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Peona, V.* ; Martelossi, J.* ; Almojil, D.* ; Bocharkina, J.* ; Brännström, I.* ; Brown, M.* ; Cang, A.* ; Carrasco-Valenzuela, T.* ; deVries, J.H.* ; Doellman, M.* ; Elsner, D.* ; Espíndola-Hernández, P. ; Montoya, G.F.* ; Gaspar, B.* ; Zagorski, D.* ; Hałakuc, P.* ; Ivanovska, B.* ; Laumer, C.* ; Lehmann, R.* ; Boštjančić, L.L.* ; Mashoodh, R.* ; Mazzoleni, S.* ; Mouton, A.* ; Nilsson, M.A.* ; 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.* ; Urzì, A.* ; Yang, H.* ; Yusuf, A.* ; Pecoraro, C.* ; Suh, A.*

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

Mob. DNA 15:10 (2024)
Verlagsversion DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
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.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Korrespondenzautor
Schlagwörter Annotation ; Genome Assembly ; Library ; Manual Curation ; Non-model Organism ; Transposable Elements; Sequence; Element; Retrotransposons; Evolution
ISSN (print) / ISBN 1759-8753
e-ISSN 1759-8753
Zeitschrift Mobile DNA
Quellenangaben Band: 15, Heft: 1, Seiten: , Artikelnummer: 10 Supplement: ,
Verlag BioMed Central
Verlagsort London
Nichtpatentliteratur Publikationen
Begutachtungsstatus Peer reviewed
Institut(e) Research Unit Comparative Microbiome Analysis (COMI)
Förderungen CSC-IT Finland
Swedish National Infrastructure for Computing (SNIC) through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) - Swedish Research Council
Uppsala University