FS

Francois Sabot

Directeur de Recherches IRD au sein de l'UMR DIADE Directeur adjoint de la Mission Science Ouverte de l'IRD
59
Documents
Affiliations actuelles
  • Diversité, adaptation, développement des plantes (UMR DIADE)
  • Diversité, adaptation, développement des plantes (UMR DIADE)
Identifiants chercheurs

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

Publications

Image document

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 Sabot et al.
Peer Community In Archaeology, 2025, 5, pp.e55. ⟨10.24072/pci.archaeo.100603⟩
Article dans une revue hal-05082078 v1
Image document

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 Sabot et al.
Peer Community Journal, 2024, 4 (e89), ⟨10.24072/pcjournal.457⟩
Article dans une revue hal-04285238 v1
Image document

An INDEL genomic approach to explore population diversity of phytoplankton : Bathycoccus , a case study

Martine Devic , Louis Dennu , Jean-Claude Lozano , Cédric Mariac , Valérie Vergé et al.
Article dans une revue hal-04286658 v2
Image document

FrangiPANe, a tool for creating a panreference using left behind reads

Christine Tranchant-Dubreuil , Clothilde Chenal , Mathieu Blaison , Laurence Albar , Valentin Klein et al.
NAR Genomics and Bioinformatics, 2023, 5 (1), pp.lqad013. ⟨10.1093/nargab/lqad013⟩
Article dans une revue hal-04049468 v1
Image document

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 Audouin et al.
Genome Biology, 2023, 24 (1), pp.63. ⟨10.1186/s13059-023-02911-2⟩
Article dans une revue hal-04291760 v1
Image document

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 Ntakirutimana et al.
BMC Genomics, 2023, 24 (1), 587 [21 p.]. ⟨10.1186/s12864-023-09695-6⟩
Article dans une revue hal-04743156 v1
Image document

CulebrONT : a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes

Julie Orjuela , Aurore Comte , Sébastien Ravel , Florian Charriat , Tram Vi et al.
Peer Community Journal, 2022, 2, e46 [9 p.]. ⟨10.24072/pcjournal.153⟩
Article dans une revue hal-04378943 v1
Image document

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. Djedatin et 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-04389871 v1
Image document

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 Fumey et al.
PLoS Computational Biology, 2021, 17 (10), pp.e1009321. ⟨10.1371/journal.pcbi.1009321⟩
Article dans une revue lirmm-03385026 v1
Image document

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 Joelle et al.
Economic Botany, 2021, ⟨10.1007/s12231-021-09515-6⟩
Article dans une revue hal-03169601 v1
Image document

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-03378164 v1
Image document

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 Mugat et al.
Cells, 2020, 9 (8), pp.1776. ⟨10.3390/cells9081776⟩
Article dans une revue hal-02905128 v1
Image document

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-02053647 v1
Image document

MooSciTIC: Training of trainers in West African research and higher education

Ménonvè Atindehou , Kifouli Adeoti , Laura Estelle Yêyinou Loko , Thierry Beulé , Emmanuel Paradis et al.
PLoS Biology, 2019, 17 (6), pp.e3000312. ⟨10.1371/journal.pbio.3000312⟩
Article dans une revue ird-02365690 v1
Image document

Long-fragment targeted capture for long-read sequencing of plastomes

Kevin Bethune , Cédric Mariac , Marie Couderc , Nora Scarcelli , Sylvain Santoni et al.
Applications in Plant Sciences, 2019, 7 (5), pp.e1243. ⟨10.1002/aps3.1243⟩
Article dans une revue hal-02620804 v1

Caractérisation phénotypique et génétique du riz africain (Oryza glaberrima Steud)

C. Gnacadja , Cécile Berthouly , S.N. Sall , Leila Zekraoui , Francois Sabot et al.
International journal of advanced research, 2018, 6 (2), pp.1389-1398. ⟨10.21474/IJAR01/6569⟩
Article dans une revue hal-03070277 v1
Image document

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 Sabot et al.
Molecular Ecology Resources, 2017, 17 (3), pp.565-580. ⟨10.1111/1755-0998.12587⟩
Article dans une revue hal-01930391 v1
Image document

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-Dubreuil et al.
Genome Biology and Evolution, 2017, 9 (1), pp.1-6. ⟨10.1093/gbe/evw253⟩
Article dans une revue hal-03208675 v1
Image document

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-03070294 v1
Image document

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 Hébrard et al.
TAG Theoretical and Applied Genetics, 2017, 130 (4), pp.807 - 818. ⟨10.1007/s00122-017-2853-0⟩
Article dans une revue hal-01522297 v1
Image document

Evolutionary forces affecting synonymous variations in plant genomes

Yves Clément , Sarah Gallien , Yan Holtz , Félix Homa , Stéphanie Pointet et al.
PLoS Genetics, 2017, 13 (5), pp.e1006799. ⟨10.1371/journal.pgen.1006799⟩
Article dans une revue hal-01608613 v2
Image document

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 Mita et al.
Rice, 2016, 9, pp.1-14. ⟨10.1186/s12284-016-0082-9⟩
Article dans une revue hal-01602248 v1
Image document

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 Sabot et al.
Sélectionneur Français, 2016, 67, pp.3-13
Article dans une revue (article de synthèse) hal-01607736 v1
Image document

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. Richard et al.
Molecular Ecology Resources, 2016, 16 (2), pp.434-445. ⟨10.1111/1755-0998.12462⟩
Article dans une revue hal-03216048 v1
Image document

The South Green portal: a comprehensive resource for tropical and Mediterranean crop genomics

Valentin Guignon , Yann Hueber , Mathieu Rouard , Stéphanie Bocs , David Couvin et al.
Current Plant Biology, 2016, 7-8, pp.6-9. ⟨10.1016/j.cpb.2016.12.002⟩
Article dans une revue hal-02631148 v1
Image document

