ArticlePlant biotechnology journal2021
Long-read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant.
Article in Plant biotechnology journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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40 citing papers in PubMed, 73 citations in OpenAlex.
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- Evolution and Comparative Analysis of Sheep Reference Genomes: From Fragmented Assemblies to Telomere-to-Telomere Genomics.Biology · 2026Review
- Accessing crop genetic diversity via pangenomics.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Genome-Wide, High-Density Genotyping Approaches for Plant Germplasm Characterisation (Methods and Applications).International journal of molecular sciences · 2025Review
- The Evolutionary Dynamics of Genetic Mutational Load Throughout Tomato Domestication History.Molecular ecology · 2025Article
- Pangenomic structural variant patterns reflect evolutionary diversification in Brassica napus.Genome biology · 2025Article
- Integrating genome assembly, structural variation map construction and GWAS reveal the impact of SVs on agronomic traits of Brassica napus.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 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
- Long-read sequencing reveals novel structural variation markers for key agronomic and quality traits of food-grade soybean.Frontiers in plant science · 2025Article
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- Construction and analysis of telomere-to-telomere genomes for 2 sweet oranges: Longhuihong and Newhall (Citrus sinensis).GigaScience · 2024Article
- Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences.Database : the journal of biological databases and curation · 2023Review
- A comprehensive lettuce variation map reveals the impact of structural variations in agronomic traits.BMC genomics · 2023Article
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- Benchmarking Oxford Nanopore read alignment-based insertion and deletion detection in crop plant genomes.The plant genome · 2023Article
- De Novo Structural Variations of Escherichia coli Detected by Nanopore Long-Read Sequencing.Genome biology and evolution · 2023Article
- Non-vernalization requirement for flowering in Brassica rapa conferred by a dominant allele of FLOWERING LOCUS T.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Accurate prediction of quantitative traits with failed SNP calls in canola and maize.Frontiers in plant science · 2023Article
- Overcoming genetic paucity ofFrontiers in plant science · 2023Review
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome structural variation (SV) contributes strongly to trait variation in eukaryotic species and may have an even higher functional significance than single-nucleotide polymorphism (SNP). In recent years, there have been a number of studies associating large chromosomal scale SV ranging from hundreds of kilobases all the way up to a few megabases to key agronomic traits in plant genomes. However, there have been little or no efforts towards cataloguing small- (30-10 000 bp) to mid-scale (10 000-30 000 bp) SV and their impact on evolution and adaptation-related traits in plants. This might be attributed to complex and highly duplicated nature of plant genomes, which makes them difficult to assess using high-throughput genome screening methods. Here, we describe how long-read sequencing technologies can overcome this problem, revealing a surprisingly high level of widespread, small- to mid-scale SV in a major allopolyploid crop species, Brassica napus. We found that up to 10% of all genes were affected by small- to mid-scale SV events. Nearly half of these SV events ranged between 100 bp and 1000 bp, which makes them challenging to detect using short-read Illumina sequencing. Examples demonstrating the contribution of such SV towards eco-geographical adaptation and disease resistance in oilseed rape suggest that revisiting complex plant genomes using medium-coverage long-read sequencing might reveal unexpected levels of functional gene variation, with major implications for trait regulation and crop improvement.
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