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Transferability of Barley Retrotransposons (Sukkula and Nikita) to Investigate Genetic Structure of Pimpinella anisum L.

Year 2018, Volume: 30 Issue: 3, 299 - 304, 30.09.2018

Sevgi Maraklı

https://doi.org/10.7240/marufbd.395068
Cited By: 5

Abstract

Transferability
of barley retrotransposons (Nikita and
Sukkula) were examined in Pimpinella
anisum L. seeds by using a
retrotransposon-based molecular marker: IRAP (inter-retrotransposon
amplified polymorphism). Furthermore, transposons’ sequences identified in medically important plants were
obtained form NCBI, and multiple alignment analyses were performed to
investigate the evolutionary relationships. These two retrotransposons were
identified in Pimpinella anisum L., showing homomorphic band profiles. In
addition, limited similar sequences were detected as a result of clustal analyses. Till
date, no study about retrotransposons evaluation using IRAP as molecular marker
has been published in aniseed. Our results are expected to contribute a new
perspective for genome architect of medically important plants in addition to
aniseed.

Keywords

Aniseed IRAP Medical Plants Mobile Genetic Elements

References

  • [1] Gülçın, İ., Oktay, M., Kıreçcı, E., & Küfrevıoǧlu, Ö.İ. (2003). Screening of antioxidant and antimicrobial activities of anise (Pimpinella anisum L.) seed extracts. Food Chemistry, 83(3), 371-382.
  • [2] Rodrigues, V.M., Rosa, P.T., Marques, M.O., Petenate, A.J., & Meireles, M.A.A. (2003). Supercritical extraction of essential oil from aniseed (Pimpinella anisum L) using CO2: solubility, kinetics, and composition data. Journal of Agricultural and Food Chemistry, 51(6), 1518-1523.
  • [3] Samojlik, I., Mijatović, V., Petković, S., Škrbić, B., & Božin, B. (2012). The influence of essential oil of aniseed (Pimpinella anisum, L.) on drug effects on the central nervous system. Fitoterapia, 83(8), 1466-1473.
  • [4] Ibrahim, M.K., Mattar, Z.A., Abdel-Khalek, H.H., & Azzam, Y.M. (2017). Evaluation of antibacterial efficacy of anise wastes against some multidrug resistant bacterial isolates. Journal of Radiation Research and Applied Sciences, 10(1), 34-43.
  • [5] Koriem, K.M., Arbid, M.S., & El-Gendy, N.F. (2016). The protective role of anise oil in oxidative stress and genotoxicity produced in favism. Journal of Dietary Supplements, 13(5), 505-521.
  • [6] Jamshidzadeh, A., Heidari, R., Razmjou, M., Karimi, F., Moein, M.R., Farshad, O., Akbarizadeh, A.R. & Shayesteh, M. R. H. (2015). An in vivo and in vitro investigation on hepatoprotective effects of Pimpinella anisum seed essential oil and extracts against carbon tetrachloride-induced toxicity. Iranian Journal of Basic Medical Sciences, 18(2), 205-211.
  • [7] Asadi, M.H., & Rahamooz-Haghighi, S. (2016). Anti-proliferative effect of the extracts and essential oil of Pimpinella anisum on gastric cancer cells. Journal of HerbMed Pharmacology, 5(4), 157-161.
  • [8] Li, L., Josef, B.A., Liu, B., Zheng, S., Huang, L., & Chen, S. (2017). Three-dimensional evaluation on ecotypic diversity of traditional chinese medicine: A Case Study of Artemisia annua L. Frontiers in Plant Science, 8, 1225.
  • [9] Wicker, T., Sabot, F., Hua-Van, A., Bennetzen, J. L., Capy, P., Chalhoub, B., Flavell, A., Leroy, P., Morgante, M., Panaud, O., Paux, E., SanMiguel, P., & Paux, E. (2007). A unified classification system for eukaryotic transposable elements. Nature Reviews Genetics, 8(12), 973-982.
  • [10] Schulman, A.H., Flavell, A.J., Paux, E., Ellis, T.H.N. (2012). The application of LTR retrotransposons as molecular markers in plants. In: Bigot, Y. (ed.), Mobile genetic elements: protocols and genomic applications. Humana Press, s. 115-153.
  • [11] Gozukirmizi, N., Temel, A., Marakli, S., Yilmaz, S. (2016). Transposon activity in plant genomes. In: Hakeem, H.R., Tombuloglu, H., Tombuloglu, G. (eds.), Plant omics: trends and applications. Springer-Verlag, Springer International Publishing Switzerland, s. 83-108.
  • [12] Gozukirmizi, N., Yilmaz, S., Marakli, S., Temel, A. (2015). Retrotransposon-based molecular markers; tools for variation analyses in plants analysis in plants. In: Taski-Adjukovic, K. (ed.), Applications of molecular markers in plant genome analysis and breeding. Research Signpost, Kerala, s. 19-45.
  • [13] Kalendar, R. (2011). The use of retrotransposon-based molecular markers to analyze genetic diversity. Ratarstvo i povrtarstvo, 48, 261-274.
  • [14] Kalendar, R., Tanskanen, J., Chang, W., Antonius, K., Sela, H., Peleg, O., & Schulman, A. H. (2008). Cassandra retrotransposons carry independently transcribed 5S RNA. Proceedings of the National Academy of Sciences, 105(15), 5833-5838.
