Long-read sequencing reveals structural variations associated with erucic acid biosynthesis in Brassica napus

Rapeseed (Brassica napus L.) is an important oilseed crop worldwide, with high erucic acid rapeseed (HEAR) cultivars valued for commercial and industrial uses. Despite the availability of multiple reference genomes, the genetic basis underlying erucic acid biosynthesis remains poorly characterized, particularly in HEAR cultivars in B. napus. Structural variations (SVs) are known to influence key agronomic traits, yet their contribution to high erucic acid accumulation has not been systematically investigated. In this study, we present a high-quality reference-aligned genome assembly of the HEAR genotype 13R4502 (UM_B.napus Ver1) using PacBio HiFi long-read sequencing. The assembly spans ~1.03 Gb across 19 pseudochromosomes, comprising 107,468 high-confidence protein-coding genes and ~60% repetitive content. Assembly completeness was confirmed with 99.6% complete BUSCO genes, and extensive repeat annotation revealed a predominance of Helitrons, indicating historical transposition events. Furthermore, systematic profiling and comparative genomics to low erucic acid cultivars (LEA) (ZS11) identified 3,450 structural variants (SVs) affecting key genes involved in fatty acid biosynthesis including (FAD2, FAE, and multiple KCS paralogs). The UM_B.napus Ver1 genome provides reference for HEAR cultivars, capturing SVs previously inaccessible with low erucic acid LEA references. The genomic resource created in this study enables functional characterization of genes controlling erucic acid biosynthesis and offers a foundation for precision breeding and metabolic engineering in B. napus. Additionally, this assembly demonstrates the utility of long-read sequencing combined with reference-guided scaffolding to attain high structural accuracy and gene completeness in complex polyploid genomes.