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Items: 35

1.

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

Atindehou M, Adéoti K, Loko LEY, Beulé T, Paradis E, Djedatin G, Tranchant-Dubreuil C, Sabot F, Lagnika L, Jaligot E.

PLoS Biol. 2019 Jun 7;17(6):e3000312. doi: 10.1371/journal.pbio.3000312. eCollection 2019 Jun.

2.

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

Bethune K, Mariac C, Couderc M, Scarcelli N, Santoni S, Ardisson M, Martin JF, Montúfar R, Klein V, Sabot F, Vigouroux Y, Couvreur TLP.

Appl Plant Sci. 2019 May 8;7(5):e1243. doi: 10.1002/aps3.1243. eCollection 2019 May.

3.

The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes.

Cubry P, Tranchant-Dubreuil C, Thuillet AC, Monat C, Ndjiondjop MN, Labadie K, Cruaud C, Engelen S, Scarcelli N, Rhoné B, Burgarella C, Dupuy C, Larmande P, Wincker P, François O, Sabot F, Vigouroux Y.

Curr Biol. 2018 Jul 23;28(14):2274-2282.e6. doi: 10.1016/j.cub.2018.05.066. Epub 2018 Jul 5.

4.

Evolutionary forces affecting synonymous variations in plant genomes.

Clément Y, Sarah G, Holtz Y, Homa F, Pointet S, Contreras S, Nabholz B, Sabot F, Sauné L, Ardisson M, Bacilieri R, Besnard G, Berger A, Cardi C, De Bellis F, Fouet O, Jourda C, Khadari B, Lanaud C, Leroy T, Pot D, Sauvage C, Scarcelli N, Tregear J, Vigouroux Y, Yahiaoui N, Ruiz M, Santoni S, Labouisse JP, Pham JL, David J, Glémin S.

PLoS Genet. 2017 May 22;13(5):e1006799. doi: 10.1371/journal.pgen.1006799. eCollection 2017 May.

5.

De Novo Assemblies of Three Oryza glaberrima Accessions Provide First Insights about Pan-Genome of African Rices.

Monat C, Pera B, Ndjiondjop MN, Sow M, Tranchant-Dubreuil C, Bastianelli L, Ghesquière A, Sabot F.

Genome Biol Evol. 2017 Jan 1;9(1):1-6. doi: 10.1093/gbe/evw253.

6.

Fine mapping of RYMV3: a new resistance gene to Rice yellow mottle virus from Oryza glaberrima.

Pidon H, Ghesquière A, Chéron S, Issaka S, Hébrard E, Sabot F, Kolade O, Silué D, Albar L.

Theor Appl Genet. 2017 Apr;130(4):807-818. doi: 10.1007/s00122-017-2853-0. Epub 2017 Jan 31.

PMID:
28144699
7.

LTRclassifier: A website for fast structural LTR retrotransposons classification in plants.

Monat C, Tando N, Tranchant-Dubreuil C, Sabot F.

Mob Genet Elements. 2016 Sep 26;6(6):e1241050. doi: 10.1080/2159256X.2016.1241050. eCollection 2016.

8.

A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives.

Sarah G, Homa F, Pointet S, Contreras S, Sabot F, Nabholz B, Santoni S, Sauné L, Ardisson M, Chantret N, Sauvage C, Tregear J, Jourda C, Pot D, Vigouroux Y, Chair H, Scarcelli N, Billot C, Yahiaoui N, Bacilieri R, Khadari B, Boccara M, Barnaud A, Péros JP, Labouisse JP, Pham JL, David J, Glémin S, Ruiz M.

Mol Ecol Resour. 2017 May;17(3):565-580. doi: 10.1111/1755-0998.12587. Epub 2016 Aug 29.

PMID:
27487989
9.

miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species.

Ta KN, Sabot F, Adam H, Vigouroux Y, De Mita S, Ghesquière A, Do NV, Gantet P, Jouannic S.

Rice (N Y). 2016 Dec;9(1):10. doi: 10.1186/s12284-016-0082-9. Epub 2016 Mar 12.

10.

TOGGLE: toolbox for generic NGS analyses.

Monat C, Tranchant-Dubreuil C, Kougbeadjo A, Farcy C, Ortega-Abboud E, Amanzougarene S, Ravel S, Agbessi M, Orjuela-Bouniol J, Summo M, Sabot F.

