Diversification, Evolution and Methylation of Short Interspersed Nuclear Element families in sugar beet and related Amaranthaceae species

Schwichtenberg K, Wenke T, Zakrzewski F, Seibt K, Minoche A, Dohm J, Weisshaar B, Himmelbauer H, Schmidt T (2016)
The Plant Journal 85(2): 229-244.

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Abstract
Short interspersed nuclear elements (SINEs) are non-autonomous non-long terminal repeat retrotransposons which are widely distributed in eukaryotic organisms. While SINEs have been intensively studied in animals, only limited information is available about plant SINEs. We analysed 22 SINE families from seven genomes of the Amaranthaceae family and identified 34806 SINEs, including 19549 full-length copies. With the focus on sugar beet (Beta vulgaris), we performed a comparative analysis of the diversity, genomic and chromosomal organization and the methylation of SINEs to provide a detailed insight into the evolution and age of Amaranthaceae SINEs. The lengths of consensus sequences of SINEs range from 113nucleotides (nt) up to 224nt. The SINEs show dispersed distribution on all chromosomes but were found with higher incidence in subterminal euchromatic chromosome regions. The methylation of SINEs is increased compared with their flanking regions, and the strongest effect is visible for cytosines in the CHH context, indicating an involvement of asymmetric methylation in the silencing of SINEs. 2015 The Authors The Plant Journal 2015 John Wiley & Sons Ltd.
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Schwichtenberg K, Wenke T, Zakrzewski F, et al. Diversification, Evolution and Methylation of Short Interspersed Nuclear Element families in sugar beet and related Amaranthaceae species. The Plant Journal. 2016;85(2):229-244.
Schwichtenberg, K., Wenke, T., Zakrzewski, F., Seibt, K., Minoche, A., Dohm, J., Weisshaar, B., et al. (2016). Diversification, Evolution and Methylation of Short Interspersed Nuclear Element families in sugar beet and related Amaranthaceae species. The Plant Journal, 85(2), 229-244.
Schwichtenberg, K., Wenke, T., Zakrzewski, F., Seibt, K., Minoche, A., Dohm, J., Weisshaar, B., Himmelbauer, H., and Schmidt, T. (2016). Diversification, Evolution and Methylation of Short Interspersed Nuclear Element families in sugar beet and related Amaranthaceae species. The Plant Journal 85, 229-244.
Schwichtenberg, K., et al., 2016. Diversification, Evolution and Methylation of Short Interspersed Nuclear Element families in sugar beet and related Amaranthaceae species. The Plant Journal, 85(2), p 229-244.
K. Schwichtenberg, et al., “Diversification, Evolution and Methylation of Short Interspersed Nuclear Element families in sugar beet and related Amaranthaceae species”, The Plant Journal, vol. 85, 2016, pp. 229-244.
Schwichtenberg, K., Wenke, T., Zakrzewski, F., Seibt, K., Minoche, A., Dohm, J., Weisshaar, B., Himmelbauer, H., Schmidt, T.: Diversification, Evolution and Methylation of Short Interspersed Nuclear Element families in sugar beet and related Amaranthaceae species. The Plant Journal. 85, 229-244 (2016).
Schwichtenberg, Katrin, Wenke, Torsten, Zakrzewski, Falk, Seibt, Kathrin, Minoche, Andre, Dohm, Juliane, Weisshaar, Bernd, Himmelbauer, Heinz, and Schmidt, Thomas. “Diversification, Evolution and Methylation of Short Interspersed Nuclear Element families in sugar beet and related Amaranthaceae species”. The Plant Journal 85.2 (2016): 229-244.
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