ArticleMobile DNA2024
Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective.
Article in Mobile DNA, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.bioRxiv : the preprint server for biology · 2026Article
- ColabCuraTE: an easy-to-use, web-based pipeline for the manual curation of transposable elements.Mobile DNA · 2025Article
- New insights into mitochondrial segregation from the Doubly Uniparental Inheritance system in bivalves.BMC biology · 2025Article
- High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae.Genome research · 2025Article
- Origin and evolutionary trajectories of brown algal sex chromosomes.Nature ecology & evolution · 2025Article
- Accumulation of a Biparentally Inherited Neptune Transposable Element in Natural Killifish Hybrids (Fundulus diaphanus × F. heteroclitus).Molecular biology and evolution · 2025Article
- Characterization of the transposable element landscape shaping the Ectocarpus genome.Genome biology · 2025Article
- TEtrimmer: a tool to automate the manual curation of transposable elements.Nature communications · 2025Article
- Repeatome diversity in sea anemone genomics (Cnidaria: Actiniaria) based on the Actiniaria-REPlib library.BMC genomics · 2025Article
- Article
- Advances and challenges in understanding evolution through genome comparison: meeting report of the European Molecular Biology Organization (EMBO) lecture course "Evolutionary and Comparative Genomics".Bioinformatics advances · 2025Article
- A Concise Guide for the Characterization and Curation of Transposable Elements in Insect Genomes.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Widespread HCD-tRNA derived SINEs in bivalves rely on multiple LINE partners and accumulate in genic regions.Mobile DNA · 2024Article
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41 authors.
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Abstract
backgroundThe 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.
resultsHere, 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.
conclusionsThe 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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