Program 2025

Preliminary program

Tuesday (May 27)

8:00 – 9:00 Registration
09:00 Welcome & Workshop Introduction  (J. Macas)
09:15 Ilia Leitch (Royal Botanic Gardens, Kew, UK) – Plant genome size diversity and how this impacts evolution, distribution, and survival
10:00 Cibele Sotero-Caio (Tree of Life Programme, Wellcome Sanger Institute, UK) – Exploring metadata and features of Earth Biogenome Project assemblies
10:30 Katja Reichel (FU Berlin, Germany) – The European Reference Genome Atlas – what is it & why participate?
11:00 Coffee break
11:40 Steven Dodsworth (Birkbeck College, University of London, UK) – Repeat annotation in Nicotiana long-read genome assemblies 
12:05 Ludwig Mann (RWTH Aachen, Germany) – TE annotation in Crocus genome assemblies: Insights in large and difficult genomes
12:30 Lunch
13:30 – (18:00) Practical training I (J. Macas, P. Novák, P. Neumann)

  • TideCluster pipeline
  • RexDB database
  • DANTE / DANTE_LTR / DANTE_TIR pipelines
  • Probe design

Wednesday (May 28)

8:30 Andrew Leitch (Queen Mary University of London, UK) – Is genome downsizing after polyploidy driven by the nutrient costs of repeats in the genome and transcriptome?
9:15 André Marques (MPI for Plant Breeding Research, Germany) – Drive to survive: bimodal centromeres in pentaploid dogroses shed light on their unique meiosis
9:50 Short presentations

  • Sophie Maiwald (RWTH Aachen, Germany) – Gonna catch them all: a blueprint for identification of non-autonomous LTR retrotransposons
  • Coffee break
  • Matej Lexa (Masaryk University, Brno, Czechia) – Understanding transposon long terminal repeats using machine learning
  • Estela Perez-Roman (University of Sussex, UK) – soloLTRseeker: a new pipeline to identify solo LTR sequences
  • Johann Confais (INRAE, France) – REPET V4.0, making life easier for de novo TE annotation
  • Jiangzhao Qian (RWTH Aachen, Germany) – TEtrimmer: a novel tool to automate the manual curation of TEs
12:30 Lunch
13:30 – (18:30) Practical training II

  • TEtrimmer demo (Jiangzhao Qian)
  • REPET (Johann Confais)
  • Repeat annotation container (Petr Novák)
19:00 – 22:00 Conference dinner at restaurant Kampa

Thursday (May 29)

8:30 Short presentations
    • Pol Fernández Mató (Institut Botànic de Barcelona, Spain) – Genome size and repetitive elements in Ferns
    • Jana Kružlicová (IBP/MUNI, Brno, Czechia) – Rumex hastatulus: one species, two karyotypes
    • Aaryan Bhatia (MPI for Plant Breeding Research, Germany) – Comparative repeatomics of Drosera plants
    • Woorin Kim (Senckenberg Research Institute and Natural History Museum, Frankfurt am Main, Germany) – Diverging repeatomes in holoparasitic Hydnoraceae uncover a playground of genome evolution
    • Coffee break
    • Lucas Costa (Universidade Estadual de Campinas, Brazil) – From legumes to bromeliads: Unveilling repeatome evolution in Brazil’s rich flora
    • Joan Pere Pascual-Díaz, Sònia Garcia (Institut Botànic de Barcelona, Spain) – Invasion within: Ogre LTR retrotransposons dominate the genome of invasive Carpobrotus
    • Filippo Giuseppe Marino (University of Pisa, Italy) – Large LTR retrotransposon-derived sequences: Insights into their structure and evolution
12:30 Lunch
13:30  Short presentations

  • Zuzana Halenková (Charles University, Prague, Czechia) – Structural variation and transposable elements in closely related passerine species
  • Adauto Cardoso (Universidade Federal do Pará/Universidad Pablo de Olavide, Brazil) – Genomic landscape of repetitive DNAs in Neotropical Electric Fishes
14:20 – (17:00)  coffee & discussions & troubleshooting & …