Programme

Preliminary workshop programme

Tuesday (May 22)

8:30 – 9:30 Registration
09:30 Principles and applications of graph-based repeat clustering (J. Macas)
10:10 RepeatExplorer pipeline  (P. Novák)
10:30 Coffee break
11:00 Using RepeatExplorer output for repeat annotation and quantification (J. Macas)
11:20 Transposon protein databases (P. Neumann)
11:40 Assembly annotation using Profrep and DANTE (N. Hoštáková)
12:00 Lunch
14:00 – (18:00) Practical training I (J. Macas, P. Novák, P. Neumann)

  • design of sequencing and repeat analysis experiments
  • introduction to Galaxy environment
  • quality control and pre-processing of NGS reads, dealing with various read formats
  • setting up clustering analysis
  • comparative clustering of multiple samples

Wednesday (May 23)

9:00 – 12:00 Short presentations of workshop participants

  • Lucia Campos-Dominguez (Royal Botanical Garden Edinburgh, UK) – Using Repeat Explorer to find the genomic factors driving speciation in Begonia
  • Steven Dodsworth (University of Bedfordshire, UK) – Repeat dynamics in the largest diploid angiosperms, Fritillaria (Liliaceae)
  • Floris C. Breman (Wageningen University, Netherlands) – The Pelargonium repeatome as a ‘DNA barcode’
  • Hanna Schneeweiss (University of Vienna, Austria) – Repeat dynamics in wild and cultivated chile peppers (genus Capsicum)
  • Daniel Vitales (Institut Botànic de Barcelona, Spain) – Transposon dynamics and chromosome reorganizations drive genome size evolution in Anacyclus
  • Veit Herklotz (Senckenberg Museum for Natural History Görlitz, Germany) – Characterization of CANR4 satellite repeat in roses
  • Danijela Greguraš (Institute of Botany, Pruhonice, Czech Republic) – Characterization of satellite and centromeric repeats in genus Hieracium
12:30 Lunch
13:30 – (18:00) Practical training II

  • identification of satellite DNA using TAREAN
  • understanding RepeatExplorer output
  • cluster annotation and repeat composition of the genome
  • comparative clustering of multiple species – data interpretation
  • repeat quantification (principles, sensitivity and reproducibility)
  • design of hybridization probes based on RE output

Thursday (May 24)

9:00 – 12:30 Short presentations of workshop participants

  • Andrew Leitch (Queen Mary University of London, UK) – The phylogenetic placement of Gnetales is important to understand patterns of genome evolution across seed plants: insights from Gnetum montanum genome 
  • Sonia Garcia (Institut Botànic de Barcelona, Spain) – Ribosomal DNA arrangements in Asteraceae: variability of 5S and 35S examined with TAREAN and RepeatExplorer
  • Aleš Kovařík (Institute of Biophysics, Brno, Czech Republic) – Diversity of rDNA repeats in gymnosperms analysed by Repeat Explorer and other tools
  • Vratislav Peška (Institute of Biophysics, Brno, Czech Republic) – Telomeres – current challenges
  • Diogo C. Cabral-de-Mello (UNESP-Universidade Estadual Paulista, Brazil) – Satellite DNAs and sex chromosomes evolution in Orthoptera
  • Nils Pilotte (Smith College, Northampton, USA) – Tropical parasites: improved diagnostics utilizing repetitive targets
12:30 Lunch
13:30 – (18:00) Practical training III

  • combining repeat clustering with ChIP-seq data
  • identification and phylogenetic analysis of retrotransposon protein domains
  • Assembly annotation
  • advanced topics, troubleshooting