Chromosome-level genome assembly of yellow lupin (Lupinus luteus) provides novel insights into genome evolution, crop adaptation and seed protein in the three most cultivated lupins

Lupinus luteus is a grain legume crop of agricultural importance due to its high seed protein content. In this study, the first chromosome-scale genome assembly of L. luteus (962.97 Mb) is presented, integrating data from Illumina, PacBio, and Hi-C platforms. The assembly exhibits exceptional completeness (98.9% BUSCO score) and a high repetition rate (76.15%). Genomic annotation identifies 36,884 protein-coding genes, including 2,492 transcription factors and 23 microRNA families. Synteny analysis with lupin species reveals important chromosomal rearrangements, indicating complex interactions between conserved regions and structural variations. Our analyses suggest that chromosome 8 may have originated from a translocation event involving two chromosomes during the speciation of L. luteus . Orthologous group characterization between L. luteus and related species indicates an enrichment in gene families associated with biotic and abiotic stress responses, secondary metabolism, and nutrient reservoir activity. Moreover, 911 resistance (R) genes are identified, highlighting their importance in pathogen defence. Exploration of alkaloid biosynthesis and regulation reveals 16 genes associated with quinolizidine alkaloids (QAs) with expression analysis revealing tissue-specific expression patterns for key enzymes in QA biosynthesis. Furthermore, secondary metabolite transporters are explored, including a Lupinus angustifolius PUP1 ortholog, providing insights into QA translocation mechanisms. This comprehensive genome analysis provides valuable resources for further understanding the genetic basis of important traits in Lupinus luteus , facilitating advancements in crop adaptation, improvement, and sustainability.