Hybrid genome and enzyme characterization uncover novel glycosyltransferases associated with benzylisoquinoline alkaloid chemodiversity in lotus

Authors

• Hedi Zhao, China Academy of Chinese Medical Sciences
• Xinyi Qi, China Academy of Chinese Medical Sciences
• Yan Liu, China Academy of Chinese Medical Sciences
• Zhuyin Chen, China Academy of Chinese Medical Sciences
• Yifan Wang, China Academy of Chinese Medical Sciences
• Jing Que, China Academy of Chinese Medical Sciences
• Yanyan Su, Amway (China) Botanical R&D Center
• Ling Yuan, University of KentuckyFollow
• Gangqiang Dong, Amway (China) Botanical R&D CenterFollow
• An Liu, China Academy of Chinese Medical SciencesFollow
• Zhennan Wang, China Academy of Chinese Medical SciencesFollow
• Sha Chen, China Academy of Chinese Medical SciencesFollow

Abstract

Introduction: Hybridization is a key evolutionary force that enriches genetic diversity and is associated with metabolic innovation. Lotus (Nelumbo), comprising Asian lotus (N. nucifera) and American lotus (N. lutea), is both a culturally important ornamental and medicinal plant rich in benzylisoquinoline alkaloids (BIAs). However, the genomic and biochemical basis of BIA glycoside biosynthesis remains poorly understood. Objectives: A high-quality hybrid lotus genome was presented to dissect the formation of benzylisoquinoline alkaloid glycosides and the mechanism underlying their synthesis. Methods: The chromosomal-level hybrid genome was constructed through PacBio HiFi, ONT Ultra-long, and Hi-C sequencing data combined assembly strategies. The metabolite and enzyme function were assayed by LC-MS. Multi-omics and molecular dynamics simulations (MD) revealed the catalytic mechanism of seven tandemly duplicated UGT75C genes. Results: Here, we present a high-quality haplotype-resolved genome of an Asian-American hybrid lotus (Nn × Nl CB), complemented by new assemblies of one N. lutea and four N. nucifera accessions. Comparative genomics revealed divergence time between the two species and extensive interspecific recombination in hybrids. Metabolite profiling uncovered armepavine-4′- O -glucoside, a novel BIA glycoside preferentially accumulated in cotyledons and hybrid cultivars. Weighted gene co-expression network analysis (WGCNA) and Gene Ontology (GO) analysis identified a cotyledon-specific module enriched in UDP-glycosyltransferases (UGTs). Seven tandemly duplicated UGT75C genes, derived from both parental genomes, were cloned and biochemically characterized. Functional assays demonstrated strict substrate and donor specificity, with NnUGT75C2 exhibiting the highest catalytic efficiency toward armepavine and norarmepavine. MD and MM/PBSA analyses identified key catalytic residues, and site-directed mutagenesis validated E321D as an activity-enhancing substitution. Conclusion: Together, these results uncover the genetic and biochemical basis of BIA glycoside biosynthesis in lotus, highlight tandem duplication and hybridization as promoters of chemodiversity, and provide molecular targets for breeding and metabolic engineering of high-value medicinal cultivars.

Document Type

Article

Publication Date

1-1-2026

Notes/Citation Information

Publisher Copyright: Copyright © 2026. Published by Elsevier B.V.

Digital Object Identifier (DOI)

10.1016/j.jare.2026.04.032

Archival?

Archival

Repository Citation

Zhao, Hedi; Qi, Xinyi; Liu, Yan; Chen, Zhuyin; Wang, Yifan; Que, Jing; Su, Yanyan; Yuan, Ling; Dong, Gangqiang; Liu, An; Wang, Zhennan; and Chen, Sha, "Hybrid genome and enzyme characterization uncover novel glycosyltransferases associated with benzylisoquinoline alkaloid chemodiversity in lotus" (2026). Plant and Soil Sciences Faculty Publications. 211.
https://uknowledge.uky.edu/pss_facpub/211