Transposon studies on Colchium chalcedonicum

Year 2019, Volume: 2 Issue: 1, 25 - 35, 21.04.2019

Elif Karlık , Merve Albayrak Erdal Uzen , Nermin Gözükırmızı

https://doi.org/10.38001/ijlsb.529237

Abstract

Colchicum chalcedonicum is one of
the endemic plants in Turkey. The aim of this study was the investigation of
the retrotransposon SIRE1, Sukkula
and Nikita presence and insertion
patterns in C. chalcedonicum. The
plant samples were collected from the botanic garden of the Istanbul
University. DNA isolation was performed from leaves by using modified
CTAB/SEVAG protocol. Retrotransposon movements were investigated using SIRE1, Sukkula and Nikita primers by Inter Retrotranposon Amplified Polymorphism PCR
technique (IRAP-PCR). Polymorphism percentages (%) were calculated based on
Jaccard Similarity Index. We observed that polymorphism ratios of SIRE1, Sukkula and Nikita
retrotransposons among all samples were 0-40%, 0-100% and 0-60%, respectively.
This is the first report to demonstrate three barley ─ SIRE1, Sukkula and Nikita─ retrotransposons presence and
movements in C. chalcedonicum which
is belonged to Colchium family, thus these IRAP primers may be
used in further characterization and diversity studies of Colchicum
family. 

 