  • [15] Cakmak, B., Marakli, S., & Gozukirmizi, N. (2015). SIRE1 retrotransposons in barley (Hordeum vulgare L.). Russian Journal of Genetics, 51(7), 661-672.
  • [16] Cakmak, B., Marakli, S., & Gozukirmizi, N. (2017). Sukkula retrotransposon movements in the human genome. Biotechnology & Biotechnological Equipment, 31(4), 756-760.
  • [17] Shirasu, K., Schulman, A.H., Lahaye, T., & Schulze-Lefert, P. (2000). A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Research, 10(7), 908-915.
  • [18] Kidwell, K.K., Osborn, T.C. (1992). Simple plant DNA isolation procedures, In: Beckmann, J.S., Osborn, T.C. (eds.) Plant genomes: methods for genetic and physical mapping. Kluwer Academic Publishers, Dordrecht, The Netherlands, s. 1-13.
  • [19] Leigh, F., Kalendar, R., Lea, V., Lee, D., Donini, P., & Schulman, A. H. (2003). Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques. Molecular Genetics and Genomics, 269(4), 464-474.
  • [20] Shojaii, A., & Abdollahi Fard, M. (2012). Review of pharmacological properties and chemical constituents of Pimpinella anisum. ISRN pharmaceutics, 2012.
  • [21] Boronnikova, S. V., & Kalendar, R. N. (2010). Using IRAP markers for analysis of genetic variability in populations of resource and rare species of plants. Russian Journal of Genetics, 46(1), 36-42.
  • [22] Soorni, A., Nazeri, V., Fattahi, R., & Khadivi-Khub, A. (2013). DNA fingerprinting of Leonurus cardiaca L. germplasm in Iran using amplified fragment length polymorphism and inter-retrotransposon amplified polymorphism. Biochemical Systematics and Ecology, 50, 438-447.
  • [23] Tomás, D., Rodrigues, J., Varela, A., Veloso, M. M., Viegas, W., & Silva, M. (2016). Use of repetitive sequences for molecular and cytogenetic characterization of Avena species from Portugal. International Journal of Molecular Sciences, 17(2), 203.
  • [24] Li, M., Cao, H., But, P. P. H., & Shaw, P. C. (2011). Identification of herbal medicinal materials using DNA barcodes. Journal of Systematics and Evolution, 49(3), 271-283.
  • [25] Chen, S., Yao, H., Han, J., Liu, C., Song, J., Shi, L., Zhu, Y. Ma, X., Gao, T., Pang, X., Luo, K., Li, Y., Li, X., Jia, X., Leon, C. (2010). Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PloS One, 5(1), e8613.
  • [26] Gao, T., Yao, H., Song, J., Liu, C., Zhu, Y., Ma, X., Pang X., Xu, H., & Chen, S. (2010). Identification of medicinal plants in the family Fabaceae using a potential DNA barcode ITS2. Journal of Ethnopharmacology, 130(1), 116-121.
  • [27] Downie, S.R., Spalik, K., Katz-Downie, D.S., & Reduron, J. P. (2010). Major clades within Apiaceae subfamily Apioideae as inferred by phylogenetic analysis of nrDNA ITS sequences. Plant Diversity and Evolution, 128(1-2), 111-136.
  • [28] Wang, Z. X., Downie, S. R., Tan, J. B., Liao, C. Y., Yu, Y., & He, X. J. (2014). Molecular phylogenetics of Pimpinella and allied genera (Apiaceae), with emphasis on Chinese native species, inferred from nrDNA ITS and cpDNA intron sequence data. Nordic Journal of Botany, 32(5), 642-657.
  • [29] Nurcahyanti, A.D., Nasser, I.J., Sporer, F., Graf, J., Bermawie, N., Reichling, J., & Wink, M. (2016). Chemical composition of the essential oil from aerial parts of Javanian Pimpinella pruatjan Molk. and its molecular phylogeny. Diversity, 8(3), 15.
  • [30] Wang, X.M., Hou, X.Q., Zhang, Y.Q., Yang, R., Feng, S. F., Li, Y., & Ren, Y. (2012). Genetic diversity of the endemic and medicinally important plant Rheum officinale as revealed by inter-simpe sequence repeat (ISSR) markers. International journal of molecular sciences, 13(3), 3900-3915.
  • [31] Kakani, R.K., Singh, S.K., Pancholy, A., Meena, R.S., Pathak, R., & Raturi, A. (2011). Assessment of genetic diversity in Trigonella foenum-graecum based on nuclear ribosomal DNA, internal transcribed spacer and RAPD analysis. Plant Molecular Biology Reporter, 29(2), 315-323.
  • [32] Sindhu, A., Tehlan, S. K., & Chaudhury, A. (2017). Analysis of genetic diversity among medicinal therapist Trigonella foenum-graecum L. genotypes through RAPD and SSR markers. Acta Physiologiae Plantarum, 39(4), 100.
  • [33] Kumar, S., Mahendi, H. A., Fougat, R. S., Sakure, A. A., & Mistry, J. G. (2014). Transferability of carrot (Daucus carota) microsatellite markers to cumin (Cuminum cyminum). International Journal Seed Spices, 4(1), 88-90.
  • [34] Zhang, Y., Fan, C., Li, S., Chen, Y., Wang, R. R. C., Zhang, X., Han, F., & Hu, Z. (2017). The Diversity of sequence and chromosomal distribution of new transposable element-related segments in the rye genome revealed by FISH and lineage annotation. Frontiers in Plant Science, 8, 1706.