BMC Bioinformatics. 2015 Nov 9;16:374. doi: 10.1186/s12859-015-0795-6.

11.

A knowledge-based molecular screen uncovers a broad-spectrum OsSWEET14 resistance allele to bacterial blight from wild rice.

Hutin M, Sabot F, Ghesquière A, Koebnik R, Szurek B.

Plant J. 2015 Nov;84(4):694-703. doi: 10.1111/tpj.13042.

12.

Intra-individual polymorphism in chloroplasts from NGS data: where does it come from and how to handle it?

Scarcelli N, Mariac C, Couvreur TL, Faye A, Richard D, Sabot F, Berthouly-Salazar C, Vigouroux Y.

Mol Ecol Resour. 2016 Mar;16(2):434-45. doi: 10.1111/1755-0998.12462. Epub 2015 Sep 20.

PMID:
26388536
13.

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

Orjuela J, Sabot F, Chéron S, Vigouroux Y, Adam H, Chrestin H, Sanni K, Lorieux M, Ghesquière A.

Theor Appl Genet. 2014 Oct;127(10):2211-23. doi: 10.1007/s00122-014-2374-z. Epub 2014 Aug 15.

PMID:
25119871
14.

Tos17 rice element: incomplete but effective.

Sabot F.

Mob DNA. 2014 Apr 1;5(1):10. doi: 10.1186/1759-8753-5-10.

15.

Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies.

Mariac C, Scarcelli N, Pouzadou J, Barnaud A, Billot C, Faye A, Kougbeadjo A, Maillol V, Martin G, Sabot F, Santoni S, Vigouroux Y, Couvreur TL.

Mol Ecol Resour. 2014 Nov;14(6):1103-13. doi: 10.1111/1755-0998.12258. Epub 2014 Apr 23.

PMID:
24690362
16.

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

Nabholz B, Sarah G, Sabot F, Ruiz M, Adam H, Nidelet S, Ghesquière A, Santoni S, David J, Glémin S.

Mol Ecol. 2014 May;23(9):2210-27. doi: 10.1111/mec.12738. Epub 2014 Apr 18.

PMID:
24684265
17.

DNA methylation and expression of the EgDEF1 gene and neighboring retrotransposons in mantled somaclonal variants of oil palm.

Jaligot E, Hooi WY, Debladis E, Richaud F, Beulé T, Collin M, Agbessi MD, Sabot F, Garsmeur O, D'Hont A, Alwee SS, Rival A.

PLoS One. 2014 Mar 17;9(3):e91896. doi: 10.1371/journal.pone.0091896. eCollection 2014.

18.

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

Carrier G, Le Cunff L, Dereeper A, Legrand D, Sabot F, Bouchez O, Audeguin L, Boursiquot JM, This P.

PLoS One. 2012;7(3):e32973. doi: 10.1371/journal.pone.0032973. Epub 2012 Mar 12.

19.

Methods and software in NGS for TE analysis.

Chaparro C, Sabot F.

Methods Mol Biol. 2012;859:105-14. doi: 10.1007/978-1-61779-603-6_6.

PMID:
22367868
20.

Transpositional landscape of the rice genome revealed by paired-end mapping of high-throughput re-sequencing data.

Sabot F, Picault N, El-Baidouri M, Llauro C, Chaparro C, Piegu B, Roulin A, Guiderdoni E, Delabastide M, McCombie R, Panaud O.

Plant J. 2011 Apr;66(2):241-6. doi: 10.1111/j.1365-313X.2011.04492.x. Epub 2011 Mar 1.

21.

The genome of Theobroma cacao.

Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN, Abrouk M, Murat F, Fouet O, Poulain J, Ruiz M, Roguet Y, Rodier-Goud M, Barbosa-Neto JF, Sabot F, Kudrna D, Ammiraju JS, Schuster SC, Carlson JE, Sallet E, Schiex T, Dievart A, Kramer M, Gelley L, Shi Z, Bérard A, Viot C, Boccara M, Risterucci AM, Guignon V, Sabau X, Axtell MJ, Ma Z, Zhang Y, Brown S, Bourge M, Golser W, Song X, Clement D, Rivallan R, Tahi M, Akaza JM, Pitollat B, Gramacho K, D'Hont A, Brunel D, Infante D, Kebe I, Costet P, Wing R, McCombie WR, Guiderdoni E, Quetier F, Panaud O, Wincker P, Bocs S, Lanaud C.

