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Publications

URGI members are underlined in authors list. In the talks sections, names in bold are the speakers.

There are different types of publications, Papers with reading comittee (ACL), Papers in books (ACT), Invited talks (INV), Talks (COM), Posters (COM), Specialised Media and Press (SMP) and Thesis.

Other
COM (communication)
 10 Nov 2022 [hal-03819882] RepetDB: a unified resource for transposable element references
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., & et al.
In ProdINRA
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COM (communication)
 09 Nov 2022 [hal-03819044] Characterization of Transposable Elements in Pangenomes
Transposable elements (TEs) are mobile DNA elements that can invade the genomes by transposition. Despite their reputation as parasitic sequences, these elements can enrich the genomes with functional novelties that foster genome evolution. Indeed, TEs can impact genes through insertional mutagenesis, supplies of new transcription factor binding sites (TFBS), or by epigenetic regulation. The impact of TEs in a genome is explored by searching for insertions events. Individuals (or accessions) of the same species independently undergo TE insertions causing inter-individual genetic variability. This variability between individuals is the basis of the natural selection that leads to an increased adaptation of individuals to their environment. A way to search for the potential role of TEs in host adaptation is through a pangenomic approach. The TE pangenome is described by (i) TE insertions present in all individuals of the species (core-genome), (ii) insertions present only among a subset of individuals (dispensable-genome) or (iii) ecogenome when the individuals share the same environment, and finally (iv) insertions specific to an individual. Current pangenome analysis methods are based on the alignment of reads from di↵erent accessions of the species to an assembled reference genome. But, the advent of the third-generation sequencing makes now possible to approach this question on several assembled genomes of the same species. I will present a new pipeline which identify the TEs pangenome compartments from several assembled genomes. There is therefore no dependency on a reference genome. This new pipeline uses a bidirectional best hits strategy to detect the copies located at the same position and shared by one or more accessions. The pipeline have been tested with Arabidopsis thaliana, Oryza sativa, and Brachypodium distachyon pangenomes.
et al.
In ProdINRA
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COM (communication)
 05 Nov 2022 [hal-03838081] REPET evolutions: faster and easier
The detection and annotation of transposable elements (TEs) are now considered mandatory to any genome sequencing project. To this aim, the REPET package integrates bioinformatics pipelines dedicated to detect, annotate and analyse TEs in genomic sequences. The two main pipelines are (i) TEdenovo, that search for interspersed repeats, build consensus sequences and classify them according to TE features and (ii) TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations. The REPET package is in continuous improvement. Several implementations and algorithms to reduce the time required for analysing large genome have been tested. With our new speed improvements and tuned annotation strategies, REPET is now able to annotate and analyse easily large genomes up to 3 Gb. Now, we chain all required steps through a process called "Repet-Factory". This process uses parameters optimized for specificity and computing time. It is capable of successively annotate several genomes in batches with all the traceability required for reproducibility. We also simplified the distribution of REPET by developing a Docker image of REPET (https://hub.docker.com/r/urgi/docker_vre_aio).
et al.
In ProdINRA
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COM (communication)
 27 Oct 2022 [hal-03807713] Traces of transposable elements in genome dark matter co-opted by flowering gene regulation networks
[...]
et al.
In ProdINRA
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COM (communication)
 21 Oct 2022 [hal-03815061] REPET evolutions: faster and easier

Transposable elements (TEs) are major players of structure and evolution of eukaryote genomes. Thanks ...
COM (communication)
 12 Oct 2022 [hal-03807727] Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila

Abstract High quality reference genomes are crucial to understanding genome function, structure and evolution. ...
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Update: 19 Nov 2010
Creation date: 01 Dec 2009