joyce et al. 2025 paper - create shared presentation
here
Day 7
Plastome assembly -
presentation,
HybPhyloMaker with chloroplast data (instructions), how to run FastPlast on MetaCentrum (txt)
Optional - wrap up, 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 ...