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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)
30 Nov 2022 [hal-03876510] Transposable elements, from their annotation to their integration into knowledge graphs
Transposable elements (TEs) are major players of structure and evolution of eukaryote genomes. Thanks to their ability to move around and to replicate within genomes, they are probably the most important contributors to genome plasticity. Individuals 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 REPET package integrates bioinformatics pipelines dedicated to detect and annotate TEs in genomes. Then the PanREPET pipeline allows to describe (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. To identify TE candidate putatively involved in local adaptation, environmental knowledge and genome annotations have been integrated in a semantic knowledge graph.
et al.
In ProdINRA
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COM (communication)
28 Nov 2022 [hal-03838843] Demo session : REPET
https://forgemia.inra.fr/urgi-anagen/wiki-repet/-/wikis/tutorial-with-Docker-image-of-REPET
et al.
In ProdINRA
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COM (communication)
19 Nov 2022 [hal-03858907] Survival and growth of 711 forest tree taxa in eight French arbore-tums from three different climate regions
Arboretums have been used for decades for scientific, educational, horticultural and aesthetic purposes. Recently, climate change concerns have renewed the interest of the scientific community for these invaluable experimental forest systems. Here, we report a dataset from eight scientific arboretums planted in three contrasted French metropolitan bioclimates: Oceanic, Mountain and Mediterranean. In total, 92,236 trees were planted in 3,678 different plots. Originating from a worldwide range of ha-bitats, from sea-level up to 3,670 m in elevation, the collection spans 711 forest tree taxa (species, subspecies and varieties) from 177 genera. Taxa often include several geographic sources (so-called provenances), often simultaneously in different arboretums, making within species analyses possible. Cool-climate temperate Pinaceae (pines, firs, spruces, hemlocks, etc.) are well represented in the Atlantic and Mountain arboretums while Mediterranean arboretums are particularly rich with genera from the Myrtaceae (mostly eucalypts) and the Pinaceae (mostly pines). Data include survival, growth (height and diameter) and health status. Planted between 1969 and 1976, 338 taxa had survived at time of assessment and occurred as at least one individual in one plot. Data can be used to assess species suitability for ecological restoration and afforestation, and to help improve functional niche modelin
et al.
In ProdINRA
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COM (communication)
18 Nov 2022 [hal-03846467] Multiple Horizontal Acquisitions of Plant Genes in the Whitefly Bemisia tabaci
Abstract The extent to which horizontal gene transfer (HGT) has shaped eukaryote evolution remains an open question. Two recent studies reported four plant-like genes acquired through two HGT events by the whitefly Bemisia tabaci, a major agricultural pest (Lapadula WJ, Mascotti ML, Juri Ayub M. 2020. Whitefly genomes contain ribotoxin coding genes acquired from plants. Sci Rep. 10(1):15503 et al.
In ProdINRA
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COM (communication)
10 Nov 2022 [hal-03819511] REPET evolutions: faster and easier
Transposable elements (TEs) are major players of structure and evolution of eukaryote genomes. Thanks to their ability to move around and to replicate within genomes, they are probably the most important contributors to genome plasticity. Their detection and annotation are considered essential and must be undertaken in any genome sequencing project. The REPET package [1, 2] integrates bioinformatics pipelines dedicated to detect, annotate and analyze TEs in genomic sequences. The two main pipelines are (i) TEdenovo, that search for interspersed repeats, build consensus sequences and classify them [3] 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 for speed by parallelizing several key bottleneck steps. In addition, several strategies which reduce the time required for analyzing large genome have been tested. With the speed improvement and adapted strategies, REPET is now able to annotate and analyze genomes such as the maize with more than 85% of TEs on a 2.3 Gb genome [4] on current computer cluster. With this tool, the PlantBioinfoPF platform ensures a TE annotation service. Indeed, we are now able to propose an automatic TE annotation of good quality through a process called "Repet-Factory". This process uses the REPET software suite with parameters optimized for TE detection specificity and computing time. This process is capable of successively annotate several genomes in batches with the required traceability and reproducibility of the analyzes. Moreover, a Virtual Research Environment (VRE) for TE annotation and its analysis has been developed on Virtual Machines (VM). An ansible script instantiate VMs with all packages and tools required for a complete genome annotation with the REPET package. This script allows this VRE to be easily re-instantiated in other infrastructures which greatly simplify the REPET package installation with all its required dependencies. We also simplified the distribution of REPET to increase its availability and portability to users, by developing a Docker image of REPET (https://hub.docker.com/r/urgi/docker_vre_aio). The REPET tool is a cornerstone of the platform. In addition to its use in the genome TE annotation service and its availability for download, it is also the basis of the RepetDB [5] database (https://urgi.versailles.inrae.fr/repetdb) hosted by the platform which provides libraries of reference TE sequences for more than 50 species. References 1. Flutre T, Duprat E, Feuillet C, Quesneville H (2011) Considering Transposable Element Diversification in De Novo Annotation Approaches. PLoS ONE 6(1): e16526. https://doi.org/10.1371/journal.pone.0016526 2. Quesneville H, Bergman CM, Andrieu O, Autard D, Nouaud D, Ashburner M, et al. (2005) Combined Evidence Annotation of Transposable Elements in Genome Sequences. PLoS Comput Biol 1(2): e22. https://doi.org/10.1371/journal.pcbi.0010022 3. Hoede C, Arnoux S, Moisset M, Chaumier T, Inizan O, Jamilloux V, et al. (2014) PASTEC: An Automatic Transposable Element Classification Tool. PLoS ONE 9(5): e91929. https://doi.org/10.1371/journal.pone.0091929 4. V. Jamilloux, J. Daron, F. Choulet and H. Quesneville, "De Novo Annotation of Transposable Elements: Tackling the Fat Genome Issue," in Proceedings of the IEEE, vol. 105, no. 3, pp. 474-481, March 2017, doi: 10.1109/JPROC.2016.2590833. 5. 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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Update: 19 Nov 2010
Creation date: 01 Dec 2009