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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
  • 36 Downloads

Abstract

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.

Keywords

RNA-seq Ajowan Terpenoid biosynthesis Transcription factor Simple sequence repeat 

Abbreviations

MEP

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

MVA

Mevalonic acid pathway

CYP

Cytochrome P450

Notes

Acknowledgements

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.

Funding

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. [https://www.ncbi.nlm.nih.gov/sra].

Supplementary material

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References

  1. Bairwa R (2012) Medicinal uses of Trachyspermum ammi: a review. Pharma Res 5:247–258Google Scholar
  2. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120.  https://doi.org/10.1093/bioinformatics/btu170 CrossRefPubMedPubMedCentralGoogle Scholar
  3. Brautigam A, Mullick T, Schliesky S, Weber AP (2011) Critical assessment of assembly strategies for non-model species mRNA-Seq data and application of next-generation sequencing to the comparison of C3 and C4 species. J Exp Bot 62:3093–3102PubMedGoogle Scholar
  4. Carretero-Paulet L, Cairo A, Botella-Pavía P, Besumbes O, Campos N, Boronat A, Rodríguez-Concepción M (2006) Enhanced flux through the methylerythritol 4-phosphate pathway in Arabidopsis plants overexpressing deoxyxylulose 5-phosphate reductoisomerase. Plant Mol Biol 62:683–695PubMedGoogle Scholar
  5. Chen Y-Y, Wang L-F, Dai L-J, Yang S-G, Tian W-M (2012) Characterization of HbEREBP1, a wound-responsive transcription factor gene in laticifers of Hevea brasiliensis Muell. Arg. Mol Biol Rep 39:3713–3719PubMedGoogle Scholar
  6. Chow KS, Mat-Isa MN, Bahari A, Ghazali AK, Alias H, Mohd-Zainuddin Z, Wan KL (2012) Metabolic routes affecting rubber biosynthesis in Hevea brasiliensis latex. J Exp Bot 63(5):1863–1871.  https://doi.org/10.1093/jxb/err363 CrossRefPubMedGoogle Scholar
  7. Clouse SD (1996) Molecular genetic studies confirm the role of brassinosteroids in plant growth and development. Plant J 10:1–8PubMedGoogle Scholar
  8. Drew DP, Dueholm B, Weitzel C, Zhang Y, Sensen CW, Simonsen HT (2013) Transcriptome analysis of Thapsia laciniata Rouy provides insights into terpenoid biosynthesis and diversity in Apiaceae. Int J Mol Sci 14:9080–9098PubMedPubMedCentralGoogle Scholar
  9. Dudareva N et al (2005) The nonmevalonate pathway supports both monoterpene and sesquiterpene formation in snapdragon flowers. Proc Natl Acad Sci USA 102:933–938PubMedGoogle Scholar
  10. Dwivedi S, Mishra R, Alava S (2012) Phytochemistry, Pharmacological studies and Traditional benefits of Trachyspermum ammi (Linn.) Sprague. Int J Pharm Life Sci 3(5):1705–1709Google Scholar
  11. Eisenreich W, Schwarz M, Cartayrade A, Arigoni D, Zenk MH, Bacher A (1998) The deoxyxylulose phosphate pathway of terpenoid biosynthesis in plants and microorganisms. Chem Biol 5:R221–R233PubMedGoogle Scholar
  12. Enfissi E, Fraser PD, Lois LM, Boronat A, Schuch W, Bramley PM (2005) Metabolic engineering of the mevalonate and non-mevalonate isopentenyl diphosphate-forming pathways for the production of health-promoting isoprenoids in tomato. Plant Biotechnol J 3:17–27PubMedGoogle Scholar
  13. Fu N, Wang Q, Shen H-L (2013) De novo assembly, gene annotation and marker development using Illumina paired-end transcriptome sequences in celery (Apium graveolens L.). PloS ONE 8:e57686PubMedPubMedCentralGoogle Scholar
  14. Gantet P, Memelink J (2002) Transcription factors: tools to engineer the production of pharmacologically active plant metabolites. Trends Pharmacol Sci 23:563–569PubMedGoogle Scholar
  15. Goldstein DB, Linares AR, Cavalli-Sforza LL, Feldman MW (1995) An evaluation of genetic distances for use with microsatellite loci. Genetics 139:463–471PubMedPubMedCentralGoogle Scholar
  16. Grabherr MG et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652PubMedPubMedCentralGoogle Scholar
  17. Haas BJ et al (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8:1494–1512PubMedGoogle Scholar
