Francois Sabot Directeur de Recherches IRD au sein de l'UMR DIADEDirecteur adjoint de la Mission Science Ouverte de l'IRD

Identifiants chercheurs

IdHAL :

francois-sabot

ORCID :

0000-0002-8522-7583

IdRef :

083268391

Présentation

From an initial formation in Molecular Genetics and Physiology, I went during my PhD on Transposable Elements, working on large plant genomes at INRA, France. During my Post-Doc at university of Helsinki, I worked on mechanics, structure and evolution of TEs, in lab then in bioinformatics and NGS. My current research interest in the French National institute for Sustainable Development (IRD) is the Pangenomics modification during speciation/domestication, especially regarding TEs, in various genomes. In this regard, I explore with my team the pangenome in all aspects: creation, modification, graph theory, vizualisation, and so on...In parallel, I spent (and continue to) large efforts on open science, through open source development, open access publication and open data dissemination, as the deputy director of the Open Science mission at IRD.

Publications

Article dans une revue (53)

Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species Daniel Siqueira de Oliveira,Anaïs Larue,William Vilas Boas Nunes,Francois Sabot,Alejandra Bodelónet al. Genome Research, 2026, 36 (3), pp.487-505. ⟨10.1101/gr.280463.125⟩ Article dans une revue hal-05539944v1
Defining biodiversity data Eric Garnier,Dominique Pelletier,Philip Roche,Rodolphe Rougerie,Eve Afonsoet al. Trends in Ecology & Evolution, 2025, 40 (8), pp.731-735. ⟨10.1016/j.tree.2025.06.004⟩ Article dans une revue hal-05230422v1
Male sterility in Drosophila mojavensis × D. arizonae hybrids is not caused by gene movements in the Y chromosome Thyago Vanderlinde,Fabiana Uno,Gabriel Goldstein,François Sabot,Claudia Cararetoet al. Evolution - International Journal of Organic Evolution, 2025, ⟨10.1093/evolut/qpaf163⟩ Article dans une revue hal-05245261v1
DateBack, an evolving open-access repository of Phoenix archaeobotanical data supporting new perspectives on the history of date palm cultivation Margot Besseiche,Elora Chambraud,Vladimir Dabrowski,Elisa Brandstatt,François Sabotet al. Peer Community In Archaeology, 2025, 5, pp.e55. ⟨10.24072/pci.archaeo.100603⟩ Article dans une revue hal-05082078v1
Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues Rita Rebollo,Pierre Gerenton,Eric Cumunel,Arnaud Mary,François Sabotet al. Peer Community Journal, 2024, 4 (e89), ⟨10.24072/pcjournal.457⟩ Article dans une revue hal-04285238v1
An INDEL genomic approach to explore population diversity of phytoplankton : Bathycoccus , a case study Martine Devic,Louis Dennu,Jean-Claude Lozano,Cédric Mariac,Valérie Vergéet al. BMC Genomics, 2024, ⟨10.1186/s12864-024-10896-w⟩ Article dans une revue hal-04286658v2
FrangiPANe, a tool for creating a panreference using left behind reads Christine Tranchant-Dubreuil,Clothilde Chenal,Mathieu Blaison,Laurence Albar,Valentin Kleinet al. NAR Genomics and Bioinformatics, 2023, 5 (1), pp.lqad013. ⟨10.1093/nargab/lqad013⟩ Article dans une revue hal-04049468v1
TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches Mourdas Mohamed,François Sabot,Marion Varoqui,Bruno Mugat,Katell Audouinet al. Genome Biology, 2023, 24 (1), pp.63. ⟨10.1186/s13059-023-02911-2⟩ Article dans une revue hal-04291760v1
Genomic introgressions from African rice (Oryza glaberrima) in Asian rice (O. sativa) lead to the identification of key QTLs for panicle architecture Hélène Adam,Andrés Gutiérrez,Marie Couderc,Francois Sabot,Fabrice Ntakirutimanaet al. BMC Genomics, 2023, 24 (1), 587 [21 p.]. ⟨10.1186/s12864-023-09695-6⟩ Article dans une revue hal-04743156v1
CulebrONT : a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes Julie Orjuela,Aurore Comte,Sébastien Ravel,Florian Charriat,Tram Viet al. Peer Community Journal, 2022, 2, e46 [9 p.]. ⟨10.24072/pcjournal.153⟩ Article dans une revue hal-04378943v1
Rice farmers' perceptions and response to climate variability, and determinants of adaptation strategies in the Republic of Benin C. D. S. J. Gbemavo,J. Toffa,C. Tchakpa,Y. L. E. Loko,G. Djedatinet al. International Journal of Climate Change Strategies and Management, 2022, 14 (4), pp.332-353. ⟨10.1108/ijccsm-06-2021-0059⟩ Article dans une revue hal-04389871v1
Ten simple rules for switching from face-to-face to remote conference: An opportunity to estimate the reduction in GHG emissions Valentin Guignon,Catherine Breton,Jérôme J. Mariette,Francois Sabot,Julien Fumeyet al. PLoS Computational Biology, 2021, 17 (10), pp.e1009321. ⟨10.1371/journal.pcbi.1009321⟩ Article dans une revue lirmm-03385026v1
On-farm management of rice diversity, varietal preference criteria, and farmers' perceptions of the African (Oryza glaberrima Steud.) versus Asian rice (Oryza sativa L.) in the Republic of Benin (West Africa): implications for breeding and conservation Loko Laura Estelle Yêyinou,Ewedje Eben-Ezer,Orobiyi Azize,Djedatin Gustave,Toffa Joelleet al. Economic Botany, 2021, ⟨10.1007/s12231-021-09515-6⟩ Article dans une revue hal-03169601v1
Panache: a Web Browser-Based Viewer for Linearized Pangenomes Éloi Durant,Francois Sabot,Matthieu Conte,Mathieu Rouard Bioinformatics, 2021, 37 (23), pp.4556-4558. ⟨10.1093/bioinformatics/btab688⟩ Article dans une revue hal-03378164v1
A transposon story : from TE content to TE dynamic invasion of Drosophila genomes using the single-molecule sequencing technology from Oxford Nanopore Mohamed Mourdas,Nguyet Thi-Minh Dang,Yuki Ogyama,Nelly Burlet,Bruno Mugatet al. Cells, 2020, 9 (8), pp.1776. ⟨10.3390/cells9081776⟩ Article dans une revue hal-02905128v1
Plant Pangenome: Impacts On Phenotypes And Evolution Christine Tranchant-Dubreuil,Mathieu Rouard,Francois Sabot Annual Plant Reviews, 2019, ⟨10.1002/9781119312994.apr0664⟩ Article dans une revue hal-02053647v1
MooSciTIC: Training of trainers in West African research and higher education Ménonvè Atindehou,Kifouli Adeoti,Laura Estelle Yêyinou Loko,Thierry Beulé,Emmanuel Paradiset al. PLoS Biology, 2019, 17 (6), pp.e3000312. ⟨10.1371/journal.pbio.3000312⟩ Article dans une revue ird-02365690v1
Long-fragment targeted capture for long-read sequencing of plastomes Kevin Bethune,Cédric Mariac,Marie Couderc,Nora Scarcelli,Sylvain Santoniet al. Applications in Plant Sciences, 2019, 7 (5), pp.e1243. ⟨10.1002/aps3.1243⟩ Article dans une revue hal-02620804v1
