ArticleThe plant genome2023
Benchmarking Oxford Nanopore read alignment-based insertion and deletion detection in crop plant genomes.
Article in The plant genome, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- European ash pangenome reveals widespread structural variation and genetic basis of low ash dieback susceptibility.Nature communications · 2026Article
- T-DNA Analyzer: A Long-Read Sequencing Pipeline for Characterizing T-DNA Insertion Sites in Transgenic Crops.International journal of molecular sciences · 2026Article
- An integrated fine-mapping, re-sequencing and transcriptome analysis provides further insights and candidate genes for silique number in oilseed rape (Brassica napus L.).BMC plant biology · 2026Article
- Pangenomic structural variant patterns reflect evolutionary diversification in Brassica napus.Genome biology · 2025Article
- Graphical pangenomics-enabled characterization of structural variant impact on gene expression in Brassica napus.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Systematic benchmarking of tools for structural variation detection using short- and long-read sequencing data in pigs.iScience · 2025Article
- Toward a standardized framework for pangenome graph evaluation: assessing crop plant pangenome variation graph construction from multiple assemblies.GigaScience · 2025Article
- Performance of somatic structural variant calling in lung cancer using Oxford Nanopore sequencing technology.BMC genomics · 2024Article
- Benchmarking Oxford Nanopore read alignment-based insertion and deletion detection in crop plant genomes.The plant genome · 2023Article
Corrections and comments
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Authors and funding
6 authors.
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Abstract
Structural variations (SVs) are larger polymorphisms (> 50 bp in length), which consist of insertions, deletions, inversions, duplications, and translocations. They can have a strong impact on agronomical traits and play an important role in environmental adaptation. The development of long-read sequencing technologies, including Oxford Nanopore, allows for comprehensive SV discovery and characterization even in complex polyploid crop genomes. However, many of the SV discovery pipeline benchmarks do not include complex plant genome datasets. In this study, we benchmarked insertion and deletion detection by popular long-read alignment-based SV detection tools for crop plant genomes. We used real and simulated Oxford Nanopore reads for two crops, allotetraploid Brassica napus (oilseed rape) and diploid Solanum lycopersicum (tomato), and evaluated several read aligners and SV callers across 5×, 10×, and 20× coverages typically used in re-sequencing studies. We further validated our findings using maize and soybean datasets. Our benchmarks provide a useful guide for designing Oxford Nanopore re-sequencing projects and SV discovery pipelines for crop plants.
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