Long-read genome assembly of high-erucic-acid Brassica napus reveals candidate structural variants in fatty acid metabolism genes

Rapeseed ( Brassica napus L.) is a globally important oilseed crop, while high-erucic-acid rapeseed (HEAR) provides a valuable source of erucic acid for diverse industrial applications. Despite the availability of several B. napus reference genomes, the structural genomic variation associated with erucic acid biosynthesis in HEAR germplasm remains insufficiently characterized. Characterizing structural variants (SVs) within fatty-acid-related genes may therefore improve understanding of the genomic variation underlying the HEAR phenotype. In this study, we present a high-quality reference-guided genome assembly of the HEAR genotype 13R4502 (UM_ B. napus Ver1) using PacBio HiFi long-read sequencing. The assembly spans ~ 1.03 Gb, with ~ 97% of the sequence anchored to 19 pseudomolecules, comprising 107,468 projected protein-coding gene models and repeatmasker annotated 60.34% of the assembly as repetitive sequence. Assembly completeness was confirmed with 99.6% complete BUSCO genes. Furthermore, assembly-independent comparison of PacBio and Oxford Nanopore read alignments identified 47,182 SVs supported by both sequencing datasets. Sixteen fatty-acid-related candidate SVs, including FAD2 , FAE1/KCS18 , KCS , KAR2 and ACX family genes, were supported by both platforms. Multi-reference genome comparisons provided additional support for four candidates, while PCR genotyping validated a 66-bp deletion in FAD2 and a 51-bp insertion in FAE1/KCS18 in 13R4502 relative to ZS11. UM_ B. napus Ver1 provides a contiguous genomic resource for the HEAR genotype 13R4502 and expands the genomic resources available for investigating fatty-acid related SVs in B. napus . Cross-platform read support, multi-reference comparisons and PCR validation strengthen the evidence for candidate SVs affecting fatty-acid-related genes. Nevertheless, their functional contributions to erucic acid accumulation require further transcriptomic, biochemical and genetic validation. This resource will facilitate comparative genomics and the investigation of genomic variation relevant to industrial rapeseed improvement.