RepeatExplorer Workshop 2019

Programme

Tuesday (May 21)

• 8:00 – 9:00 Registration
• 09:15 Principles and applications of graph-based repeat clustering J. Macas
• 10:00 RepeatExplorer pipeline P. Novák
• 10:30 Coffee break
• 11:00 REXdb database and transposon classification using conserved protein domains P. Neumann
• 11:30 Using RepeatExplorer output for repeat annotation and quantification J. Macas
• 11:50 Additional RE tools P. Novák
• 12:30 Lunch
• 13:30 – (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
• 19:00 – 22:00 Dinner at CITYgastro restaurant

Wednesday (May 22)

• 8:30 – 12:30 Short presentations of workshop participants
  • Steven Dodsworth (University of Bedfordshire, UK) – Genome size and repeat dynamics across populations of Fritillaria amabilis (Liliaceae)
  • Lucia Campos-Dominguez (Royal Botanic Gardens Edinburgh and University of Edinburgh, UK) – Using RepeatExplorer to understand genome dynamics in Begonia
  • Santelmo Vasconcelos (Vale Institute of Technology, Brazil) – Repetitive DNA and genome evolution in Philodendron s.l.
  • Sidonie Bellot (Royal Botanical Gardens Kew, UK) – Repetitive elements in palms (Arecaceae)
  • Tony Heitkam (Technische Universität Dresden, Germany) – Tandem repeat evolution during Chenopodium speciation and formation of the allotetraploid crop quinoa
  • Vildana Suljevic and Hanna Schneeweiss (University of Vienna, Austria) – Satellite DNAs and the evolution of chile pepper genomes
  • Ludwig Mann (Technische Universität Dresden, Germany) – A bioinformatic pipeline for the detection of extrachromosomal circular DNA (eccDNA) from NGS data
  • Aleš Kovařík (Institute of Biophysics, Brno, Czech Republic) – The utility of RepeatExplorer pipeline for indentification of plant hybrids and alloplyploids using clusters of 5S rDNA repeats
• 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 23)

• 8:30 – 12:30 Short presentations of workshop participants
  • Aretuza Sousa (Ludwig-Maximilians-Universität, Munich, Germany) – One step further on the understanding of why UV sex chromosomes do/do not recombine in liverworts, and how RepeatExplorer contributed to it
  • Kathrin Seibt (Technische Universität Dresden, Germany) – The Angio-SINE superfamily with a conserved 3’ domain is widely distributed across the Angiosperms and frequently associated with genes
  • Vratislav Peška (Institute of Biophysics, Brno, Czech Republic) – Comparative dissection of three giants, onion, garlic, and wild garlic
  • Jasna Puizina (University of Split, Croatia) – Analysis of repetitive DNA elements in Allium species
  • Mariana Baez (Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany) – Centromeric structure of the holocentric species Cyperus alternifolius (Cyperaceae) and Prionium serrata (Thurniaceae)
  • Nicola Schmidt (Technische Universität Dresden, Germany) – Characterization of the endogenous pararetrovirus beetEPRV3 in the genome of sugar beet (Beta vulgaris)
  • Mark Johnston (Dalhousie University, Canada) – Repetitive DNA content, intersexual selection and reproductive isolation among populations of Lobelia cardinalis
  • Horacio Naveira (Universidade da Coruña, Spain) – Revision of the evolution of satDNA families identified by genomic restriction digestion under the new light of genome-wide characterization from next generation sequence reads in lacertid lizard species
• 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