Russian Journal of Genetics

, Volume 55, Issue 1, pp 71–78 | Cite as

Determination of Barley-Specific Retrotransposons’ Movements in Pinus nigra ssp. pallasiana Varieties: pyramidata and Seneriana

  • S. MarakliEmail author
  • A. Calis
  • N. Gozukirmizi


Pinus nigra Arn. ssp. pallasiana (Lamb.) Holmboe (Anatolian black pine) is the second most widespread coniferous pine species in Turkey after the red pine. Mobile genetic elements are capable of jumping from their positions to others within the genome and constitute 15–90% of plant genomes. In this study, barley-specific BAGY2, Nikita and Sukkula retrotransposon movements were examined in the stems and needles of Anatolian endemic Pinus nigra ssp. pallasiana var. pyramidata and var. Seneriana. Moreover, multiple alignment analyses were also performed to observe the relationships among sequences found in angiosperms and gymnosperms. Polymorphisms were calculated as 0–11% for BAGY2, 0–56% for Nikita and 0–76% for Sukkula between stems and needles in var. pyramidata. There was no polymorphism in var. Seneriana. Homomorphic band profiles were observed among all needle samples in BAGY2, Nikita and Sukkula analyses both in var. pyramidata and var. Seneriana. Furthermore, we detected few similar sequences among retrotransposons identified in different plants. There is almost no research related to retrotransposons in Anatolian black pine’s endemic varieties. This is the first study to investigate the movements of barley-specific retrotransposons in Pinus nigra. Our results are expected to contribute knowledge about these endemic plants, and even the evolutionary relationships between angiosperms and gymnosperms.