Transferability of Barley Retrotransposons (Sukkula and Nikita) to Investigate Genetic Structure of Pimpinella anisum L.

Year 2018, Volume: 30 Issue: 3, 299 - 304, 30.09.2018

Sevgi Maraklı

https://doi.org/10.7240/marufbd.395068
Cited By: 5

Abstract

Transferability
of barley retrotransposons (Nikita and
Sukkula) were examined in Pimpinella
anisum L. seeds by using a
retrotransposon-based molecular marker: IRAP (inter-retrotransposon
amplified polymorphism). Furthermore, transposons’ sequences identified in medically important plants were
obtained form NCBI, and multiple alignment analyses were performed to
investigate the evolutionary relationships. These two retrotransposons were
identified in Pimpinella anisum L., showing homomorphic band profiles. In
addition, limited similar sequences were detected as a result of clustal analyses. Till
date, no study about retrotransposons evaluation using IRAP as molecular marker
has been published in aniseed. Our results are expected to contribute a new
perspective for genome architect of medically important plants in addition to
aniseed.

Keywords

Aniseed IRAP Medical Plants Mobile Genetic Elements

References

  • [1] Gülçın, İ., Oktay, M., Kıreçcı, E., & Küfrevıoǧlu, Ö.İ. (2003). Screening of antioxidant and antimicrobial activities of anise (Pimpinella anisum L.) seed extracts. Food Chemistry, 83(3), 371-382.
  • [2] Rodrigues, V.M., Rosa, P.T., Marques, M.O., Petenate, A.J., & Meireles, M.A.A. (2003). Supercritical extraction of essential oil from aniseed (Pimpinella anisum L) using CO2: solubility, kinetics, and composition data. Journal of Agricultural and Food Chemistry, 51(6), 1518-1523.
  • [3] Samojlik, I., Mijatović, V., Petković, S., Škrbić, B., & Božin, B. (2012). The influence of essential oil of aniseed (Pimpinella anisum, L.) on drug effects on the central nervous system. Fitoterapia, 83(8), 1466-1473.
  • [4] Ibrahim, M.K., Mattar, Z.A., Abdel-Khalek, H.H., & Azzam, Y.M. (2017). Evaluation of antibacterial efficacy of anise wastes against some multidrug resistant bacterial isolates. Journal of Radiation Research and Applied Sciences, 10(1), 34-43.
  • [5] Koriem, K.M., Arbid, M.S., & El-Gendy, N.F. (2016). The protective role of anise oil in oxidative stress and genotoxicity produced in favism. Journal of Dietary Supplements, 13(5), 505-521.
  • [6] Jamshidzadeh, A., Heidari, R., Razmjou, M., Karimi, F., Moein, M.R., Farshad, O., Akbarizadeh, A.R. & Shayesteh, M. R. H. (2015). An in vivo and in vitro investigation on hepatoprotective effects of Pimpinella anisum seed essential oil and extracts against carbon tetrachloride-induced toxicity. Iranian Journal of Basic Medical Sciences, 18(2), 205-211.
  • [7] Asadi, M.H., & Rahamooz-Haghighi, S. (2016). Anti-proliferative effect of the extracts and essential oil of Pimpinella anisum on gastric cancer cells. Journal of HerbMed Pharmacology, 5(4), 157-161.
  • [8] Li, L., Josef, B.A., Liu, B., Zheng, S., Huang, L., & Chen, S. (2017). Three-dimensional evaluation on ecotypic diversity of traditional chinese medicine: A Case Study of Artemisia annua L. Frontiers in Plant Science, 8, 1225.
