Journal of Plant Biochemistry and Biotechnology

, Volume 28, Issue 4, pp 496–508 | Cite as

Transcriptome analysis of Ajowan (Trachyspermum ammi L.) inflorescence

  • Mahboubeh AmiripourEmail author
  • Seyed Ahmad Sadat Noori
  • Vahid Shariati
  • Mehdi Soltani Howyzeh
Original Article


Trachyspermum ammi (L.) Sprague, commonly known as ‘Ajowan’, belongs to the family ‘Apiaceae’. Ajowan fruits yield 2–6% essential oil, and thymol is the major constituent of the oil (35–60%). T. ammi is of high medicinal value; however, the genomic resources for this medicinal plant are rare. To obtain transcript sequences of ajowan inflorescence, RNA-Seq was applied using Illumina HiSeq 2000 platform. Following de novo assembly, 68051 unigenes were produced, among which 43156 unigenes were annotated against different sequence databases. Blastx results of ajowan unigenes showed that 41950 and 29273 unigenes were hit in the NCBI non-redundant (Nr) protein and UniProt databases, respectively. Gene Ontology (GO) classification showed that 29258 unigenes were categorized into 55 GO terms, and 26002 unigenes were clustered in the Orthologous Group categories. Blastx results against the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database indicated that 14986 unigenes were represented in 127 pathways. In addition, 8751 sequences containing simple sequence repeats (SSRs) and 1180 putative transcription factor genes were also identified. As far as we know, this repository of genomic information is the first resource currently available for transcriptome characterization, gene discovery, developing SSR molecular markers and future genomic research on ajowan.


RNA-seq Ajowan Terpenoid biosynthesis Transcription factor Simple sequence repeat 



2-C-methyl-D-erythritol 4-phosphate pathway


Mevalonic acid pathway


Cytochrome P450



The authors sincerely thank Research Institute of Forests and Rangelands, Tehran, Iran for the assistance in providing our plant materials. This work was supported by Prof. M. H. Assareh, the Secretary General of National Council for Science & Technology, Development of Herbal & Traditional Medicine, Vice-Presidency for Science and Technology, Presidency of the Islamic Republic of Iran.


This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Data access

The datasets generated during the current study are available in the Sequence Read Archive (SRA) at NCBI under the accession number SRR5137050. [].

Supplementary material

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Copyright information

© Society for Plant Biochemistry and Biotechnology 2019

Authors and Affiliations

  • Mahboubeh Amiripour
    • 1
    Email author
  • Seyed Ahmad Sadat Noori
    • 1
  • Vahid Shariati
    • 2
  • Mehdi Soltani Howyzeh
    • 1
    • 3
  1. 1.Department of Agronomy and Plant Breeding Sciences, College of AbouraihanUniversity of TehranTehranIran
  2. 2.Department of Plant BiotechnologyNational Institute of Genetic Engineering and BiotechnologyTehranIran
  3. 3.Department of Genetics and Plant Breeding, Ahvaz BranchIslamic Azad UniversityAhvazIran

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