RepeatExplorer Workshop 2021

Programme

May 25

• 14:00 – 17:00 h RepeatExplorer: principles and applications
  • Opening the workshop & instructions (J. Macas)
  • RepeatExplorer pipeline and associated tools (P. Novak)
  • RepeatExplorer applications (J. Macas)
  • break
  • REXdb database and DANTE (P. Neumann)
  • Using RE output for repeat annotation and quantification (J. Macas)
  • Practical training I – assignment of tasks (P. Novak)

May 25 – May 31

• Practical training part I [conducted individually, based on the provided data and videotutorials]
  • Galaxy environment and RepeatExplorer server [VIDEO tutorial]
  • Protocol 1: Repeat analysis in a single species [VIDEO tutorial]
  • Protocol 2: Comparative repeat analysis in multiple species [VIDEO tutorial]

May 26

• 14:00 – 17:00 h Short presentations of the workshop participants (20 + 5 min each)
  • Session chair: Andrew Leitch (Queen Mary University London, UK)
  • Ana Paula Moraes (Federal Univeristy of ABC, Brazil) – Repetitive DNA in Neotropical orchid: three cases of study
  • Nicola Schmidt (Technische Universität Dresden, Germany) – Comparative analysis of repetitive sequences among Betoideae species
  • Paola Gaiero (University of the Republic, Uruguay) – Exploring the genomes of potato wild relatives from southern South America
  • break
  • Tiago Ribeiro (Federal University of Mato Grosso, Brazil) – Impact of the repeatome in the genomic divergence of Apostasia species (Apostasioideae, Orchidaceae)
  • Romain Guyot (IRD Monpellier, France) – Genome evolution of the Coffea genus
  • Emily Gu (Queen Mary University of London, UK) – Repeat transcriptome analysis of Fritillaria imperialis

May 31

• 14:00-16:00 h Troubleshooting and discussion related to practical training I
  • based on the questions posted to Slack or presented during the session

June 1

• 14:00 – 14:15 h Practical training II – assignment of tasks
• 14:15 – 17:30 h Short presentations of the workshop participants (20 + 5 min each)
  • Session chair: Tony Heitkam (Technische Universität Dresden, Germany)
  • Magdalena Vaio (University of the Republic, Uruguay) – Divergence of repetitive DNA sequences in allopolyploid species of Paspalum (Graminea)
  • Kristina Gagalova (Genome Sciences Centre, Vancouver, Canada) – Genome size increase by repeats expansion in conifers and weevil
  • Christopher Pauli (Front Range Biosciences, USA) – Repetitive elements In Cannabis
  • break
  • Ravindra Raut (National Institute of Technology Durgapur, India) – Transposon analysis of rice (Oriza sativa)
  • Alicja Macko-Podgórni (University of Agriculture in Krakow, Poland) – Identification of carrot low-copy LTR retrotransposons active in callus cultures using mobilome sequencing
  • Ludwig Mann (Technische Universität Dresden, Germany) – Extrachromosomal circular DNA (eccDNA), mobilome-Seq and the ECCsplorer pipeline

June 2

• 14:00 – 17:00 h Short presentations of the workshop participants (20 + 5 min each)
  • Session chair: Sònia Garcia (Institut Botànic de Barcelona, Spain)
  • Radka Vozárová (Institute of Biophysics, Brno, Czech Republic) – Ancient origin of two 5S rDNA families dominating in the genus Rosa and their behavior in the Canina-type meiosis
  • Zirlane Costa (University of São Paulo, Brazil) – Repetitive portion of Passiflora genomes
  • Radka Symonova (Technical University of Munich, Germany) – GC-content of transposons and of their host genomes
  • break
  • Diogo Cabral-de-Mello (São Paulo State University, Brazil) – Not ever heterochromatic and highly enriched of repeats: The B chromosome of the grasshopper Abracris flavolineata breaks the rules
  • Joan Pere Pascual-Díaz (Institut Botànic de Barcelona, Spain) – Repeat contribution to genome size ups and downs in the sunflower family

June 2 – June 7

• Practical training part II [conducted individually, based on the provided data and videotutorials]
  • Structure of the RepeatExplorer output files [VIDEO tutorial]
  • Protocols 1 + 2: evaluation and interpretation of the results, downstream analysis, data visualization tools [VIDEO tutorial]
  • Protocol 3: TAREAN analysis of satDNA and FISH probe design [VIDEO tutorial]

June 7

• 14:00-16:00 h Troubleshooting and discussion related to practical training II
  • based on the questions posted to Slack or presented during the session

June 8

• 14:00 – 14:15 h Practical training III – assignment of tasks
• 14:15 – 17:30 h Short presentations of the workshop participants (20 + 5 min each)
  • Session chair: Steven Dodsworth (University of Portsmouth, UK)
  • Sebastian Pita (University of the Republic, Uruguay) – Satellitome analysis unravels the karyotypic evolution in Triatoma kissing bugs (Hemiptera: Reduviidae)
  • Rodrigo Calegari (São Paula States University, Brazil) – Organization of satDNA of Astyanax lacustris in the Astyanax mexicanus genome
  • Damira Veseljak (Ruđer Bošković Institute, Zagreb, Croatia) – Characterization of the satellitome of the flour beetle Tribolium freemani
  • break
  • Grace Bailey (University of Edinburgh, UK) – Repetitive DNA in the developing heart
  • Juan Paolo Sicat (University of Greenwich, UK) – Challenges encountered in the characterization of transposable elements found within the B. tabaci species complex
  • Antonio Baeza (Clemson University, USA) – Using RepeatExplorer to examine repetitive elements in Crustaceans: Questions for developers

June 9 – June 10

• Practical training part III [conducted individually, based on the provided data and videotutorials]
  • Protocol 4: Identification of centromeric repeats using ChIP-seq analysis [VIDEO tutorial]
  • DANTE and JBrowse [VIDEO tutorial]

June 11

• 14:00-16:00 h Troubleshooting and discussion related to practical training III
  • based on the questions posted to Slack or presented during the session