Journal article

Authors list: Yildiz, Gözde; Zanini, Silvia F.; Afsharyan, Nazanin P.; Obermeier, Christian; Snowdon, Rod J.; Golicz, Agnieszka A.

Publication year: 2023

Journal: The Plant Genome

Volume number: 16

Issue number: 2

eISSN: 1940-3372

Open access status: Gold

DOI Link: https://doi.org/10.1002/tpg2.20314

Publisher: Wiley

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.

Harvard Citation style: Yildiz, G., Zanini, S., Afsharyan, N., Obermeier, C., Snowdon, R. and Golicz, A. (2023) Benchmarking Oxford Nanopore read alignment-based insertion and deletion detection in crop plant genomes, The Plant Genome, 16(2), Article e20314. https://doi.org/10.1002/tpg2.20314

APA Citation style: Yildiz, G., Zanini, S., Afsharyan, N., Obermeier, C., Snowdon, R., & Golicz, A. (2023). Benchmarking Oxford Nanopore read alignment-based insertion and deletion detection in crop plant genomes. The Plant Genome. 16(2), Article e20314. https://doi.org/10.1002/tpg2.20314