  18. Heidari EF, Rahimmalek M, Mohammadi S, Ehtemam MH (2016) Genetic structure and diversity of ajowan (Trachyspermum ammi) populations based on molecular, morphological markers, and volatile oil content. Ind Crops Prod 92:186–196Google Scholar
  19. Heim MA, Jakoby M, Werber M, Martin C, Weisshaar B, Bailey PC (2003) The basic helix–loop–helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Mol Biol Evol 20:735–747PubMedGoogle Scholar
  20. Hemmerlin A, Harwood JL, Bach TJ (2012) A raison d’être for two distinct pathways in the early steps of plant isoprenoid biosynthesis? Prog Lipid Res 51:95–148PubMedGoogle Scholar
  21. Iorizzo M et al (2011) De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity. BMC Genom 12:1Google Scholar
  22. Jain M (2012) Next-generation sequencing technologies for gene expression profiling in plants. Brief Funct Genom 11:63–70Google Scholar
  23. Jeet K, Devi N, Narender T, Sunil T, Shalta L, Raneev T (2012) Trachyspermum ammi (ajwain): a comprehensive review. Int Res J Pharm 3:133–138Google Scholar
  24. Jin J, Tian F, Yang DC, Meng YQ, Kong L, Luo J, Gao G (2017) PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acid Res 45(D1):D1040–D1045.  https://doi.org/10.1093/nar/gkw982 CrossRefPubMedGoogle Scholar
  25. Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M (2016) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 44(D1):D457–D462.  https://doi.org/10.1093/nar/gkv1070 CrossRefPubMedPubMedCentralGoogle Scholar
  26. Kauschmann A, Jessop A, Koncz C, Szekeres M, Willmitzer L, Altmann T (1996) Genetic evidence for an essential role of brassinosteroids in plant development. Plant J 9:701–713Google Scholar
  27. Kumpatla SP, Mukhopadhyay S (2005) Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome 48:985–998PubMedGoogle Scholar
  28. Li Z, Thomas TL (1998) PEI1, an embryo-specific zinc finger protein gene required for heart-stage embryo formation in Arabidopsis. Plant Cell 10:383–398PubMedPubMedCentralGoogle Scholar
  29. Li Y-C, Korol AB, Fahima T, Nevo E (2004) Microsatellites within genes: structure, function, and evolution. Mol Biol Evol 21:991–1007PubMedGoogle Scholar
  30. Lu X et al (2013) AaERF1 positively regulates the resistance to Botrytis cinerea in Artemisia annua. PLoS ONE 8:e57657PubMedPubMedCentralGoogle Scholar
  31. Ma D et al (2009) Isolation and characterization of AaWRKY1, an Artemisia annua transcription factor that regulates the amorpha-4, 11-diene synthase gene, a key gene of artemisinin biosynthesis. Plant and Cell Physiol 50:2146–2161Google Scholar
  32. Mirzahosseini SM, Noori SAS, Amanzadeh Y, Javid MG, Howyzeh MS (2017) Phytochemical assessment of some native ajowan (Therachyspermum ammi L.) ecotypes in Iran. Ind Crops Prod 105:142–147Google Scholar
  33. Miyamoto K et al (2014) Identification of target genes of the bZIP transcription factor OsTGAP1, whose overexpression causes elicitor-induced hyperaccumulation of diterpenoid phytoalexins in rice cells. PloS ONE 9:e105823PubMedPubMedCentralGoogle Scholar
  34. Modareskia M, Darvishzadeh R, Hassani A, Kholghi M (2013) Molecular diversity within and between Ajowan (Carum copticum L.) populations based on inter simple sequence repeat (ISSR) markers. J Plant Mol Breed 1:51–62Google Scholar
  35. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:W182–W185PubMedPubMedCentralGoogle Scholar
  36. Németh É (2003) Changes in essential oil quantity and quality influenced by ontogenetic factors. In: III WOCMAP congress on medicinal and aromatic plants-volume 1: bioprospecting and ethnopharmacology 675, pp 159–165Google Scholar
  37. Nieuwenhuizen NJ et al (2015) Natural variation in monoterpene synthesis in kiwifruit: transcriptional regulation of terpene synthases by NAC and ETHYLENE-INSENSITIVE3-like transcription factors. Plant Physiol 167:1243–1258PubMedPubMedCentralGoogle Scholar
  38. Ozsolak F, Milos PM (2011) RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 12:87–98PubMedPubMedCentralGoogle Scholar
  39. Sangwan RS, Tripathi S, Singh J, Narnoliya LK, Sangwan NS (2013) De novo sequencing and assembly of Centella asiatica leaf transcriptome for mapping of structural, functional and regulatory genes with special reference to secondary metabolism. Gene 525:58–76PubMedGoogle Scholar