Keywords

Colchicum chalcedonicum, Retrotransposons, SIRE1, Sukkula, Nikita

References

• 1. Koyuncu, M. and Ş. Alp, New geophyte taxa described from Turkey at last decade. Yüzüncü Yıl University Journal of Agriculture Science, 2014. 24 (1): p. 101-110.
• 2. Baytop, T., Therapy with plant in Turkey, İstanbul University Publication. 1984, Istanbul.
• 3. Sargın, A.S., S. Selvi, and E. Akçiçek, Investigations of ethnobotanical aspect of some geophytes growing in Alaşehir (Manisa) and surrounding area, Erciyes University Journal of Institute of Science and Technology, 2013. 29(2): p. 170-177.
• 4. Atak, A., E. Kaya, and K. Erken, Determination of quantity and purity of some geophytes collected from the flora of Turkey, Asian Journal of Plant Sciences, 2014. 13(3): p. 98-110.
• 5. Aznavour, G.Y., Note sur la flore des environs dc Constantinople. Bulletin de la Société Botanique de France, 1987. 44: p. 164-177.
• 6. Brickell, C.D., Colchicum L, In: Davis PH (ed.), Flora of Turkey and the East Aegean Islands. Vol. 8, University Press, 1984. Edinburgh.7. Küçüker, O., The morphological, anatomical and cytological studies on some Colchicum species of Istanbul area. Journal of Science Istanbul University, 1985. 50(B): p. 87-111.
• 8. Persson, K., Nomenclatural synopsis of the genus Colchicum (Colchicaceae), with some new species and combinations. Botanische Jahrbücher für Systematik, 2007. 127: p. 165–242.
• 9. Pray, L., Transposons: The jumping genes. Nature Education, 2008. 1(1): p. 204.
• 10. McClintock, B., The origin and behavior of mutable loci in maize. Proceedings of the National Academy of Sciences of the United States of America, 1950. 36(6): p. 344-355.
• 11. Liu, R., et al., A GeneTrek analysis of the maize genome. Proceedings of the National Academy of Sciences of the United States of America, 2007. 104: p. 11844–11849.
• 12. Wicker, T., et al., A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley. Plant Journal, 2009. 59: p. 712–722.
• 13. Gao, X., et al., Translational recoding signals between gag and pol in diverse LTR retrotransposons. RNA, 2003. 9(12): p. 1422–1430.
• 14. SanMiguel, P., et al., The paleontology of intergene retrotransposons of maize. Nature Genetics, 1998. 20(1): p. 43–45.
• 15. Sheen, F.M., and R.W., Levis, Transposition of the LINE-like retrotransposon TART to Drosophila chromosome termini. Proceedings of the National Academy of Sciences of the United States of America, 1994. 91: p. 12510–12514.
• 16. Frazer, K.A., et al., Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates. Genome Research, 2003. 13(3): p. 341–346.
• 17. Locke, D.P., et al., Large-scale variation among human and great ape genomes determined by array comparative genomic hybridization. Genome Research, 2003. 13(3): p. 347–357.
• 18. Jordan, E., H. Saedler, and P. Starlinger, O0 and strong-polar mutations in the gal operon are insertions. Molecular and General Genetics, 1968. 102(4): p. 353–363.
• 19. Rubin, G.M., M.G. Kidwell, and P.M. Bingham, The molecular basis of P-M hybrid dysgenesis: the nature of induced mutations. Cell, 1982. 29(3): p. 987–994.
• 20. Kazazian, H.H., et al., Haemophilia a resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Nature, 1988. 332(6160): p. 164–166.
• 21. Clegg, M.T, and M.L. Durbin, Tracing floral adaptations from ecology to molecules. Nature Reviews Genetics, 2003. 4(3): p. 206–215.
• 22. Lerman, D.N, and M.E. Feder, Naturally occurring transposable elements disrupt hsp70 promoter function in Drosophila melanogaster. Molecular Biology and Evolution, 2005. 22(3): p. 776–783.
• 23. Kidwell, M.G, and D.R. Lisch, Perspective: transposable elements, parasitic DNA, and genome evolution. Evolution, 2001. 55(1): p. 1–24.
• 24. Kazazian, H.H., Mobile elements: drivers of genome evolution. Science, 2004. 303(5664), p. 1626-1632.
• 25. Feschotte, C, and E.J. Pritham, DNA transposons and the evolution of eukaryotic genomes. Annual Review of Genetics, 2007. 41: p. 331-368.
• 26. Laten, H.M, and R.O. Morris, SIRE1, a long interspersed repetitive DNA element from soybean with weak sequence similarity to retrotransposons: initial characterization and partial sequence. Gene, 1993. 134(2): p. 153-159.
• 27. Çakmak, B., S. Marakli, and N. Gözükirmizi, SIRE1 Retrotransposons in Barley (Hordeum vulgare L.). Russian Journal of Genetics, 2015. 51(7): p.661-672.
• 28. Kalendar, R., et al., Large Retrotransposon Derivatives: Abundant, Conserved but Nonautonomous Retroelements of Barley and Related Genomes. Genetics, 2004. 166: p.1437-1450.
• 29. Leigh, F., et al., Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques. Molecular Genetics and Genomics, 2003. 269: p. 464–474.
• 30. Bento, M., et al., Polyploidization as a retractionforce in plant genome evolution: sequence rearrangements in Triticale. PLoS One, 2008. 3: p. e1402.
• 31. Bento, M., et al., Genome merger: from sequence rearrangements in Triticale to their elimination in wheat–rye addition lines. Theoretical and Applied Genetics, 2010. 121: p. 489-497.
• 32. Carvalho, A., et al., Genetic variability of Old Portuguese bread wheat cultivars assayed by IRAP and REMAP markers. Annals of Applied Biology, 2010. 156: p. 337-345.
• 33. Patel, D., et al., Somatic hybrid plants of Nicotiana X sanderae (+) N. debneyi with fungal resistance to Peronospora tabacina. Annals of Botany-London, 2011. 108: p. 809-819.
