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,Hałakuc Paweł,Ivanovska Beti,Laumer Christopher,Lehmann Robert,Boštjančić 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
Abstract
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.
Publisher
Springer Science and Business Media LLC
Cited by
1 articles.
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