Citronella is widely valued for its fragrance, medicinal potential, and defensive properties, yet the genetic basis of its characteristic citronelloid compounds has remained unclear. A new multi-omics study presents the first haplotype-resolved chromosome-level genomes of two Cymbopogon species and uncovers the evolutionary and cellular foundations of citronelloid biosynthesis. By integrating genomics, transcriptomics, metabolomics, and single-cell RNA sequencing, researchers identified key candidate genes—including members of the terpene synthase (TPS), alcohol dehydrogenase (ADH), and reductase families—strongly associated with citronellal and citronellol production. The findings provide a molecular framework explaining both species divergence and tissue-specific accumulation of these economically important metabolites.
Citronelloid compounds such as citronellal and citronellol function in plant defense and ecological communication, and they are also widely used in pharmaceuticals and essential oils. Within the Poaceae family, species of the genus Cymbopogon display striking differences in citronelloid accumulation, yet the evolutionary origin and biosynthetic regulation of these compounds have remained poorly understood. The absence of high-quality reference genomes has limited functional gene identification and comparative evolutionary analysis. Moreover, the cellular compartmentation of citronelloid biosynthesis has not been clarified. Based on these challenges, comprehensive genome assembly and integrative multi-omics analysis are urgently needed to dissect the molecular mechanisms underlying citronelloid biosynthesis.
Researchers from Sun Yat-Sen University report (DOI: 10.1093/hr/uhaf287) in Horticulture Research (2026) the first haplotype-resolved reference genomes of Cymbopogon winterianus and Cymbopogon distans. Using PacBio HiFi and Hi-C sequencing, the team assembled high-quality diploid and tetraploid genomes and performed comparative evolutionary analyses across 21 plant species. Through metabolome–transcriptome association and single-cell RNA sequencing of leaves, the study identifies candidate genes and cell-type-specific expression patterns responsible for citronelloid biosynthesis, offering new insights into terpene evolution within the Poaceae family.
The researchers assembled 1.49 Gb and 2.58 Gb genomes for diploid C. winterianus and tetraploid C. distans, respectively, achieving 99.1% completeness. Comparative analyses revealed strong chromosomal collinearity with Sorghum bicolor, indicating shared whole-genome duplication history and divergence approximately 19.2 million years ago.
Gene family analysis showed expansion of early terpenoid pathway genes—including 3-hydroxy-3-methylglutaryl-CoA synthase (HMGS), 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), and isopentenyl diphosphate isomerase (IDI)—in Poaceae species. Notably, terpene synthase (TPS) genes were markedly expanded in Cymbopogon, consistent with its rich volatile profile.
Metabolomic profiling identified 1,158 volatile compounds, with terpenoids representing the largest fraction. Citronellal, citronellol, geraniol, and related monoterpenes accumulated predominantly in leaves. Integrative correlation analysis pinpointed 19 candidate genes strongly associated with citronelloid content (R > 0.99), including seven TPS, five ADH, two OPR, and five CAR genes.
Single-cell RNA sequencing further revealed spatial specialization: most candidate TPS genes were highly expressed in mesophyll cells, suggesting this cell type as a key metabolic hub. Meanwhile, dehydrogenases and reductases displayed cell-type-specific patterns, implying metabolic compartmentation within leaves. Together, these findings map citronelloid biosynthesis from genome evolution to cellular resolution.
"This is the first time we can trace citronelloid biosynthesis from evolutionary history down to specific leaf cell types," said the corresponding author. "By integrating genome assembly with metabolomics and single-cell transcriptomics, we were able to connect gene family expansion, pathway diversification, and cellular expression specialization. These results not only clarify how citronella produces its characteristic compounds but also establish a genomic foundation for future functional validation and metabolic engineering."
The newly generated genomic resources provide a platform for molecular breeding and essential oil optimization in Cymbopogon. Identification of TPS-, ADH-, OPR-, and CAR-related candidate genes enables targeted manipulation of citronelloid composition for pharmaceutical and industrial applications. Furthermore, the discovery of cell-type-specific expression patterns opens possibilities for precision metabolic engineering by modulating pathway compartmentation. Beyond citronella, this study offers a comparative framework for understanding terpene evolution across monocots and aromatic plants. As demand for plant-derived bioactive compounds increases, integrating high-resolution genomics with cellular transcriptomics may accelerate the domestication and metabolic enhancement of other economically important species.
