RepeatExplorer Workshop 2025

The 2025 workshop focused on repetitive DNA annotation in genome assemblies, reflecting the growing availability of high-quality assemblies.

Programme

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

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

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 & …

Training materials for this workshop are in the workshop repository.