Caractérisation phénotypique et génétique du riz africain (Oryza glaberrima Steud) C. Gnacadja,Cécile Berthouly,S.N. Sall,Leila Zekraoui,Francois Sabotet al. International journal of advanced research, 2018, 6 (2), pp.1389-1398. ⟨10.21474/IJAR01/6569⟩ Article dans une revue hal-03070277v1
A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives Gautier Sarah,Félix Homa,Stéphanie Pointet,Sandy Contreras,François Sabotet al. Molecular Ecology Resources, 2017, 17 (3), pp.565-580. ⟨10.1111/1755-0998.12587⟩ Article dans une revue hal-01930391v1
De Novo Assemblies of Three Oryza glaberrima Accessions Provide First Insights about Pan-Genome of African Rices Cécile Monat,Bérengère Pera,Marie-Noelle Ndjiondjop,Mounirou Sow,Christine Tranchant-Dubreuilet al. Genome Biology and Evolution, 2017, 9 (1), pp.1-6. ⟨10.1093/gbe/evw253⟩ Article dans une revue hal-03208675v1
DuplicationDetector, a light weight tool for duplication detection using NGS data G. Djedatin,C. Monat,S. Engelen,Francois Sabot Current Plant Biology, 2017, Plant Development, 9-10, pp.23-28. ⟨10.1016/j.cpb.2017.07.001⟩ Article dans une revue hal-03070294v1
Fine mapping of RYMV3: a new resistance gene to Rice yellow mottle virus from Oryza glaberrima Hélène Pidon,Alain Ghesquière,Sophie Chéron,Souley Issaka,Eugénie Hébrardet al. TAG Theoretical and Applied Genetics, 2017, 130 (4), pp.807 - 818. ⟨10.1007/s00122-017-2853-0⟩ Article dans une revue hal-01522297v1
Effects of Sodium Azide (NaN3) on Growth of Phyllanthus odontadenius M2 and Evaluation of in vitro Antiplasmodial Activity by Elisa HRP2 Rufin Kikakedimau Nakweti,Véronique Sinou,Sébastien Luyindula Ndiku,François Sabot,Claudine Franche European Journal of Medicinal Plants, 2017, 18 (3), pp.1-10 Article dans une revue hal-05393106v1
Evolutionary forces affecting synonymous variations in plant genomes Yves Clément,Sarah Gallien,Yan Holtz,Félix Homa,Stéphanie Pointetet al. PLoS Genetics, 2017, 13 (5), pp.e1006799. ⟨10.1371/journal.pgen.1006799⟩ Article dans une revue hal-01608613v2
miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species K. N. Ta,F. Sabot,H. Adam,Y. Vigouroux,Stéphane de Mitaet al. Rice, 2016, 9, pp.1-14. ⟨10.1186/s12284-016-0082-9⟩ Article dans une revue hal-01602248v1
Intra-individual polymorphism in chloroplasts from NGS data: where does it come from and how to handle it? N. Scarcelli,C. Mariac,T. L. P. Couvreur,A. Faye,D. Richardet al. Molecular Ecology Resources, 2016, 16 (2), pp.434-445. ⟨10.1111/1755-0998.12462⟩ Article dans une revue hal-03216048v1
La diversité génétique des plantes cultivées à l'heure de l'informatique génétique à haut débit: génomique comparative de la domestication Jacques David,Sylvain Glémin,Gautier Sarah,Benoit Nabholz,Francois Sabotet al. Sélectionneur Français, 2016, 67, pp.3-13 Article dans une revue (article de synthèse) hal-01607736v1
The South Green portal: a comprehensive resource for tropical and Mediterranean crop genomics Valentin Guignon,Yann Hueber,Mathieu Rouard,Stéphanie Bocs,David Couvinet al. Current Plant Biology, 2016, 7-8, pp.6-9. ⟨10.1016/j.cpb.2016.12.002⟩ Article dans une revue hal-02631148v1
