ArticleThe plant genome2021
K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes.
Article in The plant genome, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Clusia genomes shed light on the evolution and diversity of crassulacean acid metabolism physiotypes.Nature communications · 2026Article
- Chromosome-scale genomes of two wild flowering cherries (Cerasus itosakura and Cerasus jamasakura) provide insights into structural evolution in Cerasus.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids.Plant methods · 2025Article
- Genome structure and molecular phylogeny of the only Eurasian Boechera species, Boechera falcata (Brassicaceae).G3 (Bethesda, Md.) · 2025Article
- A Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosa.Scientific data · 2025Article
- Chromosome-scale Reference Genome and RAD-based Genetic Map of Yellow Starthistle (Centaurea solstitialis) Reveal Putative Structural Variation and QTL Associated With Invader Traits.Genome biology and evolution · 2024Article
- An island of receptor-like genes at the Rrs13 locus on barley chromosome 6HS co-locate with three novel sources of scald resistance.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Origin and evolution of the bread wheat D genome.Nature · 2024Article
- The CABANA model 2017-2022: research and training synergy to facilitate bioinformatics applications in Latin America.Frontiers in education · 2024Article
- Study of Dispersed Repeats in theInternational journal of molecular sciences · 2024Article
- A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants.The plant genome · 2022Article
- Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.Nucleic acids research · 2022Article
- K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes.The plant genome · 2021Article
- Chromosome-scale reference genome ofApplications in plant sciencesArticle
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Authors and funding
6 authors.
Funding
Abstract
The annotation of repetitive sequences within plant genomes can help in the interpretation of observed phenotypes. Moreover, repeat masking is required for tasks such as whole-genome alignment, promoter analysis, or pangenome exploration. Although homology-based annotation methods are computationally expensive, k-mer strategies for masking are orders of magnitude faster. Here, we benchmarked a two-step approach, where repeats were first called by k-mer counting and then annotated by comparison to curated libraries. This hybrid protocol was tested on 20 plant genomes from Ensembl, with the k-mer-based Repeat Detector (Red) and two repeat libraries (REdat, last updated in 2013, and nrTEplants, curated for this work). Custom libraries produced by RepeatModeler were also tested. We obtained repeated genome fractions that matched those reported in the literature but with shorter repeated elements than those produced directly by sequence homology. Inspection of the masked regions that overlapped genes revealed no preference for specific protein domains. Most Red-masked sequences could be successfully classified by sequence similarity, with the complete protocol taking less than 2 h on a desktop Linux box. A guide to curating your own repeat libraries and the scripts for masking and annotating plant genomes can be obtained at https://github.com/Ensembl/plant-scripts.
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