Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective

Peona, V.; Martelossi, J.; Almojil, D.; Bocharkina, J.; Brännström, I.; Brown, M.; Cang, A.; Carrasco-Valenzuela, T.; DeVries, J.; Doellman, M.; Elsner, D.; Espindola-Hernandez, P.; Friis, G.; Gaspar, B.; Zagorski, D.; Hałakuc, P.; Ivanovska, B.; Laumer, C.; Lehmann, R.; Bostjancic, L. L.; Mashoodh, R.; Mazzoleni, S.; Mouton, A.; Janke, M. N.; Pei, Y.; Potente, G.; Provataris, P.; Pardos-Blas, J. R.; Raut, R.; Sbaffi, T.; Schwarz, F.; Stapley, J.; Stevens, L.; Sultana, N.; Symonova, R.; Tahami, M. S.; Urzi, A.; Yang, H.; Yusuf, A.; Pecoraro, C.; Suh, A.

doi:10.1101/2023.11.06.565293

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bioRxiv · 10.1101/2023.11.06.565293

Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective

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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. 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.

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Peona, V., Martelossi, J., Almojil, D., Bocharkina, J., Brännström, I., Brown, M., Cang, A., Carrasco-Valenzuela, T., DeVries, J., Doellman, M., Elsner, D., Espindola-Hernandez, P., Friis, G., Gaspar, B., Zagorski, D., Hałakuc, P., Ivanovska, B., Laumer, C., Lehmann, R., Bostjancic, L. L., Mashoodh, R., Mazzoleni, S., Mouton, A., Janke, M. N., Pei, Y., Potente, G., Provataris, P., Pardos-Blas, J. R., Raut, R., Sbaffi, T., Schwarz, F., Stapley, J., Stevens, L., Sultana, N., Symonova, R., Tahami, M. S., Urzi, A., Yang, H., Yusuf, A., Pecoraro, C., Suh, A.. 2023-11-07. Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective. https://doi.org/10.1101/2023.11.06.565293

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