TOGGLE: toolbox for generic NGS analyses Cécile Monat,Christine Tranchant-Dubreuil,Ayite Kougbeadjo,Cédric Farcy,Enrique Ortega-Abboudet al. BMC Bioinformatics, 2015, 16, pp.8. ⟨10.1186/s12859-015-0795-6⟩ Article dans une revue hal-02638152v1
A knowledge-based molecular screen uncovers a broad-spectrum OsSWEET14 resistance allele to bacterial blight from wild rice Mathilde Hutin,Francois Sabot,Alain Ghesquière,Ralf Koebnik,Boris Szurek The Plant Journal, 2015, 84 (4), pp.694-703. ⟨10.1111/tpj.13042⟩ Article dans une revue hal-03219869v1
An extensive analysis of the African rice genetic diversity through a global genotyping Julie Orjuela,Francois Sabot,Sophie Chéron,Yves Vigouroux,Hélène Adamet al. TAG Theoretical and Applied Genetics, 2014, 127 (10), pp.2211-2223. ⟨10.1007/s00122-014-2374-z⟩ Article dans une revue hal-03208697v1
DNA methylation and expression of the EgDEF1 gene and neighboring retrotransposons in mantled somaclonal variants of oil palm Estelle Jaligot,Wei Yeng Hooi,Emilie Debladis,Frédérique Richaud,Thierry Beuléet al. PLoS ONE, 2014, 9 (3), pp.e91896. ⟨10.1371/journal.pone.0091896⟩ Article dans une revue hal-03200509v1
Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice ( Oryza glaberrima ) Benoit Nabholz,Gautier Sarah,François Sabot,Manuel Ruiz,Hélène Adamet al. Molecular Ecology, 2014, 23 (9), pp.2210 - 2227. ⟨10.1111/mec.12738⟩ Article dans une revue hal-01919691v1
Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies Cédric Mariac,Nora Scarcelli,Juliette Pouzadoux,Adeline Barnaud,Claire Billotet al. Molecular Ecology Resources, 2014, 14 (6), pp.1103-1113. ⟨10.1111/1755-0998.12258⟩ Article dans une revue istex hal-02637033v1
Tos17 rice element: incomplete but effective Francois Sabot Mobile DNA, 2014, 5 (1), pp.10. ⟨10.1186/1759-8753-5-10⟩ Article dans une revue hal-03221033v1
Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L. Gregory Carrier,Loic Le Cunff,Alexis Dereeper,Delphine Legrand,François Sabotet al. PLoS ONE, 2012, 7, online (3), Non paginé. ⟨10.1371/journal.pone.0032973⟩ Article dans une revue hal-01267783v1
Transpositional landscape of the rice genome revealed by paired-end mapping of high-throughput re-sequencing data Francois Sabot,Nathalie Picault,Moaine El-Baidouri,Christel Llauro,Cristian Chaparroet al. The Plant Journal, 2011, 66 (2), pp.241-246. ⟨10.1111/j.1365-313X.2011.04492.x⟩ Article dans une revue hal-02114338v1
The genome of Theobroma cacao. Xavier Argout,Jerome Salse,Jean-Marc Aury,Mark J Guiltinan,Gaetan Drocet al. Nature Genetics, 2011, 43 (2), pp.101-8. ⟨10.1038/ng.736⟩ Article dans une revue hal-00855922v1
Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae. Anne Roulin,Benoit Piegu,Philippe M Fortune,François Sabot,Angélique d'Hontet al. BMC Evolutionary Biology, 2009, 9 (58), pp.58. ⟨10.1186/1471-2148-9-58⟩ Article dans une revue hal-00693471v1
Reply: A unified classification system for eukaryotic transposable elements should reflect their phylogeny Thomas Wicker,Francois Sabot,Aurélie Hua-Van,Jeffrey L. Bennetzen,Pierre Capyet al. Nature Reviews Genetics, 2009, 10 (4), pp.276-276. ⟨10.1038/nrg2165-c4⟩ Article dans une revue hal-01189545v1