Nat Genet. 2011 Feb;43(2):101-8. doi: 10.1038/ng.736. Epub 2010 Dec 26.

PMID:
21186351
22.

Diversity of the Ty-1 copia retrotransposon Tos17 in rice (Oryza sativa L.) and the AA genome of the Oryza genus.

Petit J, Bourgeois E, Stenger W, Bès M, Droc G, Meynard D, Courtois B, Ghesquière A, Sabot F, Panaud O, Guiderdoni E.

Mol Genet Genomics. 2009 Dec;282(6):633-52. doi: 10.1007/s00438-009-0493-z. Epub 2009 Oct 25.

PMID:
19856189
23.

Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae.

Roulin A, Piegu B, Fortune PM, Sabot F, D'Hont A, Manicacci D, Panaud O.

BMC Evol Biol. 2009 Mar 16;9:58. doi: 10.1186/1471-2148-9-58.

24.

Identification of an active LTR retrotransposon in rice.

Picault N, Chaparro C, Piegu B, Stenger W, Formey D, Llauro C, Descombin J, Sabot F, Lasserre E, Meynard D, Guiderdoni E, Panaud O.

Plant J. 2009 Jun;58(5):754-65. doi: 10.1111/j.1365-313X.2009.03813.x. Epub 2009 Feb 2. Erratum in: Plant J. 2009 Dec;60(5):929.

25.

Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats.

Wicker T, Narechania A, Sabot F, Stein J, Vu GT, Graner A, Ware D, Stein N.

BMC Genomics. 2008 Oct 31;9:518. doi: 10.1186/1471-2164-9-518.

26.

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

Chantret N, Salse J, Sabot F, Bellec A, Laubin B, Dubois I, Dossat C, Sourdille P, Joudrier P, Gautier MF, Cattolico L, Beckert M, Aubourg S, Weissenbach J, Caboche M, Leroy P, Bernard M, Chalhoub B.

J Mol Evol. 2008 Feb;66(2):138-50. doi: 10.1007/s00239-008-9066-8. Epub 2008 Feb 15.

PMID:
18274696
27.

A unified classification system for eukaryotic transposable elements.

Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH.

Nat Rev Genet. 2007 Dec;8(12):973-82. Review.

PMID:
17984973
28.
29.

Life without GAG: the BARE-2 retrotransposon as a parasite's parasite.

Tanskanen JA, Sabot F, Vicient C, Schulman AH.

Gene. 2007 Apr 1;390(1-2):166-74. Epub 2006 Oct 4.

PMID:
17107763
30.

Morgane, a new LTR retrotransposon group, and its subfamilies in wheats.

Sabot F, Sourdille P, Chantret N, Bernard M.

Genetica. 2006 Sep-Nov;128(1-3):439-47.

PMID:
17028971
31.

Parasitism and the retrotransposon life cycle in plants: a hitchhiker's guide to the genome.

Sabot F, Schulman AH.

Heredity (Edinb). 2006 Dec;97(6):381-8. Epub 2006 Sep 20. Review.

32.

Advent of a new retrotransposon structure: the long form of the Veju elements.

Sabot F, Sourdille P, Bernard M.

Genetica. 2005 Nov;125(2-3):325-32.

PMID:
16247703
33.

Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations.

Sabot F, Guyot R, Wicker T, Chantret N, Laubin B, Chalhoub B, Leroy P, Sourdille P, Bernard M.

Mol Genet Genomics. 2005 Sep;274(2):119-30. Epub 2005 Oct 11.

PMID:
16034625
34.

Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops).

Chantret N, Salse J, Sabot F, Rahman S, Bellec A, Laubin B, Dubois I, Dossat C, Sourdille P, Joudrier P, Gautier MF, Cattolico L, Beckert M, Aubourg S, Weissenbach J, Caboche M, Bernard M, Leroy P, Chalhoub B.

Plant Cell. 2005 Apr;17(4):1033-45. Epub 2005 Mar 4.

35.

Sequencing of the Triticum monococcum hardness locus reveals good microcolinearity with rice.

Chantret N, Cenci A, Sabot F, Anderson O, Dubcovsky J.

Mol Genet Genomics. 2004 May;271(4):377-86. Epub 2004 Mar 11.

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