Evidence map›Paper›PMID 39605057›Full record

ArticleBMC research notes2024

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

Nicola Schmidt, Sophie Maiwald, Ludwig Mann, Beatrice Weber, Kathrin M Seibt, Sarah Breitenbach, Susan Liedtke, Gerhard Menzel, Bernd Weisshaar, Daniela Holtgräwe and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC research notes, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Article
  2. Review
  3. Article
  4. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Nicola SchmidtFaculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany.ORCID http://orcid.org/0000-0003-0038-9581
Sophie MaiwaldFaculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany.ORCID http://orcid.org/0000-0002-0716-648X
Ludwig MannFaculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany.ORCID http://orcid.org/0000-0001-8756-8106
Beatrice WeberFaculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany.ORCID http://orcid.org/0000-0003-4012-4430
Kathrin M SeibtFaculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany.ORCID http://orcid.org/0000-0002-5435-2381
Sarah BreitenbachFaculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany.
Susan LiedtkeFaculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany.
Gerhard MenzelFaculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany.ORCID http://orcid.org/0000-0002-8912-5162
Bernd WeisshaarFakulty of Biology & CeBiTec, Universität Bielefeld, 33615, Bielefeld, Germany.ORCID http://orcid.org/0000-0002-7635-3473
Daniela HoltgräweFakulty of Biology & CeBiTec, Universität Bielefeld, 33615, Bielefeld, Germany.ORCID http://orcid.org/0000-0002-1062-4576
Tony HeitkamFaculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany. tony.heitkam@tu-dresden.de.ORCID http://orcid.org/0000-0003-0168-8428

Funding

Bundesministerium für Bildung und Forschung 031B1221
6 · The paper itself

Abstract

objectivesDespite 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.

Indexed as

Beta vulgarisGenome, PlantChenopodium quinoaDNA, PlantDNA Transposable ElementsMolecular Sequence AnnotationPolymorphism, GeneticRepetitive Sequences, Nucleic AcidDNA, PlantDNA Transposable ElementsBeta vulgarisGenome annotationPatellifoliaRepetitive DNASatellite DNAsSugar beetTransposable elements

Identifiers

PMID39605057
PMCPMC11603912

What Socratic holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.