Identification of an active LTR retrotransposon in rice. Nathalie Picault,Cristian Chaparro,Cristel Llauro,Benoit Piegu,Willfried Stengeret al. The Plant Journal, 2009, 58 (5), pp.754-65. ⟨10.1111/j.1365-313X.2009.03813.x⟩ Article dans une revue hal-00685656v1
A unified classification system for eukaryotic transposable elements should reflect their phylogeny Reply. T. Wicker,F. Sabot,A. Hua Van,J. L. Bennetzen,P. Capyet al. Nature Reviews Genetics, 2009, 10, pp.00-00 Article dans une revue hal-00462118v1
Diversity of the Ty-1 copia retrotransposon Tos17 in rice (Oryza sativa L.) and the AA genome of the Oryza genus. Julie Petit,Emmanuelle Bourgeois,Wilfried Stenger,Martine Bès,Gaétan Drocet al. Molecular Genetics and Genomics, 2009, 282 (6), pp.633-52. ⟨10.1007/s00438-009-0493-z⟩ Article dans une revue istex hal-00693499v1
Contrasted microcolinearity and gene evolution within a homoeologous region of wheat and barley species Nathalie Chantret,Jerome Salse,François Sabot,Arnaud Bellec,Bastien Laubinet al. Journal of Molecular Evolution, 2008, 66 (2), pp.138-150. ⟨10.1007/s00239-008-9066-8⟩ Article dans une revue istex hal-01189382v1
A universal classification of eukaryotic transposable elements implemented in Repbase Thomas Wicker,Francois Sabot,Aurélie Hua-Van,Jeffrey L. Bennetzen,Pierre Capyet al. Nature Reviews Genetics, 2008, 9 (5), pp.414. ⟨10.1038/nrg2165-c2⟩ Article dans une revue hal-01189557v1
A unified classification system for eukaryotic transposable elements. T. Wicker,F. Sabot,A. Hua Van,J. L. Bennetzen,P. Capyet al. Nature Reviews Genetics, 2007, 8, pp.973-982 Article dans une revue hal-00169819v1
A unified classification system for eukaryotic transposable elements should reflect their phylogeny Thomas Wicker,Francois Sabot,Aurélie Hua-Van,Jeffrey L. Bennetzen,Pierre Capyet al. Nature Reviews Genetics, 2007, 8 (12), pp.973-982. ⟨10.1038/nrg2165⟩ Article dans une revue hal-01189458v1
Morgane, a new LTR retrotransposon group, and its subfamilies in wheats François F. Sabot,Pierre Sourdille,Nathalie N. Chantret,Michel M. Bernard Genetica, 2006, 128 (1-3), pp.439-447. ⟨10.1007/s10709-006-7725-5⟩ Article dans une revue istex hal-00964272v1
Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations François F. Sabot,Romain R. Guyot,Thomas T. Wicker,Nathalie N. Chantret,Bastien B. Laubinet al. Molecular Genetics and Genomics, 2005, 274 (2), pp.119-130. ⟨10.1007/s00438-005-0012-9⟩ Article dans une revue istex hal-00964194v1
Advent of a new retrotransposon structure: the long form of the Veju elements François F. Sabot,Pierre Sourdille,Michel M. Bernard Genetica, 2005, 125 (2-3), pp.325-332 Article dans une revue hal-00964338v1
Molecular basis of evolutionary events that shaped the Hardness locus in diploid and polyploid wheat species (Triticum and Aegilops) Nathalie N. Chantret,Jerome J. Salse,François F. Sabot,Sadequr S. Rahman,Arnaud A. Bellecet al. The Plant cell, 2005, 17 (4), pp.1033-1045. ⟨10.1105/tpc.104.029181⟩ Article dans une revue hal-00964165v1
Detection of specific repeated sequences in large and complex genomes using Representative Difference Analysis (RDA) and double-probe verification Francois Sabot,Pierre Sourdille,Michel Bernard Plant Molecular Biology Reporter, 2004, 22, pp.91-95 Article dans une revue hal-02674456v1

