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Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective
V. Peona, J. Martelossi, D. Almojil, J. Bocharkina, I. Brännström, M. Brown, A. Cang, T. Carrasco-Valenzuela, J. DeVries, M. Doellman, D. Elsner, P. Espíndola-Hernández, GF. Montoya, B. Gaspar, D. Zagorski, P. Hałakuc, B. Ivanovska, C. Laumer, R....
Status not-indexed Language English Country England, Great Britain
Document type Journal Article
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BioMedCentral
from 2010-12-01
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from 2015-01-01
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- Publication type
- Journal Article MeSH
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.
Anglia Ruskin University East Rd Cambridge CB1 1PT UK
Berlin Center for Genomics in Biodiversity Research 14195 Berlin Germany
Centogene GmbH Am Strande 7 18055 Rostock Germany
Department of Bioinformatics and Genetics Swedish Natural History Museum Stockholm Sweden
Department of Biological Sciences University of Notre Dame Notre Dame IN 46556 USA
Department of Biotechnology National Institute of Technology Durgapur Durgapur India
Department of Botany Jagannath Univerity Dhaka 1100 Bangladesh
Department of Ecology and Evolution The University of Chicago Chicago IL 60637 USA
Department of Ecology and Genetics Uppsala University Uppsala Sweden
Department of Ecology Faculty of Science Charles University Prague Czech Republic
Department of Systematic and Evolutionary Botany University of Zurich Zurich Switzerland
Eurofins Genomics Europe Pharma and Diagnostics Products and Services Sales GmbH Ebersberg Germany
Evolutionary Biology and Ecology University of Freiburg Freiburg Germany
German Cancer Research Center NGS Core Facility DKFZ ZMBH Alliance 69120 Heidelberg Germany
INBIOS Conservation Genetic Lab University of Liege Liege Belgium
Institute of Botany Czech Academy of Sciences Průhonice Czech Republic
Institute of Evolution and Ecology University of Tuebingen Tuebingen Germany
LOEWE Centre for Translational Biodiversity Genomics Senckenberganlage 25 60325 Frankfurt Germany
Molecular Ecology Group Verbania Italy
Natural History Museum Oslo University Oslo Norway
New York University Abu Dhabi Saadiyat Island United Arab Emirates
Physalia courses 10249 Berlin Germany
Plant Pathology Group Institute of Integrative Biology ETH Zurich Zurich Switzerland
Reed College Portland OR United States of America
Royal Botanic Gardens Kew Richmond Surrey TW9 3AE UK
School of Biological Sciences University of East Anglia Norwich Research Park Norwich NR4 7TU UK
Skolkovo Institute of Science and Technology Moscow Russia
Swiss Ornithological Institute Vogelwarte Sempach CH 6204 Switzerland
The Natural History Museum Cromwell Road London SW6 7SJ UK
Tree of Life Wellcome Sanger Institute Cambridge CB10 1SA UK
University of Arizona Tucson AZ USA
Zell und Molekularbiologie der Pflanzen Technische Universität Dresden Dresden Germany
References provided by Crossref.org
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- $a Peona, Valentina $u Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, SE-752 36, Sweden. valentina.peona@nrm.se $u Swiss Ornithological Institute Vogelwarte, Sempach, CH-6204, Switzerland. valentina.peona@nrm.se $u Department of Bioinformatics and Genetics, Swedish Natural History Museum, Stockholm, Sweden. valentina.peona@nrm.se
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