In response to the correspondence by Vladimir V. Kapitonov and Jerzy Jurka (A universal classification of eukaryotic transposable elements implemented in Repbase. Nature Rev. Genet. 9 (2008), doi:10.1038/nrg2165-c1)1 on our Review (A unified classification system for eukaryotic transposable elements. Nature Rev. Genet. 8, 973–982 (2007))2, Repbase is a useful tool, alongside RetrOryza, the Triticeae repeat database (TREP), The Institute for Genomic Research (TIGR) repeat databases and other such resources, for organizing and accessing the complexity and commonalities of the transposable elements. Any apparent under-exposure of Repbase or other tools in our paper was unintentional. The hierarchical classification system of Repbase is consistent with that of Finnegan3 from 1989 as well those of others4,5. We have endeavored to conserve the areas of agreement within the transposable element community on transposable element taxonomy, while adding features (including a full hierarchical nomenclature) and application rules that will benefit annotators and non-experts.
References
A universal classification of eukaryotic transposable elements implemented in Repbase. Nature Rev. Genet. 9 (2008), doi:10.1038/nrg2165-c1.
A unified classification system for eukaryotic transposable elements. Nature Rev. Genet. 8, 973–982 (2007).
Finnegan, D. J. Eukaryotic transposable elements and genome evolution. Trends Genet. 5, 103–107 (1989).
Kumar, A. & Bennetzen, J. Plant retrotransposons. Ann. Rev. Genet. 33, 479–532 (1999).
Capy, P., Bazin, C., Higuet, D. & Langin, T. (eds) Dynamics and evolution of transposable elements (Library of Congress, Austin, Texas, 1998).
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Wicker, T., Sabot, F., Hua-Van, A. et al. A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet 9, 414 (2008). https://doi.org/10.1038/nrg2165-c2
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DOI: https://doi.org/10.1038/nrg2165-c2
