학술논문
Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective
Document Type
Academic Journal
Author
Peona, Valentina; Martelossi, Jacopo; Almojil, Dareen; Bocharkina, Julia; Brännström, Ioana; Brown, Max; Cang, Alice; Carrasco-Valenzuela, Tomàs; DeVries, Jon; Doellman, Meredith; Elsner, Daniel; Espíndola-Hernández, Pamela; Montoya, Guillermo Friis; Gaspar, Bence; Zagorski, Danijela; HaÅakuc, PaweÅ; Ivanovska, Beti; Laumer, Christopher; Lehmann, Robert; BoÅ¡tjanciÄ, Ljudevit Luka; Mashoodh, Rahia; Mazzoleni, Sofia; Mouton, Alice; Nilsson, Maria Anna; Pei, Yifan; Potente, Giacomo; Provataris, Panagiotis; Pardos-Blas, José Ramón; Raut, Ravindra; Sbaffi, Tomasa; Schwarz, Florian; Stapley, Jessica; Stevens, Lewis; Sultana, Nusrat; Symonova, Radka; Tahami, Mohadeseh S.; Urzì, Alice; Yang, Heidi; Yusuf, Abdullah; Pecoraro, Carlo; Suh, Alexander
Source
Mobile DNA. May 6, 2024, Vol. 15 Issue 1
Subject
Language
English
ISSN
1759-8753
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. Keywords: Transposable elements, Manual curation, Library, Annotation, Non-model organism, Genome assembly
Author(s): Valentina Peona[sup.1,2,3], Jacopo Martelossi[sup.4], Dareen Almojil[sup.5], Julia Bocharkina[sup.6], Ioana Brännström[sup.7,8], Max Brown[sup.9], Alice Cang[sup.10], Tomàs Carrasco-Valenzuela[sup.11,12], Jon DeVries[sup.13], Meredith Doellman[sup.14,15], Daniel Elsner[sup.16], Pamela Espíndola-Hernández[sup.17], Guillermo Friis Montoya[sup.18], Bence Gaspar[sup.19], [...]
Author(s): Valentina Peona[sup.1,2,3], Jacopo Martelossi[sup.4], Dareen Almojil[sup.5], Julia Bocharkina[sup.6], Ioana Brännström[sup.7,8], Max Brown[sup.9], Alice Cang[sup.10], Tomàs Carrasco-Valenzuela[sup.11,12], Jon DeVries[sup.13], Meredith Doellman[sup.14,15], Daniel Elsner[sup.16], Pamela Espíndola-Hernández[sup.17], Guillermo Friis Montoya[sup.18], Bence Gaspar[sup.19], [...]