Chapitre d'ouvrage (2)

Une histoire de la génomique des riz cultivés Philippe Cubry,Mathias Lorieux,Francois Sabot,Alain Ghesquière Pelletier, G. (ed.). Génétique des domestications, ISTE, pp.183-197, 2024, Biologie : Génétique, Epigénétique, 978-1-7894-8167-9. ⟨10.51926/ISTE.9167.ch10⟩ Chapitre d'ouvrage hal-04768659v1
Pangenomics in crop plants C. Monat,Francois Sabot Rajora, O.P. (ed.). Population genomics : crop plants, Springer, pp.3-35, 2020, Population Genomics, 978-3-031-63001-9. ⟨10.1007/13836_2020_84⟩ Chapitre d'ouvrage hal-04649495v1

Autre publication scientifique (2)

Diving, and even diging, into the wild jungle of annotation pathways for non-vertebrate animals Francois Sabot 2022, pp.100016. ⟨10.24072/pci.genomics.100016⟩ Autre publication scientifique hal-03661538v1
Using small fragments to discover old TE remnants: the Duster approach empowers the TE detection Francois Sabot 2021, pp.100004. ⟨10.24072/pci.genomics.100004⟩ Autre publication scientifique hal-03146002v1

Pré-publication, Document de travail (5)

A roadmap for the adoption of pangenomics in agronomy Stéphanie Bocs,Camille Carrette,Johann Confais,Siegfried Dubois,Ludovic Duvauxet al. 2025 Pré-publication, Document de travail (preprint/prepublication) hal-05357866v2
GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph Nina Marthe,Matthias Zytnicki,Francois Sabot 2025 Pré-publication, Document de travail (preprint/prepublication) hal-05162236v1
Identification and quantification of transposable element transcripts using Long-Read RNA-seq in &lt;i&gt;Drosophila&lt;/i&gt; germline tissues Rita Rebollo,Pierre Gerenton,Eric Cumunel,Arnaud Mary,François Sabotet al. 2024 Pré-publication, Document de travail hal-04791876v1
Transposable elements as evolutionary driving force to host shift in cactophilic Drosophila species D. Oliveira,A. Larue,W. Nunes,F. Sabot,A. Bodelónet al. 2025 Pré-publication, Document de travail hal-05060068v1
Biological and genomic resources for the cosmopolitan phytoplankton&lt;i&gt;Bathycoccus&lt;/i&gt;: Insights into genetic diversity and major structural variations Louis Dennu,Martine Devic,Janaina Rigonato,Angela Falciatore,Jean-Claude Lozanoet al. 2023 Pré-publication, Document de travail (preprint/prepublication) hal-04286701v1

Rapport (3)

Quelles stratégies de diffusion et pérennité pour les logiciels de recherche dans les établissements publics français ? Sylvie Tonda-Goldstein,Mélanie Clément-Fontaine,Nicolas Jullien,Jeanne Robineau,Francois Sabot Comité pour la science ouverte. 2025 Rapport hal-05284336v1
Report of the Working Group on Electronic Lab Notebooks Gilles Mathieu,Tovo Rabemanantsoa,Christophe Chipeaux,Simon Duvillard,Jean-François Peyratet al. Comité pour la science ouverte. 2021 Rapport hal-03959882v1
Rapport du groupe de travail sur les cahiers de laboratoires électroniques Gilles Mathieu,Dominique Pigeon,Tovo Rabemanantsoa,Christophe Chipeaux,Simon Duvillardet al. [Rapport de recherche] Comité pour la science ouverte. 2021, 68 p Rapport (rapport de recherche) hal-03563244v1

Thèse (1)

Caracterisation et évolution des éléments transposables au sein du génome des espèces du complexe Triticum/Aegilops François Sabot Sciences du Vivant [q-bio]. Université Blaise Pascal (Clermont Ferrand 2), 2004. Français. ⟨NNT : ⟩ Thèse tel-02825519v1