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Teaching transposon classification as a means to crowd source the curation of repeat annotation – a tardigrade perspective
Peona, Valentina; Martelossi, Jacopo; Almojil, Dareen et al.
2023
 

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Abstract :
[en] AbstractThe 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. Manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences. However, 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 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. Here, we present an example of such crowd sourcing effort developed through both in-person and online courses built around a collaborative peer-reviewed teaching process that can be used as teaching reference guide for similar projects. 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: A hidden treasure awaits discovery within non-model organisms.
Disciplines :
Zoology
Author, co-author :
Peona, Valentina 
Martelossi, Jacopo 
Almojil, Dareen 
Bocharkina, Julia
Brännström, Ioana 
Brown, Max 
Cang, Alice
Valenzuela, Tomas Carrasco 
DeVries, Jon
Doellman, Meredith
Elsner, Daniel
Espindola Hernandez, Pamela 
Friis Montoya, Guillermo 
Gaspar, Bence
Zagorski, Danijela
Hałakuc, Paweł
Ivanovska, Beti 
Laumer, Christopher 
Lehmann, Robert 
Boštjančić, Ljudevit Luka 
Mashoodh, Rahia 
Mazzoleni, Sofia
Mouton, Alice  ;  Université de Liège - ULiège > Département des sciences et gestion de l'environnement (Arlon Campus Environnement) > Socio-économie, Environnement et Développement (SEED)
Janke, Maria Nilsson 
Pei, Yifan 
Potente, Giacomo 
Provataris, Panagiotis
Pardos, José Ramón 
Raut, Ravindra
Sbaffi, Tomasa
Schwarz, Florian
Stapley, Jessica 
Stevens, Lewis 
Sultana, Nusrat 
Symonova, Radka 
Tahami, Mohadeseh 
Urzì, Alice
Yang, Heidi
Yusuf, Abdullah
Pecoraro, Carlo 
Suh, Alexander
More authors (31 more) Less
Language :
English
Title :
Teaching transposon classification as a means to crowd source the curation of repeat annotation – a tardigrade perspective
Publication date :
07 November 2023
Available on ORBi :
since 29 December 2023

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