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

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

Peona, Valentina (författare): Uppsala universitet,Systematisk biologi,Swiss Ornithol Inst Vogelwarte, CH-6204 Sempach, Switzerland; Swedish Nat Hist Museum, Dept Bioinformat & Genet, Stockholm, Sweden

Martelossi, Jacopo (författare): Univ Bologna, Dept Biol Geol & Environm Sci, Via Selmi 3, I-40126 Bologna, Italy.

Almojil, Dareen (författare): New York Univ Abu Dhabi, Dept Engn, Saadiyat Isl, U Arab Emirates.

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Bocharkina, Julia (författare): Skolkovo Inst Sci & Technol, Moscow, Russia.

Brännström, Ioana (författare): Uppsala universitet,Evolutionsbiologi,Univ Oslo, Nat Hist Museum, Oslo, Norway

Brown, Max (författare): Anglia Ruskin Univ, East Rd, Cambridge CB1 1PT, England.

Cang, Alice (författare): Univ Arizona, Tucson, AZ USA.

Carrasco-Valenzuela, Tomàs (författare): Leibniz Inst Zoo & Wildlife Res, Evolutionary Genet Dept, D-10315 Berlin, Germany.;Berlin Ctr Genom Biodivers Res, D-14195 Berlin, Germany.

DeVries, Jon (författare): Reed Coll, Portland, OR USA.

Doellman, Meredith (författare): Univ Chicago, Dept Ecol & Evolut, Chicago, IL 60637 USA.;Univ Notre Dame, Dept Biol Sci, Notre Dame, IN 46556 USA.

Elsner, Daniel (författare): Univ Freiburg, Evolutionary Biol & Ecol, Freiburg, Germany.

Espíndola-Hernández, Pamela (författare): Helmholtz Zent Munchen, Res Unit Comparat Microbiome Anal COMI, Ingolstadter Landstr1, D-85764 Neuherberg, Germany.

Friis Montoya, Guillermo (författare): Royal Bot Gardens, Richmond TW9 3AE, Surrey, England.

Gaspar, Bence (författare): Univ Tubingen, Inst Evolut & Ecol, Tubingen, Germany.

Zagorski, Danijela (författare): Czech Acad Sci, Inst Bot, Pruhonice, Czech Republic.

Halakuc, Pawel (författare): Univ Warsaw, Inst Evolutionary Biol, Fac Biol, Biol & Chem Res Ctr, Warsaw, Poland.

Ivanovska, Beti (författare): Hungarian Univ Agr & Life Sci, Inst Genet & Biotechnol, Budapest, Hungary.

Laumer, Christopher (författare): Nat Hist Museum, Cromwell Rd, London, England.

Lehmann, Robert (författare): King Abdullah Univ Sci & Technol KAUST, Biol & Environm Sci & Engn Div, Thuwal, Saudi Arabia.

Bostjancic, Ljudevit Luka (författare): LOEWE Ctr Translat Biodivers Genom LOEWE TBG, Senckenberganlage 25, D-60325 Frankfurt, Germany.

Mashoodh, Rahia (författare): UCL, Ctr Biodivers & Environm Res, Dept Genet Environm & Evolut, London, England.

Mazzoleni, Sofia (författare): Charles Univ Prague, Fac Sci, Dept Ecol, Prague, Czech Republic.

Mouton, Alice (författare): Univ Liege, Conservat Genet Lab, INBIOS, Liege, Belgium.

Nilsson, Maria Anna (författare): LOEWE Ctr Translat Biodivers Genom LOEWE TBG, Senckenberganlage 25, D-60325 Frankfurt, Germany.

Pei, Yifan (författare): Uppsala universitet,Systematisk biologi,Leibniz Inst Anal Biodivers Change, Ctr Mol Biodivers Res, Adenauerallee 127, D-53113 Bonn, Germany

Potente, Giacomo (författare): Univ Zurich, Dept Systemat & Evolutionary Bot, Zurich, Switzerland.

Provataris, Panagiotis (författare): German Canc Res Ctr, NGS Core Facil, DKFZ ZMBH Alliance, D-69120 Heidelberg, Germany.

Pardos-Blas, José Ramón (författare): Dept Biodivers & Biol Evolut, Museo Nacl Ciencias Nat MNCN CSIC, Jose Gutierrez Abascal 2, Madrid 28006, Spain.

Raut, Ravindra (författare): Natl Inst Technol Durgapur, Dept Biotechnol, Durgapur, India.

Sbaffi, Tomasa (författare): Water Res Inst CNR IRSA, Natl Res Council Italy, Mol Ecol Grp MEG, Verbania, Italy.

Schwarz, Florian (författare): Eurofins Genom Europe Pharm & Diagnost Prod & Serv, Ebersberg, Germany.

Stapley, Jessica (författare): Inst Integrat Biol, Plant Pathol Grp, ETH Zurich, Zurich, Switzerland.

Stevens, Lewis (författare): Wellcome Sanger Inst, Tree Life, Cambridge CB10 1SA, England.

Sultana, Nusrat (författare): Jagannath Univ, Dept Bot, Dhaka 1100, Bangladesh.

Symonova, Radka (författare): Inst Hydrobiol, Biol Ctr Czech Acad Sci, Ceske Budejovice, Czech Republic.

Tahami, Mohadeseh S. (författare): Univ Jyvaskyla, Dept Biol & Environm Sci, POB 35, Jyvaskyla 40014, Finland.

Urzì, Alice (författare): Centogene GmbH, Strande 7, D-18057 Rostock, Germany.

Yang, Heidi (författare): Univ Calif Los Angeles, Dept Ecol & Evolutionary Biol, Los Angeles, CA USA.

Yusuf, Abdullah (författare): Tech Univ Dresden, Zell & Mol Biol Pflanzen, Dresden, Germany.

Pecoraro, Carlo (författare): Physalia Courses, D-10249 Berlin, Germany.

Suh, Alexander (författare): Uppsala universitet,Systematisk biologi,Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich NR4 7TU, England

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BioMed Central (BMC), 2024
2024
Engelska.
Ingår i: Mobile DNA. - : BioMed Central (BMC). - 1759-8753. ; 15:1

Relaterad länk:: https://doi.org/10.1...; visa fler...; https://uu.diva-port... (primary) (Raw object); https://urn.kb.se/re...; https://doi.org/10.1...; visa färre...

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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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Av författaren/redakt...: Peona, Valentina; Martelossi, Jaco ...; Almojil, Dareen; Bocharkina, Juli ...; Brännström, Ioan ...; Brown, Max; visa fler...; Cang, Alice; Carrasco-Valenzu ...; DeVries, Jon; Doellman, Meredi ...; Elsner, Daniel; Espíndola-Hernán ...; Friis Montoya, G ...; Gaspar, Bence; Zagorski, Danije ...; Halakuc, Pawel; Ivanovska, Beti; Laumer, Christop ...; Lehmann, Robert; Bostjancic, Ljud ...; Mashoodh, Rahia; Mazzoleni, Sofia; Mouton, Alice; Nilsson, Maria A ...; Pei, Yifan; Potente, Giacomo; Provataris, Pana ...; Pardos-Blas, Jos ...; Raut, Ravindra; Sbaffi, Tomasa; Schwarz, Florian; Stapley, Jessica; Stevens, Lewis; Sultana, Nusrat; Symonova, Radka; Tahami, Mohadese ...; Urzì, Alice; Yang, Heidi; Yusuf, Abdullah; Pecoraro, Carlo; Suh, Alexander; visa färre...

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

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