  • [9] Wicker, T., Sabot, F., Hua-Van, A., Bennetzen, J. L., Capy, P., Chalhoub, B., Flavell, A., Leroy, P., Morgante, M., Panaud, O., Paux, E., SanMiguel, P., & Paux, E. (2007). A unified classification system for eukaryotic transposable elements. Nature Reviews Genetics, 8(12), 973-982.
  • [10] Schulman, A.H., Flavell, A.J., Paux, E., Ellis, T.H.N. (2012). The application of LTR retrotransposons as molecular markers in plants. In: Bigot, Y. (ed.), Mobile genetic elements: protocols and genomic applications. Humana Press, s. 115-153.
  • [11] Gozukirmizi, N., Temel, A., Marakli, S., Yilmaz, S. (2016). Transposon activity in plant genomes. In: Hakeem, H.R., Tombuloglu, H., Tombuloglu, G. (eds.), Plant omics: trends and applications. Springer-Verlag, Springer International Publishing Switzerland, s. 83-108.
  • [12] Gozukirmizi, N., Yilmaz, S., Marakli, S., Temel, A. (2015). Retrotransposon-based molecular markers; tools for variation analyses in plants analysis in plants. In: Taski-Adjukovic, K. (ed.), Applications of molecular markers in plant genome analysis and breeding. Research Signpost, Kerala, s. 19-45.
  • [13] Kalendar, R. (2011). The use of retrotransposon-based molecular markers to analyze genetic diversity. Ratarstvo i povrtarstvo, 48, 261-274.
  • [14] Kalendar, R., Tanskanen, J., Chang, W., Antonius, K., Sela, H., Peleg, O., & Schulman, A. H. (2008). Cassandra retrotransposons carry independently transcribed 5S RNA. Proceedings of the National Academy of Sciences, 105(15), 5833-5838.
  • [15] Cakmak, B., Marakli, S., & Gozukirmizi, N. (2015). SIRE1 retrotransposons in barley (Hordeum vulgare L.). Russian Journal of Genetics, 51(7), 661-672.
  • [16] Cakmak, B., Marakli, S., & Gozukirmizi, N. (2017). Sukkula retrotransposon movements in the human genome. Biotechnology & Biotechnological Equipment, 31(4), 756-760.
  • [17] Shirasu, K., Schulman, A.H., Lahaye, T., & Schulze-Lefert, P. (2000). A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Research, 10(7), 908-915.
  • [18] Kidwell, K.K., Osborn, T.C. (1992). Simple plant DNA isolation procedures, In: Beckmann, J.S., Osborn, T.C. (eds.) Plant genomes: methods for genetic and physical mapping. Kluwer Academic Publishers, Dordrecht, The Netherlands, s. 1-13.
  • [19] Leigh, F., Kalendar, R., Lea, V., Lee, D., Donini, P., & Schulman, A. H. (2003). Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques. Molecular Genetics and Genomics, 269(4), 464-474.
  • [20] Shojaii, A., & Abdollahi Fard, M. (2012). Review of pharmacological properties and chemical constituents of Pimpinella anisum. ISRN pharmaceutics, 2012.
  • [21] Boronnikova, S. V., & Kalendar, R. N. (2010). Using IRAP markers for analysis of genetic variability in populations of resource and rare species of plants. Russian Journal of Genetics, 46(1), 36-42.
  • [22] Soorni, A., Nazeri, V., Fattahi, R., & Khadivi-Khub, A. (2013). DNA fingerprinting of Leonurus cardiaca L. germplasm in Iran using amplified fragment length polymorphism and inter-retrotransposon amplified polymorphism. Biochemical Systematics and Ecology, 50, 438-447.
