1. Alagna, F., D'Agostino, N., Torchia, L., Servili, M., Rao, R., Pietrella, M., Giuliano, G., Chiusano, M.L., Baldoni, L. and Perrotta, G. (2009). Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development. BMC Genomics 10: 399. [DOI:10.1186/1471-2164-10-399]

2. Angeloni, F., Wagemaker, C., Jetten, M., Op den Camp, H., Janssen‐Megens, E., Francoijs, K.J., Stunnenberg, H. and Ouborg, N. (2011). De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using next‐generation sequencing techniques. Molecular Ecology Resources, 11: 662-674. [DOI:10.1111/j.1755-0998.2011.02990.x]

3. Bahmani, K., Izadi-Darbandi, A., Jafari, A.A., Noori, S.A.S. and Farajpour, M. (2012). Assessment of genetic diversity in Iranian fennels using ISSR markers. Journal of Agricultural Science, 4: 79. [DOI:10.5539/jas.v4n9p79]

4. Bairwa, R., Sodha, R. and Rajawat, B. (2012). Trachyspermum ammi. Pharmacognosy Reviews, 6: 56-60. [DOI:10.4103/0973-7847.95871]

5. Bajgain, P., Richardson, B.A., Price, J.C., Cronn, R.C. and Udall, J.A. (2011). Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata). BMC Genomics, 12: 370. [DOI:10.1186/1471-2164-12-370]

6. Barakat, A., DiLoreto, D.S., Zhang, Y., Smith, C., Baier, K., Powell, W.A., Wheeler, N., Sederoff, R. and Carlson, J.E. (2009). Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection. BMC Plant Biology, 9: 51. [DOI:10.1186/1471-2229-9-51]

7. Beier, S., Thiel, T., Münch, T., Scholz, U. and Mascher, M. (2017). MISA-web: a web server for microsatellite prediction. Bioinformatics, 33: 2583-2585. [DOI:10.1093/bioinformatics/btx198]

8. Bhandawat, A., Singh, G., Raina, A.S., Kaur, J. and Sharma, R.K. (2016). Development of genic SSR marker resource from RNA-Seq data in Dendrocalamus latiflorus. Journal of Plant Biochemistry and Biotechnology, 25: 179-190. [DOI:10.1007/s13562-015-0323-9]

9. Blanca, J., Cañizares, J., Roig, C., Ziarsolo, P., Nuez, F. and Picó, B. (2011). Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae). BMC Genomics, 12: 104. [DOI:10.1186/1471-2164-12-104]

10. Bräutigam, A., Mullick, T., Schliesky, S. and Weber, A.P. (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. Journal of Experimental Botany, 62: 3093-3102. [DOI:10.1093/jxb/err029]

11. Chen, F., Tholl, D., Bohlmann, J. and Pichersky, E. (2011). The family of terpene synthases in plants: a mid‐size family of genes for specialized metabolism that is highly diversified throughout the kingdom. The Plant Journal, 66: 212-229. [DOI:10.1111/j.1365-313X.2011.04520.x]

12. Dassanayake, M., Haas, J., Bohnert, H. and Cheeseman, J. (2009). Shedding light on an extremophile lifestyle through transcriptomics. New Phytologist, 183: 764-775. [DOI:10.1111/j.1469-8137.2009.02913.x]

13. Farajpour, M., Ebrahimi, M., Amiri, R., Noori, S., Sanjari, S. and Golzari, R. (2011). Study of genetic variation in yarrow using inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) markers. African Journal of Biotechnology, 10: 11137-11141.

14. Fu, N., Wang, Q. and 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: e57686. [DOI:10.1371/journal.pone.0057686]

15. Futschik, A. and Schlötterer, C. (2010). The next generation of molecular markers from massively parallel sequencing of pooled DNA samples. Genetics, 186: 207-218. [DOI:10.1534/genetics.110.114397]

16. Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R. and Zeng, Q. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29: 644-652. [DOI:10.1038/nbt.1883]

17. Guo, S., Liu, J., Zheng, Y., Huang, M., Zhang, H., Gong, G., He, H., Ren, Y., Zhong, S. and Fei, Z. (2011). Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles. BMC Genomics, 12: 454. [DOI:10.1186/1471-2164-12-454]

