Chromosome-level genome assembly provides insights into the genome evolution and functional importance of the phenylpropanoid-flavonoid pathway in Thymus mongolicus

Abstract

Background: Thymus mongolicus (family Lamiaceae) is a Thyme subshrub with strong aroma and remarkable environmental adaptability. Limited genomic information limits the use of this plant.

Results: Chromosome-level 605.2 Mb genome of T. mongolicus was generated, with 96.28% anchored to 12 pseudochromosomes. The repetitive sequences were dominant, accounting for 70.98%, and 32,593 protein-coding genes were predicted. Synteny analysis revealed that Lamiaceae species generally underwent two rounds of whole genome duplication; moreover, species-specific genome duplication was identified. A recent LTR retrotransposon burst and tandem duplication might play important roles in the formation of the Thymus genome. Using comparative genomic analysis, phylogenetic tree of seven Lamiaceae species was constructed, which revealed that Thyme plants evolved recently in the family. Under the phylogenetic framework, we performed functional enrichment analysis of the genes on nodes that contained the most gene duplication events (> 50% support) and of relevant significant expanded gene families. These genes were highly associated with environmental adaptation and biosynthesis of secondary metabolites. Combined transcriptome and metabolome analyses revealed that Peroxidases, Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferases, and 4-coumarate-CoA ligases genes were the essential regulators of the phenylpropanoid-flavonoid pathway. Their catalytic products (e.g., apigenin, naringenin chalcone, and several apigenin-related compounds) might be responsible for the environmental tolerance and aromatic properties of T. mongolicus.

Conclusion: This study enhanced the understanding of the genomic evolution of T. mongolicus, enabling further exploration of its unique traits and applications, and contributed to the understanding of Lamiaceae genomics and evolutionary biology.

Keywords: Thymus mongolicus; Chromosome-level genome; Genome evolution; Phenylpropanoid–flavonoid biosynthesis; Transcriptome and metabolome; Whole-genome duplication.

Fig. 1

The features of Thymus mongolicus genome. a The landscape of T. mongolicus genome. The circus plot from the outer to the inner circle represents chromosome-scale pseudochromosomes (Chr01–Chr12) (I), GC content (II), repeat element (III-1), Ty1/copia retrotransposons (III-2), Ty3/gypsy retrotransposons (III-3), gene density (IV), and each linking line in the center of the circus plot indicates the collinearity blocks panning more than 40 genes in the genome (V). b LTR assembly index (LAI) analysis for the referenced genomes. c T. mongolicus plant

Fig. 2

Evolution of T. mongolicus genome. a The dot plot of synteny blocks of T. mongolicus. b Intra- and inter-specific Ks densities of the identified synteny blocks in the analyzed genomes. c Genomic karyotype analysis of T. mongolicus, V. vinifera, and C. americana. Gray bands in the background indicate synteny blocks between the genomes. Some 1: 6 and 3: 1 blocks (V. vinifera vs. Thymus plants) are highlighted. d Estimation of the insertion of LTR retrotransposons in the analyzed genomes. e Clustering analysis of the Ty3/gypsy and Ty1/copia retrotransposons in the T. mongolicus genome

Fig. 3

Genome evolution and gene family analysis. a A phylogenetic tree was constructed based on 658 high-quality single-copy orthogroups from 10 plant species. Regions T and D represent the time of WGT and WGD in the species, respectively. The numbers of gene-family expansion and contraction on each branch are indicated by red and blue numbers, respectively. b Statistics of orthogroups on each node. Red represents all orthogroups. Blue represents orthogroups with > 50% support. c Statistics of duplicated genes on each node. Red represents all duplicated genes. Blue represents duplicated genes with > 50% support rate. d–f Wordcloud plot of KEGG enrichment analysis of the union of expanded gene families and duplicated genes at Nodes 1, 3, and 8, respectively. Word size represents gene number in a pathway

Fig. 4

Gene composition, evolution, and expression characteristics of phenylpropanoid–flavonoid (PF) biosynthetic pathway in T. mongolicus. a Composition and location of PF-biosynthetic-pathway-related genes of T. mongolicus. The circle plot represents the distribution of genes associated with the PF pathway in the T. mongolicus genome. The bar chart in the upper right corner of the circle plot indicates the origin of the PF genes in the species. DSD, dispersed duplication; PD, proximal duplication; TD, tandem duplication; TRD, transposed duplication; WGD, whole-genome duplication. b Ka/Ks ratios and Ks values of gene pairs originating from different types of gene duplication. c Genes encoding key enzymes of PF pathway in T. mongolicus and their origin from different types of gene duplication. The color and size of the bubbles represent the duplication types and numbers of genes in the pathway. d Expression profiling of DEGs from PF pathway in four tissues in T. mongolicus. Abbreviations: C4H, Cinnamate 4-monooxygenase; COMT, Caffeic acid 3-Omethyltransferase; CCR, Cinnamoyl-CoA reductase; 4CL, 4-coumarate-CoA ligase; HCT, Shikimate Ohydroxycinnamoyltransferase; REF1, Coniferyl-aldehyde dehydrogenase; CAD, Cinnamyl-alcohol dehydrogenase; CHI, chalcone isomerase; CHS, chalcone synthase; CCoAOMT, caffeoyl-CoA 3-O-methyltransferase; DFR, dihydroflflavonol 4-reductase; F3H, naringenin 3-dioxygenase; F5H, ferulate 5-hydroxylase; PAL, phenylalanine ammonia-lyase; POD, peroxidase; C3ʹH, 5-O-(4-coumaroyl)-D-quinate 3ʹ-monooxygenase; F3ʹH, flavonoid 3'-monooxygenase; FLS, flavonol synthase; CSE, caffeoylshikimate esterase; ANS, leucoanthocyanidin dioxygenase. e Metabolome characteristics of PF pathway in T. mongolicus. The colored circles represent the abundance of the metabolites identified in the PF pathway in four tissues

Fig. 5

Gene co-expression network and transcription factor (TF) identification. a Weighted gene co-expression network analysis of genes and metabolites identified in the PF pathway in T. mongolicus. b and c Transcriptional regulatory network of PF-pathway-related genes and TFs in green and yellow modules. Diamonds and circles represent PF-pathway-related genes and their regulated TFs, respectively. Lines indicate correlation