  • [23] Tomás, D., Rodrigues, J., Varela, A., Veloso, M. M., Viegas, W., & Silva, M. (2016). Use of repetitive sequences for molecular and cytogenetic characterization of Avena species from Portugal. International Journal of Molecular Sciences, 17(2), 203.
  • [24] Li, M., Cao, H., But, P. P. H., & Shaw, P. C. (2011). Identification of herbal medicinal materials using DNA barcodes. Journal of Systematics and Evolution, 49(3), 271-283.
  • [25] Chen, S., Yao, H., Han, J., Liu, C., Song, J., Shi, L., Zhu, Y. Ma, X., Gao, T., Pang, X., Luo, K., Li, Y., Li, X., Jia, X., Leon, C. (2010). Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PloS One, 5(1), e8613.
  • [26] Gao, T., Yao, H., Song, J., Liu, C., Zhu, Y., Ma, X., Pang X., Xu, H., & Chen, S. (2010). Identification of medicinal plants in the family Fabaceae using a potential DNA barcode ITS2. Journal of Ethnopharmacology, 130(1), 116-121.
  • [27] Downie, S.R., Spalik, K., Katz-Downie, D.S., & Reduron, J. P. (2010). Major clades within Apiaceae subfamily Apioideae as inferred by phylogenetic analysis of nrDNA ITS sequences. Plant Diversity and Evolution, 128(1-2), 111-136.
  • [28] Wang, Z. X., Downie, S. R., Tan, J. B., Liao, C. Y., Yu, Y., & He, X. J. (2014). Molecular phylogenetics of Pimpinella and allied genera (Apiaceae), with emphasis on Chinese native species, inferred from nrDNA ITS and cpDNA intron sequence data. Nordic Journal of Botany, 32(5), 642-657.
  • [29] Nurcahyanti, A.D., Nasser, I.J., Sporer, F., Graf, J., Bermawie, N., Reichling, J., & Wink, M. (2016). Chemical composition of the essential oil from aerial parts of Javanian Pimpinella pruatjan Molk. and its molecular phylogeny. Diversity, 8(3), 15.
  • [30] Wang, X.M., Hou, X.Q., Zhang, Y.Q., Yang, R., Feng, S. F., Li, Y., & Ren, Y. (2012). Genetic diversity of the endemic and medicinally important plant Rheum officinale as revealed by inter-simpe sequence repeat (ISSR) markers. International journal of molecular sciences, 13(3), 3900-3915.
  • [31] Kakani, R.K., Singh, S.K., Pancholy, A., Meena, R.S., Pathak, R., & Raturi, A. (2011). Assessment of genetic diversity in Trigonella foenum-graecum based on nuclear ribosomal DNA, internal transcribed spacer and RAPD analysis. Plant Molecular Biology Reporter, 29(2), 315-323.
  • [32] Sindhu, A., Tehlan, S. K., & Chaudhury, A. (2017). Analysis of genetic diversity among medicinal therapist Trigonella foenum-graecum L. genotypes through RAPD and SSR markers. Acta Physiologiae Plantarum, 39(4), 100.
  • [33] Kumar, S., Mahendi, H. A., Fougat, R. S., Sakure, A. A., & Mistry, J. G. (2014). Transferability of carrot (Daucus carota) microsatellite markers to cumin (Cuminum cyminum). International Journal Seed Spices, 4(1), 88-90.
  • [34] Zhang, Y., Fan, C., Li, S., Chen, Y., Wang, R. R. C., Zhang, X., Han, F., & Hu, Z. (2017). The Diversity of sequence and chromosomal distribution of new transposable element-related segments in the rye genome revealed by FISH and lineage annotation. Frontiers in Plant Science, 8, 1706.
There are 34 citations in total.