18. Hao, D., Ma, P., Mu, J., Chen, S., Xiao, P., Peng, Y., Huo, L., Xu, L. and Sun, C. (2012). De novo characterization of the root transcriptome of a traditional Chinese medicinal plant Polygonum cuspidatum. Science China Life Sciences, 55: 452-466. [DOI:10.1007/s11427-012-4319-6]

19. Heidari, E.F., Rahimmalek, M., Mohammadi, S. and Ehtemam, M.H. (2016). Genetic structure and diversity of ajowan (Trachyspermum ammi) populations based on molecular, morphological markers, and volatile oil content. Industrial Crops and Products, 92: 186-196. [DOI:10.1016/j.indcrop.2016.08.014]

20. Hiremath, P.J., Farmer, A., Cannon, S.B., Woodward, J., Kudapa, H., Tuteja, R., Kumar, A., BhanuPrakash, A., Mulaosmanovic, B. and Gujaria, N. (2011). Large‐scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi‐arid tropics of Asia and Africa. Plant Biotechnology Journal, 9: 922-931. [DOI:10.1111/j.1467-7652.2011.00625.x]

21. Kaliswamy, P., Vellingiri, S., Nathan, B. and Selvaraj, S. (2015). Microsatellite analysis in the genome of Acanthaceae: An in silico approach. Pharmacognosy Magazine, 11: 152-156. [DOI:10.4103/0973-1296.149731]

22. Karimbeigi, H., Nazarian-Firouzabadi, F., Khademi, M. and Mousav, E. (2016) Assessment of genetic diversity among some oilseed rape (Brassica nupus L.) plants, using single sequence repeats (SSR) molecular markers. Plant Genetic Researches, 3(1): 45-56 (In Persian). [DOI:10.29252/pgr.3.1.45]

23. Kumpatla, S.P. and Mukhopadhyay, S. (2005). Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome, 48: 985-998. [DOI:10.1139/g05-060]

24. Li, D., Deng, Z., Qin, B., Liu, X. and Men, Z. (2012). De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). BMC Genomics, 13: 192. [DOI:10.1186/1471-2164-13-192]

25. Li, Y.C., Korol, A.B., Fahima, T. and Nevo, E. (2004). Microsatellites within genes: structure, function, and evolution. Molecular Biology and Evolution, 21: 991-1007. [DOI:10.1093/molbev/msh073]

26. Li, Y., Sun, C., Luo, H., Li, X., Niu, Y. and Chen, S. (2010). Transcriptome characterization for Salvia miltiorrhiza using 454 GS FLX. Yao xue xue bao. Acta Pharmaceutica Sinica, 45: 524-529.

27. Li, Y.C., Korol, A.B., Fahima, T., Beiles, A. and Nevo, E. (2002). Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Molecular Ecology, 11: 2453-2465. [DOI:10.1046/j.1365-294X.2002.01643.x]

28. Lin, X., Zhang, J., Li, Y., Luo, H., Wu, Q., Sun, C., Song, J., Li, X., Wei, J. and Lu, A. (2011). Functional genomics of a living fossil tree, Ginkgo, based on next‐generation sequencing technology. Physiologia Plantarum, 143: 207-218. [DOI:10.1111/j.1399-3054.2011.01500.x]

29. Lu, F.H., Cho, M.C. and Park, Y.J. (2012). Transcriptome profiling and molecular marker discovery in red pepper, Capsicum annuum L. TF68. Molecular Biology Reports, 39: 3327-3335. [DOI:10.1007/s11033-011-1102-x]

30. Luo, H., Sun, C., Sun, Y., Wu, Q., Li, Y., Song, J., Niu, Y., Cheng, X., Xu, H. and Li, C. (2011). Analysis of the transcriptome of Panax notoginseng root uncovers putative triterpene saponin-biosynthetic genes and genetic markers. BMC Genomics, 12: S5. [DOI:10.1186/1471-2164-12-S5-S5]

31. Mirzahosseini, S.M., Noori, S.A.S., Amanzadeh, Y., Javid, M.G. and Howyzeh, M.S. (2017). Phytochemical assessment of some native ajowan (Therachyspermum ammi L.) ecotypes in Iran. Industrial Crops and Products, 105: 142-147. [DOI:10.1016/j.indcrop.2017.04.052]

32. Modareskia, M., Darvishzadeh, R., Hassani, A. and Kholghi, M. (2013). Molecular diversity within and between Ajowan (Carum copticum L.) populations based on inter simple sequence repeat (ISSR) markers. Journal of Plant Molecular Breeding, 1: 51-62.

33. Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A.C. and Kanehisa, M. (2007). KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Research, 35: W182-W185. [DOI:10.1093/nar/gkm321]

34. Noori, S.A.S., Norouzi, M., Karimzadeh, G., Shirkool, K. and Niazian, M. (2017). Effect of colchicine-induced polyploidy on morphological characteristics and essential oil composition of ajowan (Trachyspermum ammi L.). Plant Cell, Tissue and Organ Culture (PCTOC), 130(3): 543-551. [DOI:10.1007/s11240-017-1245-0]

35. Parida, S.K., Pandit, A., Gaikwad, K., Sharma, T.R., Srivastava, P.S., Singh, N.K. and Mohapatra, T. (2010). Functionally relevant microsatellites in sugarcane unigenes. BMC Plant Biology, 10: 251. [DOI:10.1186/1471-2229-10-251]

36. Primmer, C.R. (2009). From conservation genetics to conservation genomics. Annals of the New York Academy of Sciences, 1162: 357-368. [DOI:10.1111/j.1749-6632.2009.04444.x]

37. Sadati, S., Sadat-Noori, S.A., Ramshini, H., Soltani, E. and Foghi, B. (2016). Towards conservation and breeding of Ajowan (Trachyspermum ammi) by assessing ISSR, morphological traits and germination variability. Iranian Journal of Genetics and Plant Breeding, 5: 8-21.

38. Sargazi, A. (2016). Genetic diversity of some population of medicinal Ajowan (Trachyspermum copticum) using RAPD marker. M.Sc. Thesis. Faculty of Agriculture, University of Zabol, Zabol, Iran (In Persian).

39. Shuorvazdi, A., Mohammadi, S.A., Norozi, M. and Sadeghzadeh, B. (2014) Molecular analysis of genetic diversity and relationships of barley landraces based on microsatellite markers. Plant Genetic Researches, 1(1): 51-64 (In Persian). [DOI:10.29252/pgr.1.1.51]

40. Soltani Howyzeh, M., Sadat Noori, S.A. and Shariati, J.V. (2018a). Essential oil profiling of Ajowan (Trachyspermum ammi) industrial medicinal plant. Industrial Crops and Products, 119: 255-259. [DOI:10.1016/j.indcrop.2018.04.022]

41. Soltani Howyzeh, M., Sadat Noori, S.A., Shariati J.V. and Niazian, M. (2018b). Essential oil chemotype of Iranian Ajowan (Trachyspermum ammi L.). Journal of Essential Oil Bearing Plants, 21: 273-276. [DOI:10.1080/0972060X.2018.1433074]

42. Strickler, S.R., Bombarely, A. and Mueller, L.A. (2012). Designing a transcriptome next-generation sequencing project for a nonmodel plant species1. American Journal of Botany, 99: 257-266. [DOI:10.3732/ajb.1100292]

43. Vasemägi, A., Nilsson, J. and Primmer, C.R. (2005). Expressed sequence tag-linked microsatellites as a source of gene-associated polymorphisms for detecting signatures of divergent selection in Atlantic salmon (Salmo salar L.). Molecular Biology and Evolution, 22: 1067-1076. [DOI:10.1093/molbev/msi093]

44. Wei, W., Qi, X., Wang, L., Zhang, Y., Hua, W., Li, D., Lv, H. and Zhang, X. (2011). Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics, 12: 451. [DOI:10.1186/1471-2164-12-451]

45. Xu, M., Liu, X., Wang, J.W., Teng, S.Y., Shi, J.Q., Li, Y.Y. and Huang, M.R. (2017). Transcriptome sequencing and development of novel genic SSR markers for Dendrobium officinale. Molecular Breeding, 37: 18. [DOI:10.1007/s11032-016-0613-5]

46. Zhang, J., Liang, S., Duan, J., Wang, J., Chen, S., Cheng, Z., Zhang, Q., Liang, X. and Li, Y. (2012). De novo assembly and characterisation of the transcriptome during seed development, and generation of genic-SSR markers in peanut (Arachis hypogaea L.). BMC Genomics, 13: 90. [DOI:10.1186/1471-2164-13-90]