Transcriptome Landscape Variation in the Genus Thymus

Abstract

Among the Lamiaceae family, the genus Thymus is an economically important genera due to its medicinal and aromatic properties. Most Thymus molecular research has focused on the determining the phylogenetic relationships between different species, but no published work has focused on the evolution of the transcriptome across the genus to elucidate genes involved in terpenoid biosynthesis. Hence, in this study, the transcriptomes of five different Thymus species were generated and analyzed to mine putative genes involved in thymol and carvacrol biosynthesis. High-throughput sequencing produced ~43 million high-quality reads per sample, which were assembled de novo using several tools, then further subjected to a quality evaluation. The best assembly for each species was used as queries to search within the UniProt, KEGG (Kyoto Encyclopedia of Genes and Genomes), COG (Clusters of Orthologous Groups) and TF (Transcription Factors) databases. Mining the transcriptomes resulted in the identification of 592 single-copy orthogroups used for phylogenetic analysis. The data showed strongly support a close genetic relationship between Thymus vulgaris and Thymus daenensis. Additionally, this study dates the speciation events between 1.5–2.1 and 9–10.2 MYA according to different methodologies. Our study provides a global overview of genes related to the terpenoid pathway in Thymus, and can help establish an understanding of the relationship that exists among Thymus species.

Thymus zygis subsp. zygis an Endemic Portuguese Plant: Phytochemical Profiling, Antioxidant, Anti-Proliferative and Anti-Inflammatory Activities

“…The genus Thymus , belonging to the Lamiaceae family, includes ca. 350 species of perennial, subshrubs, and aromatic herbs native to Europe and North Africa, with many of them being endemic to the Mediterranean region [ 1 , 2 , 3 ]. Thymus plants are heliophylous, thus they grow well in a climate with moderate to warm temperatures, in well-drained to dry soils (usually they grow on rocks, stones, or sand), and in sunny places [ 4 ].…”

Transcriptome profiling of spike provides expression features of genes related to terpene biosynthesis in lavender

“…In this study, we applied the RNA-Seq approach to explore the transcriptome dynamics in two local lavender cultivars at three developmental stages in spikes and investigated the expression differences in genes related to EO synthesis. In comparison with other published transcriptome including several aromatic plants 29,31,32 , less than 80% SCO revealed that the assembly quality of lavender transcriptome could be further improved. In view of the complexity of lavender genome, our transcriptome data is acceptable.…”

“…Biosynthesis of Lavandula terpenes include mono, sesqui, di and triterpenes, which are catalysed by all kinds of terpene synthases 28 . Gene expression analysis through RNA-Seq from several aromatic plants revealed that genes related to terpene biosynthesis displayed a parallel expression pattern with the emission of some monoterpenes, indicating its regulatory role in monoterpene biosynthesis during flower development 2,29,31,32 . Here, two LaGPPS, one GGPPS, two rLinS were upregulated from Bud I to flowering stage 50%, and the expression pattern coincided with the production of EOs in two cultivars (Figs.…”

Transcriptome and phytochemical analyses provide insights into the organic sulfur pathway in Allium hirtifolium

“…In contrast, NAC family members participate in regulating plant growth and developmental processes 27,28 . Although the previous studies have revealed TFs are associated with secondary metabolism pathways 29,30 , little is about the TFs involved in the biosynthetic pathway of sulfur compounds. However, previous research has demonstrated www.nature.com/scientificreports/ that MYB, NAC, WRKY, and AP2/ERF are the most represented TFs in the transcriptome data of root, stem, bulb, and leaves of different Allium species 31 .…”