New genome assembly of narrow-leafed lupin (Lupinus angustifolius) and its pan-genome. Pan-genome of narrow leaf lupin

The lack of sufficient genetic variation in crop varieties due to a domestication bottleneck is an increasing concern for sustaining global food supplies. Countering this concern requires a clear understanding of the domestication process and dynamics of domestication bottlenecks. The long and complicated domestication process in major crops makes it difficult to identify components of the bottleneck. Narrow-leafed lupin (Lupinus angustifolius) has experienced rapid domestication and become the newest crop with key domestication traits being fixed from mutations in natural populations within 50 years. Here, we assemble the third-generation reference genome of narrow-leafed lupin cultivar Tanjil, comprising 20 pseudochromosomes with a total genome size of 772.1 Mb and contig N50 = 5.65 Mb. We identify the key mutation resulting in low seed alkaloid levels that initiated the domestication of narrow-leafed lupin. A comparative analysis of genomic diversity in cultivars and wild types identified an apparent domestication bottleneck, as predicted by the original model of the bottleneck effect on genetic variability in populations. Our findings provide the first direct genomic evidence for a domestication bottleneck and open up the possibility of knowledge-driven de novo domestication of wild plants as an avenue to broaden crop plant diversity to enhance food security and sustainable low-carbon emission agriculture.