References
- Asif, J. M., Othman, F. Y. (2005). Characterization of fusarium wilt-resistant and fusarium wilt-susceptible somaclones of banana cultivar Rastali (Musa AAB) by random amplified polymorphic DNA and retrotransposon markers. Plant Mol. Biol. Rep., 23 (3), 241–249.
- Bairu, M. W., Aremu, A. O., Staden, J. V. (2011). Somaclonal variation in plants: Causes and detection methods. Plant Growth Regul., 63, 147–173.
- Baranek, M., Meszaros, M., Sochorova, J., Cechova, J., Raddova, J. (2012). Utility of retrotransposon-derived marker systems for differentiation of presumed clones of the apricot cultivar Velkopavlovická. Sci. Horticult., 143, 1–6.
- Bayram, E., Yilmaz, S., Hamat-Mecbur, H., Kartal-Alacam, G., Gozukirmizi, N. (2012). Nikita retrotransposon movements in callus cultures of barley (Hordeum vulgare L.). Plant Omics Journal (POJ), 5 (3), 211–215.
- Benachenhou, F., Sperber, G. O., Bongcam-Rudloff, E., Andersson, G., Boeke, J. D., Blomberg, J. (2013). Conserved structure and inferred evolutionary history of long terminal repeats (LTRs). Mobile DNA, doi: 10.1186/1759-8753-4-5.
- Berg, D. E., Howe, M. H. (eds.) (1989). Mobile DNA. Washington, D.C.: American Society for Microbiology Press.
- Birnboim, H. C., Doly, J. (1979). A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucl. Acids Res., 7 (6), 1513–1523.
- Brandes, A., Heslop-Harrison, J. S., Kamm, A., Kubis, S., Doudrick, R. L., Schmidt, T. (1997). Comparative analysis of the chromosomal and genomic organization of Ty1-copia -like retrotransposons in pteridophytes, gymnosperms and angiosperms. Plant Mol. Biol., 33 (1), 11–21.
- Campbell, B. C., LeMare, S., Piperidis, G., Godwin, I. D. (2011). IRAP, a retrotransposon-based marker system for the detection of somaclonal variation in barley. Mol. Breed., 27, 193–206.
- Capy, P. (2005). Classification and nomenclature of retrotransposable elements. Cytogenet. Gen. Res., 110 (1–4), 457–461.
- Capy, P., Gasperi, G., Biemont, C., Bazin, C. (2000). Stress and transposable elements: Co-evolution or useful parasites? Heredity, 85, 101–106.
- Carvalho, A., Guedes-Pinto, H., Lima-Brito, J. E. (2012). Genetic diversity in old Portuguese durum wheat cultivars assessed by retrotransposon-based markers. Plant Mol. Biol. Rep., 30, 578–589.
- Castro, I., D’Onofrio, C., Martín, J. P., Ortiz, J. M., De Lorenzis, G., Ferreira, V., Pinto-Carnide, O. (2012). Effectiveness of AFLPs and retrotransposon-based markers for the identification of Portuguese grapevine cultivars and clones. Mol. Biotechnol., 52 (1), 26–39.
- D’Onofrio, C., De Lorenzis, G., Giordani, T., Natali, L., Cavallini, A., Scalabrelli, G. (2010). Retrotransposon-based molecular markers for grapevine species and cultivars identification. Tree Genet. Gen., 6, 451–466.
- Feschotte, C., Jiang, N., Wessler, S. R. (2002). Plant transposable elements: Where genetics meets genomics. Nat. Rev. Genet., 3, 329–341.
- Finnegan, D. J. (1989). Eukaryotic transposable elements and genome evolution. Trends. Genet., 5, 103–107.
- Flavell, A. J., Pearce, S. R., Kumar, A. (1994). Plant transposable elements and the genome. Curr. Opin. Genet. Dev., 4, 838–844.
- Friesen, N., Brandes, A., Heslop-Harrison, J. S. (2001). Diversity, origin and distribution of retrotransposons (gypsy and copia) in conifers. Mol. Biol. Evol., 18 (7), 1176–1188.
- Gao, D., Chen, J., Chen, M., Meyers, B. C., Jackson, S. (2012). A highly conserved, small LTR retrotransposon that preferentially targets genes in grass genomes. PloS One, doi:10.1371/journal.pone.0032010.
- Grandbastien, M. A., Lucas, H., Morel, J. B., Corinne, M. C., Vernhettes, S., Casacuberta, J. M. (1997). The expression of the tobacco Tnt1 retrotransposon is linked to plant defense responses. Genetica, 100, 241–252.
- Inoue, H., Nojima, H., Okayama, H. (1990). High efficiency transformation of Escherichia coli with plasmids. Gene, 96, 23–28.
