Benchmarking Oxford Nanopore read alignment‐based insertion and deletion detection in crop plant genomes

• Published in: The plant genome 2023-06, Vol.16 (2), p.e20314-n/a
• Main Authors: Yildiz, Gözde, Zanini, Silvia F., Afsharyan, Nazanin P., Obermeier, Christian, Snowdon, Rod J., Golicz, Agnieszka A.
• Format: Article
• Language: English
• Subjects: Accuracy; Algorithms; Benchmarking; Benchmarks; Brassica napus; Corn; Crops; Datasets; Diploids; Gene deletion; Genome, Plant; Genomes; High-Throughput Nucleotide Sequencing; Insertion; Nanopores; Polyploidy; Sequence Analysis, DNA; Simulation; Software; Solanum lycopersicum; Translocation
• ISSN: 1940-3372; 1940-3372
• DOI: 10.1002/tpg2.20314

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. Core Ideas Structural variants (SVs) have strong impact on crop traits and play an important role in environmental adaptation. Long read based SV discovery tools have not been comprehensively evaluated in crops. We benchmarked popular SV discovery tools using real and simulated data for two contrasting crop genomes. Our benchmarks provide a guide for choosing insertion and deletion discovery tools for low to medium sequencing coverage experiments.