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 (Schmidt et al., 2024; a detailed list with all corresponding references can be found in 'BeetRepeatDB_v2.0-Content.docx'). Additionally, we provide a GFF annotaion file containing structural components (e.g., protein domains; 'BeetRepeatDB_v2.0_annotation.gff') as well as annotation of the repeats within the three different sugar beet assemblies RefBeet-3.0 (Dohm et al., 2025), EL10 (McGrath et al., 2023), and 2320BvONT_v1.0 (Sielemann et al., 2023) as GFF files. We provide separate annotations for centromeric repeats ('[...]centromericONLY.gff') to facilitate the identification of centromeres within the assemblies.

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 35 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, RepeatExplorer2, and TEtrimmer pipelines and can be used directly for any repeat annotation and repeat polymorphism detection purposes.

Update from BeetRepeatDB_v1.0 to BeetRepeatDB_v2.0: Using the recently published sugar beet assembly RefBeet-3.0 (Dohm et al., 2025), we applied the automatic TE refinement approach provided by the TEtrimmer pipeline (Qian et al., 2025) using the TE sequences from BeetRepeatDB_v1.0 (Schmidt et al., 2024). The refined sequences were manually curated, consolidated, and used to update the BeetRepeats database with respect to the new, more complete RefBeet-3.0 genome assembly, providing many consensus sequences where previously only individual copies were available. Newly identified repeats were included and revised repeat family classifications were implemented.

Schmidt N, Maiwald S, Mann L, Weber B, Seibt KM, Breitenbach S, et al. BeetRepeats: reference sequences for genome and polymorphism annotation in sugar beet and wild relatives. BMC Res Notes. 2024;17:351.

Dohm JC, Holzweber T, Pensch RA, Himmelbauer H. Sugar beet long-read reference assembly of genotype KWS2320. NAR Genom Bioinform. 2025;7:lqaf142.

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.

Qian J, Xue H, Ou S, Mann L, Storer J, Fürtauer L, et al. TEtrimmer: a tool to automate the manual curation of transposable elements. Nat commun. 2025;16:8429.