A haplotype-resolved genome reveals intron expansion and enzyme innovation associated with the starch-to-fructan shift in Polygonatum cyrtonema.

Huangjing (Polygonati Rhizoma) is a traditional food-medicine substance in China, which can serve as a grain substitute historically. However, its material basis is not starch but agavin-type fructans with dual regulatory effects on energy and biological activity, which also constituted the staple diet component of prehistoric Mesoamerican humans. Yet, the formation mechanism of these compounds remains unclear. Here we presented a haplotype-resolved assembly of the Polygonatum cyrtonema giant genome, spanning two phased haplotypes of ∼7.18 Gb and 7.05 Gb respectively. Genomic analyses revealed two WGD events in P. cyrtonema including monocot ancient and Polygonatum-Dracaena shared. We demonstrated that specific LTR retrotransposon insertions into starch genes are associated with extreme intron elongation (mean ∼61 kb) and lower gene expression levels in the starch biosynthesis pathway. Resequencing of 261 Polygonatum accessions indicated seven genetic lineages and three geographic subgroups of P. cyrtonema, with genome wide association analysis identifying a significantly SNP associating fructan gene cluster region. More importantly, we uncovered a gain-of-function mechanism where a neofunctionalized enzyme, Pc6SFTL (P023394), acquired novel sucrose:fructan 6-fructosyltransferase (6-SFT) activity to catalyze the formation of highly branched agavins. Our findings illuminated TE-associated structural variation and enzymatic innovation contributing to carbon allocation of starch and fructan, establishing agavins as a promising candidate for starch-deficient functional staple foods.