Long‐read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant

• DOI: 10.1111/pbi.13456
• Publication Date: 2020-08-01T05:41:00Z
• Authors: Harmeet Singh Chawla; HueyTyng Lee; Iulian Gabur; Paul Vollrath; Suriya Tamilselva...; Christian Obermeier; Sarah V. Schiessl; Jia‐Ming Song; Kede Liu; Liang Guo; Isobel A. P. Parkin; Rod J. Snowdon
• Keywords: Structural Variation; Trait

Summary Genome structural variation (SV) contributes strongly to trait in eukaryotic species and may have an even higher functional significance than single‐nucleotide polymorphism (SNP). In recent years, there been a number of studies associating large chromosomal scale SV ranging from hundreds kilobases all the way up few megabases key agronomic traits plant genomes. However, little or no efforts towards cataloguing small‐ (30–10 000 bp) mid‐scale (10 000–30 their impact on evolution adaptation‐related plants. This might be attributed complex highly duplicated nature genomes, which makes them difficult assess using high‐throughput genome screening methods. Here, we describe how long‐read sequencing technologies can overcome this problem, revealing surprisingly high level widespread, major allopolyploid crop species, Brassica napus . We found that 10% genes were affected by events. Nearly half these events ranged between 100 bp 1000 bp, challenging detect short‐read Illumina sequencing. Examples demonstrating contribution such eco‐geographical adaptation disease resistance oilseed rape suggest revisiting genomes medium‐coverage reveal unexpected levels gene variation, with implications for regulation improvement.