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@ARTICLE{Peona:290058,
      author       = {V. Peona and J. Martelossi and D. Almojil and J. Bocharkina
                      and I. Brännström and M. Brown and A. Cang and T.
                      Carrasco-Valenzuela and J. DeVries and M. Doellman and D.
                      Elsner and P. Espíndola-Hernández and G. F. Montoya and B.
                      Gaspar and D. Zagorski and P. Hałakuc and B. Ivanovska and
                      C. Laumer and R. Lehmann and L. L. Boštjančić and R.
                      Mashoodh and S. Mazzoleni and A. Mouton and M. A. Nilsson
                      and Y. Pei and G. Potente and P. Provataris$^*$ and J. R.
                      Pardos-Blas and R. Raut and T. Sbaffi and F. Schwarz and J.
                      Stapley and L. Stevens and N. Sultana and R. Symonova and M.
                      S. Tahami and A. Urzì and H. Yang and A. Yusuf and C.
                      Pecoraro and A. Suh},
      title        = {{T}eaching transposon classification as a means to crowd
                      source the curation of repeat annotation - a tardigrade
                      perspective.},
      journal      = {Mobile DNA},
      volume       = {15},
      number       = {1},
      issn         = {1759-8753},
      address      = {London},
      publisher    = {BioMed Central},
      reportid     = {DKFZ-2024-00963},
      pages        = {10},
      year         = {2024},
      note         = {DKFZ-ZMBH Alliance},
      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. Moreover, manual
                      curation of raw repeat libraries is deemed essential due to
                      the frequent incompleteness of automatically generated
                      consensus sequences.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.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     = {Annotation (Other) / Genome assembly (Other) / Library
                      (Other) / Manual curation (Other) / Non-model organism
                      (Other) / Transposable elements (Other)},
      cin          = {W190},
      ddc          = {570},
      cid          = {I:(DE-He78)W190-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:38711146},
      doi          = {10.1186/s13100-024-00319-8},
      url          = {https://inrepo02.dkfz.de/record/290058},
}