angiosperms Anatolian endemic varieties gymnosperms IRAP mobile elements 


  1. 1.
    Nystedt, B., Street, N.R., Wetterbom, A., et al., The Norway spruce genome sequence and conifer genome evolution, Nature, 2013, vol. 497, pp. 579—584.CrossRefGoogle Scholar
  2. 2.
    Voronova, A., Jansons, A., and Rungis, D., Expression of retrotransposon-like sequences in Scots pine (Pinus sylvestris) in response to heat stress, Environ. Exp. Biol., 2011, vol. 9, pp. 121—127.Google Scholar
  3. 3.
    Kovach, A., Wegrzyn, J.L., Parra, G., et al., The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences, BMC Genomics, 2010, vol. 11, pp. 1—14.CrossRefGoogle Scholar
  4. 4.
    Gülsoy, A.D., Gülsoy, A.M., Çengel, B., and Kaya, Z., The evolutionary divergence of Pinus nigra subsp. pallasiana and its varieties based on noncoding trn regions of chloroplast genome, Turk. J. Bot., 2014, vol. 38, pp. 627—636.CrossRefGoogle Scholar
  5. 5.
    Yucel, E., Ecological properties of Pinus nigra ssp. pallasiana var. seneriana, Silvae Genet., 2000, vol. 49, pp. 264—277.Google Scholar
  6. 6.
    Boydak, M., A new variety of Pinus nigra J.F. Arnold subsp. pallasiana (Lamb.) Holmboe from Anatolia, Karaca Arbor. Mag., 2001, vol. 6, pp. 15—23.Google Scholar
  7. 7.
    Ünaldı, U.E., The distribution of an endemic Pinus nigra species Ebe Black Pine (Pinus nigra ssp. pallasiana var. seneriana) around domanic area, NE part of Aegean region, Fırat Univ. J. Soc. Sci., 2005, vol. 15, pp. 33—42.Google Scholar
  8. 8.
    Shirasu, K., Schulman, A.H., Lahaye, T., and Schulze-Lefert, P., A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion, Genome Res., 2000, vol. 10, pp. 908—915.CrossRefGoogle Scholar
  9. 9.
    Pervaiz, Z.H., Turi, N.A., Khaliq, I., et al., A modified method for high-quality DNA extraction for molecular analysis in cereal plants, Genet. Mol. Res., 2011, vol. 10, pp. 1669—1673.CrossRefGoogle Scholar
  10. 10.
    Jaccard, P., Nouvelles recherches sur la distribution florale, Bull. Soc. Vaud. Sci. Nat., 1908, vol. 44, pp. 223—270.Google Scholar
  11. 11.
    Pavel, A.B. and Vasile, C.I., PyElph—a software tool for gel images analysis and phylogenetics, BMC Bionf., 2012, vol. 13, pp. 1—6.Google Scholar
  12. 12.
    Heras, J., Dominguez, C., Mata, E., et al., GelJ—a tool for analyzing DNA fingerprint gel images, BMC Genomics, 2015, vol. 16, pp. 1—8.CrossRefGoogle Scholar
  13. 13.
    Voronova, A. and Rungis, D., Development and characterisation of IRAP markers from expressed retrotransposon-like sequences in Pinus sylvestris L., Proc. Latv. Acad. Sci., 2013, vol. 67, pp. 485—492.Google Scholar
  14. 14.
    Gozukirmizi, N., Yilmaz, S., Marakli, S., and Temel, A., Retrotransposon-based molecular markers; tools for variation analyses in plants, in Applications of Molecular Markers in Plant Genome Analysis and Breeding, Taski-Ajdukovic, K., Ed., Kerala: Research Signpost, 2015, pp. 19—45.Google Scholar
  15. 15.
    Slotkin, R.K., Vaugh, M., Borgers, F., et al., Epigenetic reprogramming and small RNA silencing of transposable elements in pollen, Cell, 2009, vol. 136, pp. 461—472.CrossRefGoogle Scholar
  16. 16.
    Fernandez, L., Torregrosa, L., Segura, V., et al., Transposon-induced gene activation as a mechanism generating cluster shape somatic variation in grapevine, Plant J., 2010, vol. 61, pp. 545—557.CrossRefGoogle Scholar
  17. 17.
    Leigh, F., Kalendar, R., Lea, V., et al., Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques, Mol. Genet. Genomics, 2003, vol. 269, pp. 464—474.CrossRefGoogle Scholar
  18. 18.
    Guo, D.-L., Guo, M.-X., Hou, X.-G., and Zhang, G.-H., Molecular diversity analysis of grape varieties based on iPBS markers, Biochem. Syst. Ecol., 2014, vol. 52, pp. 27—32.CrossRefGoogle Scholar
  19. 19.
    Bayram, E., Yilmaz, S., Hamat-Mecbur, H., et al., Nikita retrotransposon movements in callus cultures of barley (Hordeum vulgare L.), Plant Omics, 2012, vol. 5, pp. 211—215.Google Scholar
  20. 20.
    Yigider, E., Taspinar, M.S., Sigmaz, B., et al., Humic acids protective activity against manganese induced LTR (long terminal repeat) retrotransposon polymorphism and genomic instability effects in Zea mays, Plant Gene, 2016, vol. 6, pp. 13—17.CrossRefGoogle Scholar
  21. 21.
    Mamaghani, R.A., Mohammadi, S.A., and Aharizad, S., Transferability of barley retrotransposon primers to analyze genetic structure in Iranian Hypericum perforatum L. populations, Turk. J. Bot., 2015, vol. 39, pp. 664—672.CrossRefGoogle Scholar
  22. 22.
    Wicker, T. and Keller, B., Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families, Genome Res., 2007, vol. 17, pp. 1072—1081.CrossRefGoogle Scholar
  23. 23.
    Morse, A.M., Peterson, D.G., Islam-Faridi, M.N., et al., Evolution of genome size and complexity in Pinus, PLoS One, 2009, vol. 4, pp. 1—11.CrossRefGoogle Scholar
  24. 24.
    Fan, F., Cui, B., Zhang, T., et al., LTR-retrotransposon activation, IRAP marker development and its potential in genetic diversity assessment of Masson pine (Pinus massoniana), Tree Genet. Genomes, 2014, vol. 10, pp. 213—222.CrossRefGoogle Scholar
  25. 25.
    Rocheta, M., Cordeiro, J., Oliveira, M., and Miguel, C., PpRT1: The first complete gypsy-like retrotransposon isolated in Pinus pinaster, Planta, 2007, vol. 225, pp. 551—562.CrossRefGoogle Scholar
  26. 26.
    Voronova, A., Belevich, V., Korica, A., and Rungis, D., Retrotransposon distribution and copy number variation in gymnosperm genomes, Tree Genet. Genomes, 2017, vol. 13, pp. 1—23.CrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Inc. 2019

Authors and Affiliations

  1. 1.Molecular Biology and Genetics Department, Istanbul UniversityVezneciler-IstanbulTurkey

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