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bioRxiv · 10.64898/2026.02.17.706310

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

Tyagi, S.·Gupta, V.·Verma, S.·Negi, N. P.·Kumar, S.·Trivedi, P. K.
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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.

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Tyagi, S., Gupta, V., Verma, S., Negi, N. P., Kumar, S., Trivedi, P. K.. 2026-02-18. First haplotype-resolved genome assembly of citral-rich lemongrass Cymbopogon flexuosus var. Krishna. https://doi.org/10.64898/2026.02.17.706310

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