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. 2019 Aug 16;10(8):620.
doi: 10.3390/genes10080620.

Transcriptome Landscape Variation in the Genus Thymus

Aboozar Soorni  1 , Tahereh Borna  2 , Ali Alemardan  2 , Manohar Chakrabarti  3 , Arthur G Hunt  3 , Aureliano Bombarely  4   5
Affiliations

Transcriptome Landscape Variation in the Genus Thymus

Aboozar Soorni et al. Genes (Basel). .

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.

Keywords: Thymus; phylotranscriptome; terpenoid biosynthesis; transcriptome.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Venn diagram showing the number of overlapping proteins between the five Thymus transcriptome assemblies.
Figure 2
Figure 2
Gene ontology (GO) classification map derived from Thymus transcriptomes. The results are summarized in three GO categories: biological process, molecular function, and cellular component. The x-axis indicates the percentage of sequences in each category.
Figure 3
Figure 3
COG classification map. The abscissa represents 24 COG group names, while the vertical axis represents the number of unigenes annotated into each group.
Figure 4
Figure 4
Distribution of transcripts in different transcription factor (TF) families showing over-representation in bHLH.
Figure 5
Figure 5
Maximum likelihood (ML) phylogeny of putative TPS genes in Thymus species compared to other species of TPS subfamilies.
Figure 6
Figure 6
Phylogenetic relationships among five Thymus species inferred from 592 single-copy orthogroups. (A) Maximum likelihood tree. (B) Bayesian tree.
Figure 7
Figure 7
Ks distribution plots for T. daenensis and T. persicus. The components are (1) background gene duplications (green), (2) putative whole-genome duplications (purple), (3) alleles or sequencing errors resulting in high identity transcripts (blue), and (4) potential whole-genome duplications with low support (black).
See this image and copyright information in PMC

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