• 34. Wessler, S.R., T.E. Bureau, and S.E. White, LTRretrotransposons and MITEs: important players in the evolution of plant genomes. Current Opinion in Genetics and Development, 1995. 5(6): p. 814-821.
• 35. Vicient, C.M., et al., Retrotransposon BARE-1 and Its Role in Genome Evolution in the Genus Hordeum. Plant Cell, 1999. 11: p. 1769-1784.
• 36. Schulman, A.H, and R. Kalendar, A movable feast: diverse retrotransposons and their contribution to barley genome Dynamics. Cytogenetic and Genome Research, 2005. 110: p. 598-605.
• 37. Kalendar, R, and A.H. Schulman, IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nature Protocols, 2006. 1(5): p. 2478-2484.
• 38. Kalendar, R, and A.H. Schulman, Transposon based tagging: IRAP, REMAP, and iPBS. Methods in Molecular Biology, 2014. 1115: p. 233-255.
• 39. Chesnay, C., A. Kumar, and S.R. Pearce, Genetic diversity of SIRE1 retroelements in annual and parennial glycine species revealed using SSAP. Cellular and Molecular Biology Letters, 2007. 12: p. 103-110.
• 40. Rodriguez, M., et al., Integration of Retrotransposons-Based Markers in a Linkage Map of Barley, Molecular Breeding, 2006. 17: p. 173-184.
• 41. Zein, I., M. Jawhar, and M.I.E. Arabi, Efficiencyof IRAP and ITS-RFLP marker systems in accessing genetic variation of Pyrenophora graminea. Genetics and Molecular Biology, 2010. 33(2): p. 328-332.
• 42. Jaccard, P., Nouvelles recherches sur la distribution florale [New research on floral distrubition]. Bulletin de la Société Vaudoise des Sciences Naturelles, 1908. 44: p. 223–270.
• 43. Heras, J., et al., GelJ- a tool for analyzing DNA fingerprint gel images. BioMed Central Bioinformatics, 2015. 16: p. 270.
• 44. Mascher, M., et al., A chromosome conformation capture ordered sequence of the barley genome. Nature, 2017. 544: p. 427–433.
• 45. Fedoroff, N, Transposons and genome evolution in plants. Proceedings of the National Academy of Sciencies of the United States of America, 2000. 97(13): p. 7002-7007.
• 46. Baumel, A., et al., Retrotransposons and genomic stability in populations of the young allopolyploid species Spartina anglica C.E. Hubbard (Poaceae). Molecular Biology and Evolution, 2002. 19(8): p. 1218-1227.
• 47. Alavi-Kia, S.S., et al., Analysis of genetic diversity and phylogenetic relationships in Crocus genus of Iran using Inter Retrotransposon Amplified Polymorphism. Biotechnology and Biotechnological Equipment, 2008. 22: p. 795-800.
• 48. Belyayev, A., et al., Transposable elements in a marginal plant population: temporal fluctuations provide new insights into genome evolution of wild diploid wheat. Mobile DNA, 2010. 1: p. 1-16.
• 49. Giray, B, Türkiye’deki Doğal Çiçek Soğanları ile ilgili Gelişmeler. Tarım ve Köyişleri Bakanlığı Dergisi. 139. 2001. Ankara.
• 50. Dahlgren, R.M.T., H.T. Clifford, and P.F. Yeo, The Families of the Monocotyledons -Structure, Evolution and Taxonomy. 1985. Springer-Verlag Berlin Heidelberg: New York.
• 51. Persson, K, The Genus Colchicum in Turkey I. New Species. Edinburgh Journal of Botany, 1999. 56(1): p. 85-102.
• 52. Akan, H, and I. Eker, Check-list of the genus Colchicum in the flora of Turkey. Turkish Journal of Botany, 2005. 29: p. 327-331.
• 53. Flavell, A.J., S.R. Pearce, and A. Kumar, Plant transposable elements and the genome. Current Opinion in Genetics and Development, 1994. 4(6): p. 838–844.
• 54. Fedoroff, N.V., D.B. Furtek, and O.E. Nelson Jr., (1984) Cloning of the bronze locus in maize by a simple generalizable procedure using the transposable controlling element Activator (Ac). Proceedings of the National Academy of Sciencies of the United States of America, 1984. 81: p. 3825-3829.
• 55. Banks, J.A, and N. Fedoroff, Patterns of developmental and heritable change in methylation of the Suppressor-mutator transposable element. Developmental Genetics, 1989. 10: p. 425-437.
• 56. Kumar, A, and J.L. Bennetzen, Plant retrotransposons. Annual Review of Genetics, 1999. 33: p. 479-532.
• 57. Feschotte, C., N. Jiang, and S.R. Wessler, Plant transposable elements: Where genetics meets genomics. Nature, 2002. 3: p. 329-341.
• 58. Deininger, P.L., et al., Mobile elements and mammalian genome evolution. Current Opinion in Genetics and Development, 2003. 13: p. 651-658.
• 59. Havecker, E.R., X. Gao, and D.F. Voytas, The diversity of LTR retrotransposons. Genome Biology, 2004. 5: p. 225.
• 60. Hymowitz, T, and C.A. Newell, Taxonomy of the genus Glycine: domestication and uses of soybeans. Economic Botany, 1981. 35: p. 272-288.
• 61. Carvalho, A., H. Guedes-Pinto, and J.E. Lima-Brito, Genetic diversity in old Portuguese durum wheat cultivars assessed by retrotransposon-based markers. Plant Molecular Biology Reporter, 2012. 30: p. 578–589.
• 62. Nasri, S., et al., Retrotransposon insertional polymorphism in Iranian bread wheat cultivars and breeding lines revealed by IRAP and REMAP markers. Biochemical Genetics, 2013. 51: p. 927–943.
• 63. Kartal-Alacam, G., et al., Sukkula retrotransposon insertion polymorphism in barley. Russian Journal of Plant Physiology, 2014. 61: p. 828–833.
• 64. Cakmak, B., S. Marakli, and N. Gozukirmizi, Sukkula retrotransposon movements in the human genome. Biotechnology and Biotechnological Equipment, 2017. 31(5): p. 900-905.
• 65. Bayram, E., et al., Nikita Retrotransposon Movements in Callus Cultures of Barley (Hordeum vulgare L.). Plantomics, 2012. 5: p. 211-215.
• 66. Marakli, S, Transferability of Barley Retrotransposons (Sukkula and Nikita) to Investigate Genetic Structure of Pimpinella anisum L.. Marmara Fen Bilimleri Dergisi, 2018. 30: p. 299-304.