First haplotype-resolved genome assembly of citral-rich lemongrass Cymbopogon flexuosus var. Krishna

Abstract

Cymbopogon flexuosus var. Krishna (lemongrass) is an aromatic grass valued for its high citral content, which is widely used in the fragrance, flavor, and pharmaceutical industries. C. flexuosus, a member of the Poaceae family, is a predominantly outcrossing species characterized by a highly heterozygous genome. Despite its economic importance and widespread cultivation, a high-quality reference genome has been lacking. Here, we report the first chromosome-scale genome assembly of lemongrass, generated using PacBio HiFi long-read sequencing combined with Omni-C chromatin conformation capture data. The resulting pseudo-haploid assembly spans approximately 798 Mb, organized into 10 chromosomes, and exhibits a scaffold N50 of 64.35 Mb. The assembly demonstrates high completeness, with 99.8% BUSCO recovery, and comprises [~]37,254 predicted protein-coding genes. In addition, we generated haplotype-resolved assemblies that capture the allelic diversity of this heterozygous genome. The haplotypes have sizes of [~]750 Mb and [~]726 Mb, representing 95-98% of the pseudo-haploid genome, and together they provide phase-resolved information for gene families and biosynthetic pathways. These high-quality assemblies establish a foundational genomic resource for advancing molecular breeding, comparative genomics, and metabolic engineering of lemongrass and related aromatic grasses.