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RepetDB: A TE database

Authors
  • Francillonne, Nicolas
  • Wan, Mariène
  • Choisne, Nathalie
  • Alfama, Françoise
  • Flores, Raphaël
  • Amselem, Joelle
  • Confais, Johann
  • Quesneville, Hadi
Publication Date
Apr 20, 2024
Source
HAL-Descartes
Keywords
Language
English
License
Unknown
External links

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 more species of plants andfungi 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 (‘googlelike search’) or make more complex queries using the Querybuilder to display various desiredinformation. 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.

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