Mobile DNA (May 2024)
Teaching transposon classification as a means to crowd source the curation of repeat annotation – a tardigrade perspective
- Valentina Peona,
- Jacopo Martelossi,
- Dareen Almojil,
- Julia Bocharkina,
- Ioana Brännström,
- Max Brown,
- Alice Cang,
- Tomàs Carrasco-Valenzuela,
- Jon DeVries,
- Meredith Doellman,
- Daniel Elsner,
- Pamela Espíndola-Hernández,
- Guillermo Friis Montoya,
- Bence Gaspar,
- Danijela Zagorski,
- Paweł Hałakuc,
- Beti Ivanovska,
- Christopher Laumer,
- Robert Lehmann,
- Ljudevit Luka Boštjančić,
- Rahia Mashoodh,
- Sofia Mazzoleni,
- Alice Mouton,
- Maria Anna Nilsson,
- Yifan Pei,
- Giacomo Potente,
- Panagiotis Provataris,
- José Ramón Pardos-Blas,
- Ravindra Raut,
- Tomasa Sbaffi,
- Florian Schwarz,
- Jessica Stapley,
- Lewis Stevens,
- Nusrat Sultana,
- Radka Symonova,
- Mohadeseh S. Tahami,
- Alice Urzì,
- Heidi Yang,
- Abdullah Yusuf,
- Carlo Pecoraro,
- Alexander Suh
Affiliations
- Valentina Peona
- Department of Organismal Biology – Systematic Biology, Evolutionary Biology Centre, Uppsala University
- Jacopo Martelossi
- Department of Biological Geological and Environmental Science, University of Bologna
- Dareen Almojil
- New York University Abu Dhabi
- Julia Bocharkina
- Skolkovo Institute of Science and Technology
- Ioana Brännström
- Natural History Museum, Oslo University
- Max Brown
- Anglia Ruskin University
- Alice Cang
- University of Arizona
- Tomàs Carrasco-Valenzuela
- Evolutionary Genetics Department, Leibniz Institute for Zoo and Wildlife Research
- Jon DeVries
- Reed College
- Meredith Doellman
- Department of Ecology and Evolution, The University of Chicago
- Daniel Elsner
- Evolutionary Biology & Ecology, University of Freiburg
- Pamela Espíndola-Hernández
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München
- Guillermo Friis Montoya
- Royal Botanic Gardens
- Bence Gaspar
- Institute of Evolution and Ecology, University of Tuebingen
- Danijela Zagorski
- Institute of Botany, Czech Academy of Sciences
- Paweł Hałakuc
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw
- Beti Ivanovska
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences
- Christopher Laumer
- The Natural History Museum
- Robert Lehmann
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST)
- Ljudevit Luka Boštjančić
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG)
- Rahia Mashoodh
- Department of Genetics, Environment & Evolution, Centre for Biodiversity & Environment Research, University College London
- Sofia Mazzoleni
- Department of Ecology, Faculty of Science, Charles University
- Alice Mouton
- INBIOS-Conservation Genetic Lab, University of Liege
- Maria Anna Nilsson
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG)
- Yifan Pei
- Department of Organismal Biology – Systematic Biology, Evolutionary Biology Centre, Uppsala University
- Giacomo Potente
- Department of Systematic and Evolutionary Botany, University of Zurich
- Panagiotis Provataris
- German Cancer Research Center, NGS Core Facility, DKFZ-ZMBH Alliance
- José Ramón Pardos-Blas
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC)
- Ravindra Raut
- Department of Biotechnology, National Institute of Technology Durgapur
- Tomasa Sbaffi
- Molecular Ecology Group (MEG), National Research Council of Italy – Water Research Institute (CNR-IRSA)
- Florian Schwarz
- Eurofins Genomics Europe Pharma and Diagnostics Products & Services Sales GmbH
- Jessica Stapley
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich
- Lewis Stevens
- Tree of Life, Wellcome Sanger Institute
- Nusrat Sultana
- Department of Botany, Jagannath Univerity
- Radka Symonova
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences
- Mohadeseh S. Tahami
- Department of Biological and Environmental Science, University of Jyväskylä
- Alice Urzì
- Centogene GmbH
- Heidi Yang
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles
- Abdullah Yusuf
- Zell- und Molekularbiologie der Pflanzen, Technische Universität Dresden
- Carlo Pecoraro
- Physalia-courses
- Alexander Suh
- Department of Organismal Biology – Systematic Biology, Evolutionary Biology Centre, Uppsala University
- DOI
- https://doi.org/10.1186/s13100-024-00319-8
- Journal volume & issue
-
Vol. 15,
no. 1
pp. 1 – 12
Abstract
Abstract Background The advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the significance of in-depth analyses of repetitive elements, transposable elements (TEs) in particular, is increasingly recognized in understanding genome evolution. Despite the plethora of available bioinformatic tools for identifying and annotating TEs, the phylogenetic distance of the target species from a curated and classified database of repetitive element sequences constrains any automated annotation effort. Moreover, manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences. Results Here, we present an example of a crowd-sourcing effort aimed at curating and annotating TE libraries of two non-model species built around a collaborative, peer-reviewed teaching process. Manual curation and classification are time-consuming processes that offer limited short-term academic rewards and are typically confined to a few research groups where methods are taught through hands-on experience. Crowd-sourcing efforts could therefore offer a significant opportunity to bridge the gap between learning the methods of curation effectively and empowering the scientific community with high-quality, reusable repeat libraries. Conclusions The collaborative manual curation of TEs from two tardigrade species, for which there were no TE libraries available, resulted in the successful characterization of hundreds of new and diverse TEs in a reasonable time frame. Our crowd-sourcing setting can be used as a teaching reference guide for similar projects: A hidden treasure awaits discovery within non-model organisms.
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