RepeatExplorer Workshop 2017

Programme

Tuesday (May 23)

• 8:30 – 9:30 Registration
• 09:30 Principles and applications of graph-based repeat clustering J. Macas
• 10:10 RepeatExplorer pipeline version 2.0 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 New tools N. Hoštáková, P. Novák
• 12:00 Lunch
• 13:30 – 14:00 (short presentation)Steven Dodsworth (Royal Botanic Gardens, Kew, UK) – Phylogenetic signal in repeat abundances: Angiosperm examples from tomatoes to orchids
• 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 24)

• 9:00 – 12:00 Short presentations of workshop participants
  • Gustavo Souza (Federal University of Pernambuco, Brazil) – Using genomic repeat abundance and cytogenomic approaches to infer phylogenetic relationships in Caesalpinia sensu lato (Fabaceae)
  • Maria Gonzalez (Instituto Multidisciplinario de Biologia Vegetal, Argentina) – Chromosome evolution of South American and Antarctic species of Deschampsia (Poaceae)
  • Beatrice Weber (Dresden University of Technology, Germany) – Chromoviruses in the genome of sugar beet Beta vulgaris
  • Danijela Greguraš (Institute of Botany, Prague, Czech Republic) – Repeatome dynamics in the earliest evolutionary stages of apomictic plants
  • Alevtina Ruban (IPK Gatersleben, Germany) – Why does the genome size differ between roots and shoots in some Aegilops speltoides plants?
  • Nusrat Sultana (Omer Halisdemir University, Turkey) – Bioinformatics and molecular characterization of Vaccinium corymbosum genome
  • Christiaan Henkel (Leiden University, Netherlands) – Can we sequence a repeat-rich, 35 Gbp tulip genome?
• 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 25)

• 9:00 – 12:30 Short presentations of workshop participants
  • Amanda Grusz (University of Minnesota Duluth, USA) – Genome evolution in the fern family Pteridaceae
  • Andrew Leitch (Queen Mary University of London, UK) – The placement of Gnetales amongst seed plants
  • Sonia Garcia, Daniel Vitales (Institut Botanic de Barcelona, Spain) – Concerted evolution under the microscope: rDNA arrangements in three Asteraceae genera
  • Ales Kovarik (Institute of Biophysics, Brno, Czech Republic) – Higher-order repeat structure of 5S rRNA genes of Esox lucius (fish) determined from long PacBio reads
  • Tanja Vojvoda Zeljko (Rudjer Boskovic Institute, Croatia) – Characterization of transposable elements containing internal tandem repeats in the genome of the Pacific oyster Crassostrea gigas
  • Rodolpho Menezes (Universidade de São Paulo, Brazil) – Cytogenetics meets phylogeography and phylogenomics: exploring the evolutionary history of Neotropical swarm-founding social wasps
  • Abhijeet Shah (University of Jena, Germany) – Mobile DNA in Acrididae grasshoppers
• 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
  • SeqGrapheR – visualization and annotation of the cluster graphs
  • advanced topics, troubleshooting