Details

Primary Language English
Subjects Engineering
Journal Section Research Articles
Authors

Sevgi Maraklı

Publication Date September 30, 2018
Acceptance Date August 13, 2018
Published in Issue Year 2018 Volume: 30 Issue: 3

Cite

APA Maraklı, S. (2018). Transferability of Barley Retrotransposons (Sukkula and Nikita) to Investigate Genetic Structure of Pimpinella anisum L. Marmara Fen Bilimleri Dergisi, 30(3), 299-304. https://doi.org/10.7240/marufbd.395068
AMA Maraklı S. Transferability of Barley Retrotransposons (Sukkula and Nikita) to Investigate Genetic Structure of Pimpinella anisum L. MAJPAS. September 2018;30(3):299-304. doi:10.7240/marufbd.395068
Chicago Maraklı, Sevgi. “Transferability of Barley Retrotransposons (Sukkula and Nikita) to Investigate Genetic Structure of Pimpinella Anisum L”. Marmara Fen Bilimleri Dergisi 30, no. 3 (September 2018): 299-304. https://doi.org/10.7240/marufbd.395068.
EndNote Maraklı S (September 1, 2018) Transferability of Barley Retrotransposons (Sukkula and Nikita) to Investigate Genetic Structure of Pimpinella anisum L. Marmara Fen Bilimleri Dergisi 30 3 299–304.
IEEE S. Maraklı, “Transferability of Barley Retrotransposons (Sukkula and Nikita) to Investigate Genetic Structure of Pimpinella anisum L”., MAJPAS, vol. 30, no. 3, pp. 299–304, 2018, doi: 10.7240/marufbd.395068.
ISNAD Maraklı, Sevgi. “Transferability of Barley Retrotransposons (Sukkula and Nikita) to Investigate Genetic Structure of Pimpinella Anisum L”. Marmara Fen Bilimleri Dergisi 30/3 (September 2018), 299-304. https://doi.org/10.7240/marufbd.395068.
JAMA Maraklı S. Transferability of Barley Retrotransposons (Sukkula and Nikita) to Investigate Genetic Structure of Pimpinella anisum L. MAJPAS. 2018;30:299–304.
MLA Maraklı, Sevgi. “Transferability of Barley Retrotransposons (Sukkula and Nikita) to Investigate Genetic Structure of Pimpinella Anisum L”. Marmara Fen Bilimleri Dergisi, vol. 30, no. 3, 2018, pp. 299-04, doi:10.7240/marufbd.395068.
Vancouver Maraklı S. Transferability of Barley Retrotransposons (Sukkula and Nikita) to Investigate Genetic Structure of Pimpinella anisum L. MAJPAS. 2018;30(3):299-304.

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Marmara Journal of Pure and Applied Sciences

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