Haplotype-resolved chromosome-level genome sequence of Elsholtzia splendens (Nakai ex F.Maek.)

Abstract

Elsholtzia splendens, a perennial herb native to East Asia, is valued for its ornamental and medicinal uses, particularly in treating inflammatory and febrile conditions. Recent studies have highlighted its antibacterial, anti-inflammatory, antidepressant, antithrombotic, and lipid-lowering properties of its compounds. Additionally, E. splendens shows potential for phytoremediation owing to its ability to hyperaccumulate copper (Cu), lead (Pb), zinc (Zn), and cadmium (Cd). However, its role in remediation conflicts with its medicinal use because of the risk of heavy metal accumulation. Genome sequencing will be key to boosting beneficial compound production and reducing heavy metal risks. In this study, we generated a high-resolution, haplotype-resolved, chromosome-scale genome sequence of E. splendens using PacBio Revio long-read, Illumina short-read, and Hi-C sequencing technologies. The haplotype genome assemblies, spanned 275.4 and 265.0 Mbp with a scaffold N50 of 33.9 and 33.8 Mbp for haplotype 1 and 2, respectively. This assembly provides valuable insights into medicinal compound biosynthesis and supports genetic conservation efforts, facilitating future genetic and biotechnological applications of E. splendens for medicinal and ecological uses.

Fig. 1

The appearance of Elsholtzia splendens plant. The picture was taken from the plant grown for four months.

Fig. 2

The K-mer frequency distribution of E. splendens genome.

Fig. 3

The Hi-C interaction map of haplotype-resolved chromosome level assembly of E. splendens genome. Hi-C interaction between 16 chromosomes was depicted. Note that the chrosomes were ordered by the size, and unplaced contigs were excluded in the Hi-C interaction map.

Fig. 4

Circular map of the genomic features of E. splendens. (a) Density of total repetitive sequences. (b) Density of Copia-type LTR elements. (c) Density of Gypsy-type LTR elements. (d) Density of high-confident E. splendens gene models. (e) GC contents. (f) Syntenic relationships between homologous chromosomes. (g) Syntenic relationships between non-homologous chromosomes. Density of genomic features were measured on the non-overlapping 100 kbp windows.

Fig. 5

Impact of repetitive sequences on the chromosomal length disparity between homologous chromosome sets. Correlation between the difference in (a) the amount and (b) the total genomic span of repetitive sequences and the length disparity between homologous chromosome pairs is visualized.