- Ito, H., Gaubert, H., Bucher, E., Mirouze, M., Vaillant, I., Paszkowski, J. (2011). An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature, 472, 115–118.
- Kalendar, R., Antonius, K., Smykal, P., Schulman, A.H. (2010). iPBS: A universal method for DNA fingerprinting and retrotransposon isolation. Theor. Appl. Genet., doi:10.1007/s00122-010-1398-2.
- Kalendar, R., Grob, T., Regina, M., Suoniemi, A., Schulman, A. (1999). IRAP and REMAP: Two new retrotransposon-based DNA fingerprinting techniques. Theor. Appl. Genet., 98, 704–711.
- Kalendar, R., Schulman, A. H. (2007). IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nat. Protoc., 1 (5), 2478–2484.
- Kamm, A., Doudric, R. L., Heslop-Harrison, J. S., Schmidt, T. (1996). The genomic and physical organization of Ty1-copia -like sequences as a component of large genomes in Pinus elliottii var. elliottii and other gymnosperms. Proc. Natl. Acad. Sci. USA, 93, 2708–2713.
- Knight, C. A., Ackerly, D. D. (2002). Variation in nuclear DNA content across environmental gradients: A quantile regression analysis. Ecol. Lett., 5, 66–76.
- Kohany, O., Gentles, A. J., Hankus, L., Jurka, J. (2006). Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics, doi:10.1186/1471-2105-7-474.
- Kossack, D. S., Kinlaw, C. S. (1999). IFG, a gypsy -like retrotransposon in Pinus (Pinaceae), has an extensive history in pines. Plant Mol. Biol., 39, 417–426.
- Kovach, A., Wegrzyn, J. L., Parra, G., Holt, C., Bruening, G. E., Loopstra, C. A., Hartigan, J., Yandell, M., Langley, C. H., Korf, I., Neale, D. B. (2010). The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics, doi: 10.1186/1471-2164-11-420.
- Kumar, A., Bennetzen, J. L. (1999). Plant Retrotransposons. Annu. Rev. Genet., 33, 479–532.
- Kumar, A., Hirochika, H. (2001). Applications of retrotransposons as genetic tools in plant biology. Trends Plant Sci., 6 (3), 127–134.
- Kumar, A., Pearce, S. R., McLean, K., Harrison, G., Heslop-Harrison, J. S., Waugh, R., Flavell, A. J. (1997). The Ty1-copia group of retrotransposons in plants: Genomic organisation, evolution, and use as molecular markers. Genetica, 100 (1–3), 205–217.
- L’Homme, Y., Seguin, A., Tremblay, F. M. (2000). Different classes of retrotransposons in coniferous spruce species. Genome, 43, 1084–1089.
- Leitch, I. J., Bennett, M. D. (2004). Genome downsizing in polyploid plants. Biol. J. Linn. Soc., 82, 651–663.
- Lightbourn, G. J., Jelesko, J. G., Veilleux, R. E. (2007). Retrotransposonbased markers from potato monoploids used in somatic hybridization. Genome, 50 (5), 492–501.
- Mak, J., Kleiman, L. (1997). Primer tRNAs for reverse transcription. J. Virol., 71 (11), 8087–8095.
- McClintock, B. (1984). The significance of responses of the genome to challenge. Science, 226, 792–801.
- Mignone, F., Grillo, G., Licciulli, F., Iacono, M., Liuni, S., Kersey, P. J., Duarte, J., Saccone, C. Pesole, G. (2005). UTRdb and UTRsite: A collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucl. Acids Res., 33, D141–146.
- Miguel, C., Simoes, M., Oliveira, M. M., Rocheta, M. (2008). Envelope-like retrotransposons in the plant kingdom: Evidence of their presence in Gymnosperms (Pinus pinaster). J. Mol. Evol., 67, 517–525.
- Murray, B.G. (1998). Nuclear DNA amounts in gymnosperms. Ann. Bot., 82, 3–15.
- Murray, B.G. (2005). When does intraspecific C-value variation become taxonomically significant? Ann. Bot., 95, 119–125.
- Neumann, P., Pozárková, D., Macas, J. (2003). Highly abundant pea LTR Retrotransposon Ogre is constitutively transcribed and partially spliced. Plant. Mol. Biol., 53 (3), 399–410.
