RepeatExplorer Workshop 2022

Programme

Tuesday (May 24)

• 8:00 – 9:00 Registration
• 09:00 Principles and history of RepeatExplorer J. Macas
• 10:00 Diagnostic features of repetitive elements – Part I P. Neumann
• 10:30 Coffee break
• 11:00 Diagnostic features of repetitive elements – Part II P. Neumann
• 11:15 RepeatExplorer tools for genome annotation P. Novák
• 12:30 Lunch
• 13:30 – (18:00) Practical training I J. Macas, P. Novák, P. Neumann
  • Basic Protocols 1-4: troubleshooting & advanced data analysis
• 19:00 – 22:00 Dinner at CITYgastro restaurant

Wednesday (May 25)

• 8:30 – 12:30 Short presentations of workshop participants
  • Nicola Schmidt (Technische Universität Dresden, Germany) – The fancy ones are spotted first: an update on repeats in beets
  • Ludwig Mann (Technische Universität Dresden, Germany) – Comparative repeat analysis of saffron (Crocus sativus) and its progenitor species
  • Zirlane Portugal da Costa (University of Sao Paulo, Brazil) – The repetitive portion of Passifloraceae genomes
  • coffee break
  • Pol Fernández Mató (Institut Botànic de Barcelona, Spain) – Understanding genus wide genome size differences in Phoradendron
  • Yennifer Mata-Sucre (Federal University of Pernambuco, Brazil) – Insight into the evolution of the repetitive fraction of the monocentric genus Juncus
  • Nusrat Sultana (Technische Universität Dresden, Germany) – Development of molecular cytogenetics tools for the characterization of mango (Mangifera indica)
• 12:30 Lunch
• 13:30 – (18:00) Practical training II – Genome annotation tools
  • using RE output for annotating genome assemblies
  • REXdb and DANTE
  • structure-based annotation of complete LTR-retrotransposons

Thursday (May 26)

• 8:30 – 12:30 Short presentations of workshop participants
  • Matej Lexa (Masaryk University, Brno, Czech Republic) – TE-greedy-nester: a tool to detect nested LTR-TEs in assembled genomes
  • Monika Čechová (Masaryk University, Brno, Czech Republic) – HiC-TE: a Nextflow pipeline to study repeat interactions in the 3D genome
  • Sophie Maiwald (Technische Universität Dresden, Germany) – Hidden repeats: identifying non-autonomous LTR retrotransposons
  • Vratislav Peška (Institute of Biophysics, Brno, Czech Republic) – New telomeres and telomerases
  • coffee break
  • Camila do Nascimento Moreira (Universidade Estadual Paulista, Brazil) – Comparative analysis of repetitive content in genomes of a rodent and a fish species with and without B chromosomes
  • Veit Herklotz (Senckenberg Museum of Natural History Görlitz, Germany) – Repeatomic fingerprint – a statistical approach to track phylogenetic signals from comparative cluster analysis
  • Alice Krumpolcová (Institute of Biophysics, Brno, Czech Republic) – Reconstruction of phylogenies in liverworts (Marchantiophyta) using a repeatome fingerprint
• 12:30 Lunch
• 13:30 – (18:00) Practical training III – Advanced topics
  • reconstructing phylogenetic relationships based on repeat sequence similarities (Steven Dodsworth, University of Portsmouth, UK)
  • local installation and running RE tools from a command line
  • topics proposed by the participants & individual consultations