The chromosome-based lavender genome provides new insights into Lamiaceae evolution and terpenoid biosynthesis

Abstract

The aromatic shrub Lavandula angustifolia produces various volatile terpenoids that serve as resources for essential oils and function in plant-insect communication. To better understand the genetic basis of the terpenoid diversity in lavender, we present a high-quality reference genome for the Chinese lavender cultivar "Jingxun 2" using PacBio and Hi-C technologies to anchor the 894.50 Mb genome assembly into 27 pseudochromosomes. In addition to the γ triplication event, lavender underwent two rounds of whole-genome duplication (WGD) during the Eocene-Oligocene (29.6 MYA) and Miocene-Pliocene (6.9 MYA) transitions. As a result of tandem duplications and lineage-specific WGDs, gene families related to terpenoid biosynthesis in lavender are substantially expanded compared to those of five other species in Lamiaceae. Many terpenoid biosynthesis transcripts are abundant in glandular trichomes. We further integrated the contents of ecologically functional terpenoids and coexpressed terpenoid biosynthetic genes to construct terpenoid-gene networks. Typical gene clusters, including TPS-TPS, TPS-CYP450, and TPS-BAHD, linked with compounds that primarily function as attractants or repellents, were identified by their similar patterns of change during flower development or in response to methyl jasmonate. Comprehensive analysis of the genetic basis of the production of volatiles in lavender could serve as a foundation for future research into lavender evolution, phytochemistry, and ecology.

Fig. 1. Genomic landscape of lavender.

a Photo of L. angustifolia ‘Jingxun 2’ cultivated in Beijing. b Lavender genomic landscape. (I) Circular representation of the pseudomolecule. (II–IV) Gene density (500kb window), percent repeats (500kb window), and ncRNA content (500kb window). (V) Locations of tandem duplicated genes. Each line in the center of the circle connects a pair of homologous genes

Fig. 2. Lavender genome evolution.

a Phylogenetic tree with 59 single-copy orthologs from 13 species identified by OrthoMCL to show divergence times. The distribution of genes in each species is shown in the right panel. b Synonymous substitution rate (Ks) distributions of syntenic blocks for lavender paralogs and orthologs with Vvin and some species (Smil, Sspl, Sbai and Tgra) in Lamiaceae. Lang, L. angustifolia; Smil, Salvia miltiorrhiza; Sspl, Salvia splendens; Slyc, Solanum lycopersicum; Sbai, Scutellaria baicalensis; Tgra, Tectona grandis; Sind, Sesamum indicum; Cros, Catharanthus roseus; Rchi, Rosa chinensis; Hann, Helianthus annuus; Aann, Artemisia annua; Ptri, Populus trichocarpa, Vvin, Vitis vinifera; Atha, Arabidopsis thaliana. c The syntenic blocks among Lang, Vvin, and Sbai. d Summary of tandem duplications in lavender and four other Lamiaceae species. e The number of each type of tandem block in lavender and four other Lamiaceae species

Fig. 3. The sites, types, contents, and putative functions of volatile production in lavender.

a, b Surface and cross-section of the calyx of a blossom floret. These images were captured by CT. The glandular trichomes (GTs) of lavender are colored purple. c Top view and side view of a single GT separated from a flower at blossom. The GTs are composed of eight secretory cells and one secretory cavity. d–i Scanning electron microscopy images. The GTs of the flower (LAF), leaf (LAL), and stem (LAS) are colored purple, and non-GTs are in yellow. Scale bars = 1 mm (a, b); 50 μm (c–e, g, i); and 100 μm (f, h). j, k The relative and absolute contents of volatile terpenoids in LAF, LAL, and LAS. l The ecological function of the main volatiles emitted by opening flowers, flower buds, leaves, and stems. A large proportion of linalool, linalyl acetate, and lavandulyl acetate in opening flowers function as attractants for pollinators. At the flower bud stage, α-pinene, β-pinene, and β-ocimene, etc. provide defense against herbivores and predators. Borneol, camphor, 1,8-cineole, camphene, and bornyl acetate are the main compounds in leaves and stems and are always repellents to pests.

Fig. 4. Biosynthesis of volatile terpenoid in lavender.

a There are four steps required to produce diverse terpenoids. Enzymes involved at each step of the volatile terpenoid biosynthesis pathway are shown in blue, and intermediates are shown in black. Relative expression profiles of genes implicated in volatile terpenoid biosynthesis among various tissues (LAR, root; LAS, stem; LAL, leaf; LAF, flower; LAGT, glandular trichome) are presented as heatmaps (cyan–purple scale). Copy number variations of genes involved in volatile terpenoid biosynthesis in the ten plant species (from left to right: Lang, Sspl, Tgra, Smil, Sbai, Sind, Slyc, Hann, Rchi, and Atha) are shown in orange font. b–d Phylogeny of TPS subfamilies (b), CYP450 clans (c), and BAHD subfamilies (d) in lavender based on protein sequences. The gene numbers clustered into one category are indicated in green font. e Ks values and duplication/divergence times of genes involved in terpenoid biosynthesis in lavender. f Representative gene cluster with a physical link. Clusters TPS-TPS, TPS-BAHD, and TPS-CYP450 are shown.

Fig. 5. Gene-terpenoid network of candidates strongly associated with attractive and defensive terpenoids in lavender.

a Coexpression modules of terpenoid biosynthetic genes clustered by WGCNA. b Candidates strongly associated with attractive and defensive terpenoids in lavender. The large circles indicate the main terpenoids in lavender. Linalool, linalyl acetate, and lavandulyl acetate have sweet floral and refreshing odors and mainly function as attractants for pollinators; borneol, camphor, 1,8-cineole, camphene, and bornyl acetate are always repellents to pests. Genes clustered into different modules are filled in green, blue, turquoise, yellow, and brown. Circles and hexagons represent genes involved in one and two steps of terpenoid biosynthesis. TPSs, BAHDs, and genes belonging to the CYP71 clan are indicated by diamonds, triangles, and squares, respectively. Edges represent the correlation between terpenoids and genes. Purple lines indicate a positive correlation, whereas cyan lines indicate a negative correlation

Fig. 6. Transcriptional changes in representative genes in clusters in response to methyl jasmonate or during flower development.

Gene expression patterns among various tissues (LAR, LAS, LAL, LAF, and LAGT) were verified by qRT-PCR. Relative expression levels of these genes after leaf or flower treatment with methyl jasmonate (CKL, JAL, CKF, and JAF) and in flowers at different developmental stages (FB0, FB1, FB2, F3, F4, and F5) were determined. Values shown are mean ± SE of three replicates