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

The present repository provides a BeetRepeats fasta resource representing a comprehensive compilation of all characterized repeat families in the genome of sugar beet and wild relatives (a detailed list with all corresponding references can be found in 'BeetRepeatDB_v1.0-Content.docx'). Additionally, we provide an annotation of these repeats within the three different sugar beet assemblies EL10 (McGrath et al., 2023), 2320BvONT_v1.0 (Sielemann et al., 2023), and RefBeet1.5 (https://jbrowse.cebitec.uni-bielefeld.de/RefBeet1.5) as GFF files.

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 more than 30 years and many repeat-based studies, over a thousand  reference repeat sequences for beet genomes have been identified and experimentally characterized (i.e. physically located on the chromosomes). 
The BeetRepeats 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.

McGrath JM, Funk A, Galewski P, Ou S, Townsend B, Davenport K, et al. A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.). DNA Res. 2023;30:dsac033.

Sielemann K, Pucker B, Orsini E, Elashry A, Schulte L, Viehoever P, et al. Genomic characterization of a nematode tolerance locus in sugar beet. BMC Genomics. 2023;24:748.