TOGGLE: toolbox for generic NGS analyses

Cécile Monat , Christine Tranchant-Dubreuil , Ayite Kougbeadjo , Cédric Farcy , Enrique Ortega-Abboud et al.
BMC Bioinformatics, 2015, 16, pp.8. ⟨10.1186/s12859-015-0795-6⟩
Article dans une revue hal-02638152 v1

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-03219869 v1
Image document

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 Beulé et al.
PLoS ONE, 2014, 9 (3), pp.e91896. ⟨10.1371/journal.pone.0091896⟩
Article dans une revue hal-03200509 v1

An extensive analysis of the African rice genetic diversity through a global genotyping

Julie Orjuela , Francois Sabot , Sophie Chéron , Yves Vigouroux , Hélène Adam et al.
TAG Theoretical and Applied Genetics, 2014, 127 (10), pp.2211-2223. ⟨10.1007/s00122-014-2374-z⟩
Article dans une revue hal-03208697 v1
Image document

Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice ( Oryza glaberrima )

Benoit Nabholz , Gautier Sarah , François Sabot , Manuel Ruiz , Hélène Adam et al.
Molecular Ecology, 2014, 23 (9), pp.2210 - 2227. ⟨10.1111/mec.12738⟩
Article dans une revue hal-01919691 v1
Image document

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-03221033 v1

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 Billot et al.
Molecular Ecology Resources, 2014, 14 (6), pp.1103-1113. ⟨10.1111/1755-0998.12258⟩
Article dans une revue istex hal-02637033 v1
Image document

Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L.

Gregory Carrier , Loic Le Cunff , Alexis Dereeper , Delphine Legrand , François Sabot et al.
PLoS ONE, 2012, 7, online (3), Non paginé. ⟨10.1371/journal.pone.0032973⟩
Article dans une revue hal-01267783 v1

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 Chaparro et al.
The Plant Journal, 2011, 66 (2), pp.241-246. ⟨10.1111/j.1365-313X.2011.04492.x⟩
Article dans une revue hal-02114338 v1

The genome of Theobroma cacao.

Xavier Argout , Jerome Salse , Jean-Marc Aury , Mark J Guiltinan , Gaetan Droc et al.
Nature Genetics, 2011, 43 (2), pp.101-8. ⟨10.1038/ng.736⟩
Article dans une revue hal-00855922 v1

Identification of an active LTR retrotransposon in rice.

Nathalie Picault , Cristian Chaparro , Cristel Llauro , Benoit Piegu , Willfried Stenger et al.
The Plant Journal, 2009, 58 (5), pp.754-65. ⟨10.1111/j.1365-313X.2009.03813.x⟩
Article dans une revue hal-00685656 v1
Image document

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'Hont et al.
BMC Evolutionary Biology, 2009, 9 (58), pp.58. ⟨10.1186/1471-2148-9-58⟩
Article dans une revue hal-00693471 v1

Reply: A unified classification system for eukaryotic transposable elements should reflect their phylogeny

Thomas Wicker , Francois Sabot , Aurélie Hua-Van , Jeffrey L. Bennetzen , Pierre Capy et al.
Nature Reviews Genetics, 2009, 10 (4), pp.276-276. ⟨10.1038/nrg2165-c4⟩
Article dans une revue hal-01189545 v1

A unified classification system for eukaryotic transposable elements should reflect their phylogeny Reply.

T. Wicker , F. Sabot , A. Hua Van , J. L. Bennetzen , P. Capy et al.
Nature Reviews Genetics, 2009, 10, pp.00-00
Article dans une revue hal-00462118 v1

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 Droc et al.
Molecular Genetics and Genomics, 2009, 282 (6), pp.633-52. ⟨10.1007/s00438-009-0493-z⟩
Article dans une revue istex hal-00693499 v1

Contrasted microcolinearity and gene evolution within a homoeologous region of wheat and barley species

Nathalie Chantret , Jerome Salse , François Sabot , Arnaud Bellec , Bastien Laubin et al.
Journal of Molecular Evolution, 2008, 66 (2), pp.138-150. ⟨10.1007/s00239-008-9066-8⟩
Article dans une revue istex hal-01189382 v1

A universal classification of eukaryotic transposable elements implemented in Repbase

Thomas Wicker , Francois Sabot , Aurélie Hua-Van , Jeffrey L. Bennetzen , Pierre Capy et al.
Nature Reviews Genetics, 2008, 9 (5), pp.414. ⟨10.1038/nrg2165-c2⟩
Article dans une revue hal-01189557 v1

A unified classification system for eukaryotic transposable elements.

T. Wicker , F. Sabot , A. Hua Van , J. L. Bennetzen , P. Capy et al.
Nature Reviews Genetics, 2007, 8, pp.973-982
Article dans une revue hal-00169819 v1

A unified classification system for eukaryotic transposable elements should reflect their phylogeny

Thomas Wicker , Francois Sabot , Aurélie Hua-Van , Jeffrey L. Bennetzen , Pierre Capy et al.
Nature Reviews Genetics, 2007, 8 (12), pp.973-982. ⟨10.1038/nrg2165⟩
Article dans une revue hal-01189458 v1

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-00964272 v1

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. Laubin et al.
Molecular Genetics and Genomics, 2005, 274 (2), pp.119-130. ⟨10.1007/s00438-005-0012-9⟩
Article dans une revue istex hal-00964194 v1

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-00964338 v1

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. Bellec et al.
The Plant cell, 2005, 17 (4), pp.1033-1045. ⟨10.1105/tpc.104.029181⟩
Article dans une revue hal-00964165 v1

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-02674456 v1

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-04768659 v1

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-04649495 v1