BeetRepeats: reference sequences for genome and polymorphism annotation in sugar beet and wild relatives

BMC Research Notes, vol. 17, pp. 351

Abstract

OBJECTIVES: Despite the advances in genomics, repetitive DNAs (repeats) are still difficult to sequence, assemble, and identify. This is due to their high abundance and diversity, with many repeat families being unique to the organisms in which they were described. In sugar beet, repeats make up a significant portion of the genome (at least 53%), with many repeats being restricted to the beet genera, Beta and Patellifolia. Over the course of over 30 years and many repeat-based studies, over a thousand reference repeat sequences for beet genomes have been identified and many experimentally characterized (e.g. physically located on the chromosomes). Here, we present the collection of these reference repeat sequences for beets. DATA DESCRIPTION: The BeetRepeats_v1.0 resource is a comprehensive compilation of all characterized repeat families, including satellite DNAs, ribosomal DNAs, transposable elements and endogenous viruses. The genomes covered are those of sugar beet and closely related wild beets (genera Beta and Patellifolia) as well as Chenopodium quinoa and Spinacia oleracea (all belonging to the Amaranthaceae). The reference sequences are in fasta format and comprise well-characterized repeats from both repeat categories (dispersed/mobile as well as tandemly arranged). The database is suitable for the RepeatMasker and RepeatExplorer2 pipelines and can be used directly for any repeat annotation and repeat polymorphism detection purposes.

Authors 10

1. Nicola Schmidt

   Technische Universität Dresden

   Affiliation as printed

   Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany

2. Sophie Maiwald

   Technische Universität Dresden

   Affiliation as printed

   Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany

3. Ludwig Mann

   Technische Universität Dresden

   Affiliation as printed

   Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany

4. Kathrin M. Seibt

   Technische Universität Dresden

   Affiliation as printed

   Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany

5. Sarah Breitenbach

   Technische Universität Dresden

   Affiliation as printed

   Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany

6. Susan Liedtke

   Technische Universität Dresden

   Affiliation as printed

   Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany

7. Gerhard Menzel

   Technische Universität Dresden

   Affiliation as printed

   Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany

8. Bernd Weißhaar

   Bielefeld University

   Affiliation as printed

   Fakulty of Biology & CeBiTec, Universität Bielefeld, 33615, Bielefeld, Germany

9. Daniela Holtgräwe

   Bielefeld University

   Affiliation as printed

   Fakulty of Biology & CeBiTec, Universität Bielefeld, 33615, Bielefeld, Germany

10. Tony Heitkam corresponding Aachen Institute of Biology I

    Technische Universität Dresden · RWTH Aachen University

    Affiliation as printed

    Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany. tony.heitkam@tu-dresden.de

    Institute of Biology I, RWTH Aachen University, 52056, Aachen, Germany. tony.heitkam@tu-dresden.de

    Institute of Biology I, RWTH Aachen University, 52056, Aachen, Germany