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Conference Papers Year : 2019

RepetDB: a unified resource for transposable element references

Abstract

Transposable elements (TEs) are major players in the structure and evolution of eukaryote genomes. Thanks to their ability to move around and replicate within genomes, they are probably the most important contributors to genome plasticity. The insertion of TEs close to genes can affect gene structure, expression and function, contributing to the genetic diversity underlying species adaptation. Many studies have shown that TEs are generally silenced through epigenetic defense mechanisms, and that these elements play an important role in epigenetic genome regulation. Their detection and annotation are considered essential and must be undertaken in the frame of any genome sequencing project. Here, we will present the new version of RepetDB [1] (Amselem et al., Mobile DNA, 2019), (https://urgi.versailles.inrae.fr/repetdb) our TE database developed to store and retrieve detected, classified and annotated TEs in a standardized manner. This RepetDB v2 new version was updated with 31 more species of plants and fungi and provides TE consensi with evidences able to justify their classification. RepetDB v2 is a customized implementation of InterMine [2,3], an open-source data warehouse framework used here to store, search, browse, analyze and compare all the data recorded for each TE reference sequence. InterMine provides powerful capabilities to query and visualize all biological information on TE. It allows to make simple search on the database using the QuickSearch (‘google like search’) or make more complex queries using the Querybuilder to display various desired information. RepetDB v2 is designed to be a TE knowledge base populated with full de novo TE annotations of complete (or near-complete) genome sequences. Indeed, the description and classification of TEs facilitates the exploration of specific TE families, superfamilies or orders across a large range of species. It also makes possible cross-species searches and comparisons of TE family content between genomes. References 1. Amselem, J., Cornut, G., Choisne, N., Alaux, M., Alfama-Depauw, F., Jamilloux, V., Maumus, F., Letellier, T., Luyten, I., Pommier, C., Adam-Blondon, A. F., & Quesneville, H. (2019). RepetDB: a unified resource for transposable element references. Mobile DNA, 10, 6. https://doi.org/10.1186/s13100-019-0150-y 2. InterMine: extensive web services for modern biology. Kalderimis A, Lyne R, Butano D, Contrino S, Lyne M, Heimbach J, Hu F, Smith R, Stˇepán R, Sullivan J, Micklem G. Nucleic Acids Res. 2014 Jul; 42 (Web Server issue): W468-72 3. InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. Smith RN, Aleksic J, Butano D, Carr A, Contrino S, Hu F, Lyne M, Lyne R, Kalderimis A, Rutherford K, Stepan R, Sullivan J, Wakeling M, Watkins X, Micklem G. Bioinformatics (2012) 28 (23): 3163-3165.
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Dates and versions

hal-03819882 , version 1 (08-11-2022)

Identifiers

  • HAL Id : hal-03819882 , version 1

Cite

Mariène Wan, Nicolas Francillonne, Raphaël Flores, Françoise Alfama, Johann Confais, et al.. RepetDB: a unified resource for transposable element references. Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM) 2022, SFBI; IFB; GDR BIM, Jul 2022, Rennes, France. ⟨hal-03819882⟩
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