- Nystedt, B., Street, N. R., Wetterbom, A., Zuccolo, A., Lin, Y. C., Scofield, D. G., Vezzi, F., Delhomme, N., Giacomello, S., Alexeyenko, A., Vicedomini, R., Sahlin, K., Sherwood, E., Elfstrand, M., Gramzow, L., Holmberg, K., Hällman, J., Keech, O., Klasson, L., Koriabine, M., Kucukoglu, M., Käller, M., Luthman, J., Lysholm, F., Niittylä, T., Olson, A., Rilakovic, N., Ritland, C., Rosselló, J.A., Sena, J., Svensson, T., Talavera-López, C., Theißen, G., Tuominen, H., Vanneste, K., Wu, Z. Q., Zhang, B., Zerbe, P., Arvestad, L., Bhalerao, R., Bohlmann, J., Bousquet, J., Garcia, G. R., Hvidsten, T. R., de Jong, P., MacKay, J., Morgante, M., Ritland, K., Sundberg, B., Thompson, S. L., Van de Peer, Y., Andersson, B., Nilsson, O., Ingvarsson, P.K., Lundeberg, J., Jansson, S. (2013). The Norway spruce genome sequence and conifer genome evolution. Nature, doi:10.1038/nature12211.
- Peakall, R., Smouse, P. E. (2006). GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes, 6, 288–295.
- Porebski, S., Bailey, G. L., Baum, B. R. (1997). Modification of a CTAB DNA extraction protocol for plants containing high polysaharide and polyphenol componenets. Plant Mol. Biol. Rep., 15 (1), 8–15.
- Rocheta, M., Cordeiro, J., Oliveira, M., Miguel, C. (2007). PpRT1: The first complete gypsy -like retrotransposon isolated in Pinus pinaster. Planta, 225, 551–562.
- Saeidi, H., Rahiminejad, M. R., Heslop-Harrison, J. S. (2008). Retroelement insertional polymorphisms, diversity and phylogeography within diploid, D-genome Aegilops tauschii (Triticeae, Poaceae) sub-taxa in Iran. Ann. Bot., 101 (6), 855–861.
- Schlüter, P. M., Harris, S. A. (2006). Analysis of multilocus fingerprinting data sets containing missing data. Mol. Ecol. Notes, 6, 569–572.
- Schulman, A. H. (2007). Molecular markers to assess genetic diversity. Euphytica, 158, 313–321.
- Schulman, A. H., Flavell, A. J., Ellis, T. H. (2004). The application of LTR retrotransposons as molecular markers in plants. Meth. Mol. Biol., 260, 145–173.
- Schulman, A. H., Flavell, A. J., Paux, E., Ellis, T. H. (2012). The application of LTR retrotransposons as molecular markers in plants. Meth. Mol. Biol., 859, 115–153.
- Solovyev, V. V. (2002). Structure, properties and computer identification of eukaryotic genes. In: Bioinformatics Genomes to Drugs, Basic Technologies (59–111 pp.). Lengauer, T. (ed.). Wiley.
- Solovyev, V. V., Shahmuradov, I. A. (2003). PromH: Promoters identification using orthologous genomic sequences. Nucl. Acids Res., 31 (13), 3540–3545.
- Soranzo, N., Provan, J., Powell, W. (1998). Characterization of microsatellite loci in Pinus sylvestris L. Mol. Ecol., 7, 1247–1263.
- Stuart-Rogers, C., Flavell, A. J. (2001). The evolution of Ty1-copia group retrotransposons in gymnosperms. Mol. Biol. Evol., 18 (2), 155–163.
- Subudhi, P., Magpantay, G., Karan, R. (2013) A retrotransposon-based probe for fingerprinting and evolutionary studies in rice (Oryza sativa). Genet. Res. Crop. Evol., 60 (4), 1263–1273.
- Tam, S. M., Mhiri, C., Vogelaar, A., Kerkveld, M., Pearce, S. R., Grandbastien, M. A. (2005). Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR. Theor. Appl. Genet., 110 (5), 819–831.
- Vicient, C. M., Kalendar, R., Schulman, A. H. (2005). Variability, recombination and mosaic evolution of the barley BARE-1 retrotransposon. J. Mol. Evol., 61, 275–291.
- Voronova, A., Jansons, A., Ruòìis, D. (2011). Expression of retrotransposon-like sequences in Scots pine (Pinus sylvestris L.) in response to heat stress. Environ. Exper. Biol., 9, 121–127.
- Wessler, S. R. (1996). Plant retrotransposons: Turned on by stress. Curr. Biol., 6 (8), 959–961.
- 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., Schulman, A. H. (2007) A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet., 8 (12), 973–982.
- Xiong, Y., Eickbush, T. H. (1990). Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J., 9, 3353–3362.
- Ye, J., Coulouris, G., Zaretskaya, I., Cutcutache, I., Rozen, S., Madden, T. (2012). Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics, doi:10.1186/1471-2105-13-134.