A1 Journal article (refereed)
Teaching transposon classification as a means to crowd source the curation of repeat annotation : a tardigrade perspective (2024)
Peona, V., Martelossi, J., Almojil, D., Bocharkina, J., Brännström, I., Brown, M., Cang, A., Carrasco-Valenzuela, T., DeVries, J., Doellman, M., Elsner, D., Espíndola-Hernández, P., Montoya, G. F., Gaspar, B., Zagorski, D., Hałakuc, P., Ivanovska, B., Laumer, C., Lehmann, R., . . . Suh, A. (2024). Teaching transposon classification as a means to crowd source the curation of repeat annotation : a tardigrade perspective. Mobile DNA, 15, Article 10. https://doi.org/10.1186/s13100-024-00319-8
JYU authors or editors
Publication details
All authors or editors: Peona, Valentina; Martelossi, Jacopo; Almojil, Dareen; Bocharkina, Julia; Brännström, Ioana; Brown, Max; Cang, Alice; Carrasco-Valenzuela, Tomàs; DeVries, Jon; Doellman, Meredith; et al.
Journal or series: Mobile DNA
eISSN: 1759-8753
Publication year: 2024
Publication date: 06/05/2024
Volume: 15
Article number: 10
Publisher: BioMed Central
Publication country: United Kingdom
Publication language: English
DOI: https://doi.org/10.1186/s13100-024-00319-8
Publication open access: Openly available
Publication channel open access: Open Access channel
Publication is parallel published (JYX): https://jyx.jyu.fi/handle/123456789/95043
Publication is parallel published: https://doi.org/10.3929/ethz-b-000672225
Web address of parallel published publication (pre-print): https://doi.org/10.1101/2023.11.06.565293
Abstract
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.
Keywords: genomics; molecular genetics; Tardigrada; sequencing; transposons; annotation; curation (collections); libraries; bioinformatics; crowdsourcing
Contributing organizations
Ministry reporting: Yes
Preliminary JUFO rating: 1