  40. Sargazi A (2016) Genetic diversity of some population of medicinal Ajowan (Trachyspermum copticum) using RAPD marker. University of Zabol, ZabolGoogle Scholar
  41. Sasse JM (2003) Physiological actions of brassinosteroids: an update. J Plant Growth Regul 22:276–288PubMedGoogle Scholar
  42. Schmidt J, Voigt B, Adam G (1995) 2-Deoxybrassinolide—a naturally occurring brassinosteroid from Apium graveolens. Phytochemistry 40:1041–1043Google Scholar
  43. Schmidt J, Porzel A, Adam G (1998) Brassinosteroids and a pregnane glucoside from Daucus carota. Phytochem Anal 9:14–20Google Scholar
  44. Singh KB, Foley RC, Oñate-Sánchez L (2002) Transcription factors in plant defense and stress responses. Curr Opin Plant Biol 5:430–436PubMedGoogle Scholar
  45. Soltani Howyzeh M, Sadat Noori SA, Shariati JV, Niazian M (2018) Essential oil chemotype of Iranian Ajowan (Trachyspermum ammi L.). J Essent Oil Bear Plants 21:273–276Google Scholar
  46. Sondhi N, Bhardwaj R, Kaur S, Chandel M, Kumar N, Singh B (2010) Inhibition of H2O2-induced DNA damage in single cell gel electrophoresis assay (comet assay) by castasterone isolated from leaves of Centella asiatica. Health 2:595Google Scholar
  47. Song T et al (2015) Comparative transcriptome of rhizome and leaf in Ligusticum chuanxiong. Plant Syst Evol 301:2073–2085Google Scholar
  48. Sousa SF, Fernandes PA, Ramos MJ (2008) Enzyme flexibility and the catalytic mechanism of farnesyltransferase: targeting the relation. J Phys Chem B 112:8681–8691PubMedGoogle Scholar
  49. Spyropoulou EA, Haring MA, Schuurink RC (2014) RNA sequencing on Solanum lycopersicum trichomes identifies transcription factors that activate terpene synthase promoters. BMC Genom 15:1Google Scholar
  50. Sui C et al (2011) Transcriptome analysis of Bupleurum chinense focusing on genes involved in the biosynthesis of saikosaponins. BMC Genom 12:1Google Scholar
  51. Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28:33–36PubMedPubMedCentralGoogle Scholar
  52. Wang C, Wu J, Mei X (2001) Enhancement of taxol production and excretion in Taxus chinensis cell culture by fungal elicitation and medium renewal. Appl Microbiol Biotechnol 55:404–410PubMedGoogle Scholar
  53. Wang Q, Reddy VA, Panicker D, Mao HZ, Kumar N, Rajan C, Sarojam R (2016) Metabolic engineering of terpene biosynthesis in plants using a trichome-specific transcription factor MsYABBY5 from spearmint (Mentha spicata). Plant Biotechnol J 14(7):1619–1632.  https://doi.org/10.1111/pbi.12525 CrossRefPubMedPubMedCentralGoogle Scholar
  54. Wei W et al (2011) Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genom 12:1Google Scholar
  55. Wildung MR, Croteau RB (2005) Genetic engineering of peppermint for improved essential oil composition and yield. Transgenic Res 14:365–372PubMedGoogle Scholar
  56. Xie Z, Kapteyn J, Gang DR (2008) A systems biology investigation of the MEP/terpenoid and shikimate/phenylpropanoid pathways points to multiple levels of metabolic control in sweet basil glandular trichomes. Plant J 54:349–361PubMedGoogle Scholar
  57. Xu Y-H, Wang J-W, Wang S, Wang J-Y, Chen X-Y (2004) Characterization of GaWRKY1, a cotton transcription factor that regulates the sesquiterpene synthase gene (+)-δ-cadinene synthase-A. Plant Physiol 135:507–515PubMedPubMedCentralGoogle Scholar
  58. Yanhui C et al (2006) The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family. Plant Mol Biol 60:107–124PubMedGoogle Scholar
  59. Ye J et al (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34:W293–W297PubMedPubMedCentralGoogle Scholar
  60. Yu Z-X, Li J-X, Yang C-Q, Hu W-L, Wang L-J, Chen X-Y (2012) The jasmonate-responsive AP2/ERF transcription factors AaERF1 and AaERF2 positively regulate artemisinin biosynthesis in Artemisia annua L. Mol Plant 5:353–365PubMedGoogle Scholar
  61. Zhang L et al (2004) Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana. Bioinformatics 20:1081–1086PubMedGoogle Scholar
  62. Zhang F et al (2015) A basic leucine zipper transcription factor, AabZIP1, connects abscisic acid signaling with artemisinin biosynthesis in Artemisia annua. Mol Plant 8:163–175PubMedGoogle Scholar

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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