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Transcriptome Landscape Variation in the Genus Thymus

Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan 84156-83111, Iran
Department of Horticultural Science, College of Agriculture and Natural Resources, University of Tehran, Karaj 31587-11167, Iran
Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, USA
School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24060, USA
Department of Bioscience, University of Milano, 20133 Milan, Italy
Authors to whom correspondence should be addressed.
Genes 2019, 10(8), 620;
Received: 10 May 2019 / Revised: 31 July 2019 / Accepted: 12 August 2019 / Published: 16 August 2019
(This article belongs to the Section Plant Genetics and Genomics)
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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. View Full-Text
Keywords: Thymus; terpenoid biosynthesis; transcriptome; phylotranscriptome Thymus; terpenoid biosynthesis; transcriptome; phylotranscriptome

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Soorni, A.; Borna, T.; Alemardan, A.; Chakrabarti, M.; Hunt, A.G.; Bombarely, A. Transcriptome Landscape Variation in the Genus Thymus. Genes 2019, 10, 620.

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