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

Autor: Yildiz G; Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany., Zanini SF; Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany., Afsharyan NP; Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany., Obermeier C; Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany., Snowdon RJ; Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany., Golicz AA; Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany.
Jazyk: angličtina
Zdroj: The plant genome [Plant Genome] 2023 Jun; Vol. 16 (2), pp. e20314. Date of Electronic Publication: 2023 Mar 29.
DOI: 10.1002/tpg2.20314
Abstrakt: 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.
(© 2023 The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)
Databáze: MEDLINE
Externí odkaz: