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Items: 17

1.

Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression.

Arnaiz O, Van Dijk E, Bétermier M, Lhuillier-Akakpo M, de Vanssay A, Duharcourt S, Sallet E, Gouzy J, Sperling L.

BMC Genomics. 2017 Jun 26;18(1):483. doi: 10.1186/s12864-017-3887-z.

2.

Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes.

Blanc-Mathieu R, Perfus-Barbeoch L, Aury JM, Da Rocha M, Gouzy J, Sallet E, Martin-Jimenez C, Bailly-Bechet M, Castagnone-Sereno P, Flot JF, Kozlowski DK, Cazareth J, Couloux A, Da Silva C, Guy J, Kim-Jo YJ, Rancurel C, Schiex T, Abad P, Wincker P, Danchin EGJ.

PLoS Genet. 2017 Jun 8;13(6):e1006777. doi: 10.1371/journal.pgen.1006777. eCollection 2017 Jun.

3.

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution.

Badouin H, Gouzy J, Grassa CJ, Murat F, Staton SE, Cottret L, Lelandais-Brière C, Owens GL, Carrère S, Mayjonade B, Legrand L, Gill N, Kane NC, Bowers JE, Hubner S, Bellec A, Bérard A, Bergès H, Blanchet N, Boniface MC, Brunel D, Catrice O, Chaidir N, Claudel C, Donnadieu C, Faraut T, Fievet G, Helmstetter N, King M, Knapp SJ, Lai Z, Le Paslier MC, Lippi Y, Lorenzon L, Mandel JR, Marage G, Marchand G, Marquand E, Bret-Mestries E, Morien E, Nambeesan S, Nguyen T, Pegot-Espagnet P, Pouilly N, Raftis F, Sallet E, Schiex T, Thomas J, Vandecasteele C, Varès D, Vear F, Vautrin S, Crespi M, Mangin B, Burke JM, Salse J, Muños S, Vincourt P, Rieseberg LH, Langlade NB.

Nature. 2017 Jun 1;546(7656):148-152. doi: 10.1038/nature22380. Epub 2017 May 22.

PMID:
28538728
4.

Reprogramming of DNA methylation is critical for nodule development in Medicago truncatula.

Satgé C, Moreau S, Sallet E, Lefort G, Auriac MC, Remblière C, Cottret L, Gallardo K, Noirot C, Jardinaud MF, Gamas P.

Nat Plants. 2016 Oct 31;2(11):16166. doi: 10.1038/nplants.2016.166.

PMID:
27797357
5.

A Laser Dissection-RNAseq Analysis Highlights the Activation of Cytokinin Pathways by Nod Factors in the Medicago truncatula Root Epidermis.

Jardinaud MF, Boivin S, Rodde N, Catrice O, Kisiala A, Lepage A, Moreau S, Roux B, Cottret L, Sallet E, Brault M, Emery RJ, Gouzy J, Frugier F, Gamas P.

Plant Physiol. 2016 Jul;171(3):2256-76. doi: 10.1104/pp.16.00711. Epub 2016 May 23.

6.

Effector Polymorphisms of the Sunflower Downy Mildew Pathogen Plasmopara halstedii and Their Use to Identify Pathotypes from Field Isolates.

Gascuel Q, Bordat A, Sallet E, Pouilly N, Carrere S, Roux F, Vincourt P, Godiard L.

PLoS One. 2016 Feb 4;11(2):e0148513. doi: 10.1371/journal.pone.0148513. eCollection 2016.

7.

Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi.

Ropars J, Rodríguez de la Vega RC, López-Villavicencio M, Gouzy J, Sallet E, Dumas É, Lacoste S, Debuchy R, Dupont J, Branca A, Giraud T.

Curr Biol. 2015 Oct 5;25(19):2562-9. doi: 10.1016/j.cub.2015.08.025. Epub 2015 Sep 24.

8.

The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome.

Formey D, Sallet E, Lelandais-Brière C, Ben C, Bustos-Sanmamed P, Niebel A, Frugier F, Combier JP, Debellé F, Hartmann C, Poulain J, Gavory F, Wincker P, Roux C, Gentzbittel L, Gouzy J, Crespi M.

Genome Biol. 2014 Sep 24;15(9):457. doi: 10.1186/s13059-014-0457-4.

9.

A Medicago truncatula rdr6 allele impairs transgene silencing and endogenous phased siRNA production but not development.

Bustos-Sanmamed P, Hudik E, Laffont C, Reynes C, Sallet E, Wen J, Mysore KS, Camproux AC, Hartmann C, Gouzy J, Frugier F, Crespi M, Lelandais-Brière C.

Plant Biotechnol J. 2014 Dec;12(9):1308-18. doi: 10.1111/pbi.12230. Epub 2014 Jul 24.

10.

EuGene-PP: a next-generation automated annotation pipeline for prokaryotic genomes.

Sallet E, Gouzy J, Schiex T.

Bioinformatics. 2014 Sep 15;30(18):2659-61. doi: 10.1093/bioinformatics/btu366. Epub 2014 May 30.

PMID:
24880686
11.

An integrated analysis of plant and bacterial gene expression in symbiotic root nodules using laser-capture microdissection coupled to RNA sequencing.

Roux B, Rodde N, Jardinaud MF, Timmers T, Sauviac L, Cottret L, Carrère S, Sallet E, Courcelle E, Moreau S, Debellé F, Capela D, de Carvalho-Niebel F, Gouzy J, Bruand C, Gamas P.

Plant J. 2014 Mar;77(6):817-37. doi: 10.1111/tpj.12442. Epub 2014 Feb 24.

12.

Multiple recent horizontal transfers of a large genomic region in cheese making fungi.

Cheeseman K, Ropars J, Renault P, Dupont J, Gouzy J, Branca A, Abraham AL, Ceppi M, Conseiller E, Debuchy R, Malagnac F, Goarin A, Silar P, Lacoste S, Sallet E, Bensimon A, Giraud T, Brygoo Y.

Nat Commun. 2014;5:2876. doi: 10.1038/ncomms3876.

13.

Next-generation annotation of prokaryotic genomes with EuGene-P: application to Sinorhizobium meliloti 2011.

Sallet E, Roux B, Sauviac L, Jardinaud MF, Carrère S, Faraut T, de Carvalho-Niebel F, Gouzy J, Gamas P, Capela D, Bruand C, Schiex T.

DNA Res. 2013 Aug;20(4):339-54. doi: 10.1093/dnares/dst014. Epub 2013 Apr 18.

14.

The Medicago genome provides insight into the evolution of rhizobial symbioses.

Young ND, Debellé F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H, Van de Peer Y, Proost S, Cook DR, Meyers BC, Spannagl M, Cheung F, De Mita S, Krishnakumar V, Gundlach H, Zhou S, Mudge J, Bharti AK, Murray JD, Naoumkina MA, Rosen B, Silverstein KA, Tang H, Rombauts S, Zhao PX, Zhou P, Barbe V, Bardou P, Bechner M, Bellec A, Berger A, Bergès H, Bidwell S, Bisseling T, Choisne N, Couloux A, Denny R, Deshpande S, Dai X, Doyle JJ, Dudez AM, Farmer AD, Fouteau S, Franken C, Gibelin C, Gish J, Goldstein S, González AJ, Green PJ, Hallab A, Hartog M, Hua A, Humphray SJ, Jeong DH, Jing Y, Jöcker A, Kenton SM, Kim DJ, Klee K, Lai H, Lang C, Lin S, Macmil SL, Magdelenat G, Matthews L, McCorrison J, Monaghan EL, Mun JH, Najar FZ, Nicholson C, Noirot C, O'Bleness M, Paule CR, Poulain J, Prion F, Qin B, Qu C, Retzel EF, Riddle C, Sallet E, Samain S, Samson N, Sanders I, Saurat O, Scarpelli C, Schiex T, Segurens B, Severin AJ, Sherrier DJ, Shi R, Sims S, Singer SR, Sinharoy S, Sterck L, Viollet A, Wang BB, Wang K, Wang M, Wang X, Warfsmann J, Weissenbach J, White DD, White JD, Wiley GB, Wincker P, Xing Y, Yang L, Yao Z, Ying F, Zhai J, Zhou L, Zuber A, Dénarié J, Dixon RA, May GD, Schwartz DC, Rogers J, Quétier F, Town CD, Roe BA.

Nature. 2011 Nov 16;480(7378):520-4. doi: 10.1038/nature10625.

15.

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
16.

Genome-wide Medicago truncatula small RNA analysis revealed novel microRNAs and isoforms differentially regulated in roots and nodules.

Lelandais-Brière C, Naya L, Sallet E, Calenge F, Frugier F, Hartmann C, Gouzy J, Crespi M.

Plant Cell. 2009 Sep;21(9):2780-96. doi: 10.1105/tpc.109.068130. Epub 2009 Sep 18.

17.

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.

Abad P, Gouzy J, Aury JM, Castagnone-Sereno P, Danchin EG, Deleury E, Perfus-Barbeoch L, Anthouard V, Artiguenave F, Blok VC, Caillaud MC, Coutinho PM, Dasilva C, De Luca F, Deau F, Esquibet M, Flutre T, Goldstone JV, Hamamouch N, Hewezi T, Jaillon O, Jubin C, Leonetti P, Magliano M, Maier TR, Markov GV, McVeigh P, Pesole G, Poulain J, Robinson-Rechavi M, Sallet E, Ségurens B, Steinbach D, Tytgat T, Ugarte E, van Ghelder C, Veronico P, Baum TJ, Blaxter M, Bleve-Zacheo T, Davis EL, Ewbank JJ, Favery B, Grenier E, Henrissat B, Jones JT, Laudet V, Maule AG, Quesneville H, Rosso MN, Schiex T, Smant G, Weissenbach J, Wincker P.

Nat Biotechnol. 2008 Aug;26(8):909-15. doi: 10.1038/nbt.1482. Epub 2008 Jul 27.

PMID:
18660804

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