<b>Revisiting the genome assembly of </b><b>Lupinus </b><b>species reveals differential diploidization after a shared whole-genome duplication</b>

Accurate genome assemblies are essential for comparative genomics, yet Hi-C-guided scaffolding can introduce structural errors that misrepresent chromosome architecture and bias evolutionary inferences. Here, we identified pervasive scaffolding errors - including artificial fusions, internal inversions, and incomplete contig mounting - in two previously published Lupinus genomes (L. cosentiniiand L. digitatus) using a segmentation method based on LTR retrotransposon density. We re-assembled both genomes, producing chromosome-level references of 472.7Mb (16 chromosomes) and 427.2Mb (21 chromosomes), with BUSCO completeness >98.5%. Synteny validation and re-application of LTR profiling confirmed that all prior errors were resolved.