Fast and cost-effective chromosome-scale scaffolding of low-coverage wheat assemblies using in silico optical maps

Abstract Bread wheat ( Triticum aestivum L., AABBDD) poses major challenges for genome assembly because of its large, polyploid, and highly repetitive genome. Although advances in long-read sequencing have improved contig assembly, generating chromosome-scale assemblies from low-coverage data remains difficult. Here, we explored whether low-coverage HiFi sequencing combined with in silico optical maps could provide a fast and computationally efficient option for chromosome-scale scaffolding and exploratory screening of candidate structural variants (SVs) in wheat. Reanalysis of HiFi data from the wheat cultivar ‘Lumai15’ produced a hifiasm contig assembly with an N50 of 6.90 Mb, after which in silico optical maps were used to anchor and order the contigs into chromosome-scale pseudomolecules. Across four wheat assemblies, the optical-map approach completed chromosome anchoring in 3–4 h, compared with 74–85 h for RagTag, while requiring similar peak memory, although anchoring rates were lower for some assemblies. An exploratory simulation-based assessment showed higher recall for ‘inversions’ ranging from 0.5 to 10 Mb than for interchromosomal ‘translocations’, indicating that the approach is more suitable for preliminary screening of large-scale rearrangements than for comprehensive SV detection. These results support the feasibility of using in silico optical maps as a practical option for rapid, reference-guided chromosome anchoring in selected applications.