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1. Full Text The Rosa genome provides new insights into the domestication of modern roses
by Raymond, Olivier and Gouzy, Jérôme and Just, Jérémy and Badouin, Hélène and Verdenaud, Marion and Lemainque, Arnaud and Vergne, Philippe and Moja, Sandrine and Choisne, Nathalie and Pont, Caroline and Carrère, Sébastien and Caissard, Jean-Claude and Couloux, Arnaud and Cottret, Ludovic and Aury, Jean-Marc and Szécsi, Judit and Latrasse, David and Madoui, Mohammed-Amin and François, Léa and Fu, Xiaopeng and Yang, Shu-Hua and Dubois, Annick and Piola, Florence and Larrieu, Antoine and Perez, Magali and Labadie, Karine and Perrier, Lauriane and Govetto, Benjamin and Labrousse, Yoan and Villand, Priscilla and Bardoux, Claudia and Boltz, Véronique and Lopez-Roques, Céline and Heitzler, Pascal and Vernoux, Teva and Vandenbussche, Michiel and Quesneville, Hadi and Boualem, Adnane and Bendahmane, Abdelhafid and Liu, Chang and Le Bris, Manuel and Salse, Jérôme and Baudino, Sylvie and Benhamed, Moussa and Wincker, Patrick and Bendahmane, Mohammed
Nature Genetics, ISSN 1061-4036, 06/2018, Volume 50, Issue 6, pp. 772 - 777
Roses have high cultural and economic importance as ornamental plants and in the perfume industry. We report the rose whole-genome sequencing and assembly and... 
SCENT COMPOUNDS | READ ALIGNMENT | PROTEIN | BIOSYNTHESIS | ANNOTATION | GENETICS & HEREDITY | WIDE PREDICTION | ARABIDOPSIS | IDENTIFICATION | TRANSCRIPTION FACTOR | FLOWERING TIME | Genomes | Analysis | Genes | Genomics | Plant genetics | Hybrids | Economic importance | Domestication | Hybridization | Multivariate analysis | Gene expression | Metabolism | Gene sequencing | Plant diversity | Ornamental plants | Vigor | Flowers & plants | Bioinformatics | Genotypes | Life Sciences | Plants genetics | Genetics | Environmental Sciences
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2. Full Text The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution
by Badouin, Hélène and Gouzy, Jérôme and Grassa, Christopher J and Murat, Florent and Staton, S. Evan and Cottret, Ludovic and Lelandais-Brière, Christine and Owens, Gregory L and Carrère, Sébastien and Mayjonade, Baptiste and Legrand, Ludovic and Gill, Navdeep and Kane, Nolan C and Bowers, John E and Hubner, Sariel and Bellec, Arnaud and Bérard, Aurélie and Bergès, Hélène and Blanchet, Nicolas and Boniface, Marie-Claude and Brunel, Dominique and Catrice, Olivier and Chaidir, Nadia and Claudel, Clotilde and Donnadieu, Cécile and Faraut, Thomas and Fievet, Ghislain and Helmstetter, Nicolas and King, Matthew and Knapp, Steven J and Lai, Zhao and Le Paslier, Marie-Christine and Lippi, Yannick and Lorenzon, Lolita and Mandel, Jennifer R and Marage, Gwenola and Marchand, Gwenaëlle and Marquand, Elodie and Bret-Mestries, Emmanuelle and Morien, Evan and Nambeesan, Savithri and Nguyen, Thuy and Pegot-Espagnet, Prune and Pouilly, Nicolas and Raftis, Frances and Sallet, Erika and Schiex, Thomas and Thomas, Justine and Vandecasteele, Céline and Varès, Didier and Vear, Felicity and Vautrin, Sonia and Crespi, Martin and Mangin, Brigitte and Burke, John M and Salse, Jérôme and Muños, Stéphane and Vincourt, Patrick and Rieseberg, Loren H and Langlade, Nicolas B
Nature, ISSN 0028-0836, 06/2017, Volume 546, Issue 7656, pp. 148 - 152
The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields... 
PHOSPHATIDATE PHOSPHATASE | WILD | ACID | CULTIVATED SUNFLOWER | ANNOTATION | MULTIDISCIPLINARY SCIENCES | SEQUENCE | GENES | HELIANTHUS-ANNUUS | DOMESTICATION | ASTERACEAE | Genome, Plant - genetics | Stress, Physiological - genetics | Genomics | Helianthus - metabolism | Transcriptome - genetics | Sequence Analysis, DNA | Genetic Variation | Sunflower Oil | Gene Expression Regulation, Plant | Plant Oils - metabolism | Gene Duplication - genetics | Flowers - physiology | Acclimatization - genetics | Helianthus - classification | Flowers - genetics | Evolution, Molecular | Helianthus - genetics | Genetic aspects | Gene expression | Observations | Sunflowers | Networks | Climate | Oil and gas exploration | Transcription | Research programs | Genes | Genomes | Gene sequencing | Mining | Botany | Evolution | Genetics | Flowering | Flowers & plants | Assembly | Adaptation | Duplicating milling machines | Reconstruction | Stresses | Architecture | Breeding | Crops | Organs | Genetic diversity | Metabolism | Real time | Stress | Environmental conditions | Resilience | Quantitative genetics | Climate change | Oil | Plant breeding | Oils & fats | Compatibility | Life Sciences | Vegetal Biology
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3. Full Text MyGenomeBrowser: Building and sharing your own genome browser
by Carrere, Sébastien and Gouzy, Jérôme
Bioinformatics, ISSN 1367-4803, 04/2017, Volume 33, Issue 8, pp. 1255 - 1257
myGenomeBrowser is a web-based environment that provides biologists with a way to build, query and share their genome browsers. This tool, that builds on... 
Data Mining | Software | Internet | Genome | Genomics | Bioinformatics | Computer Science | Applications Notes
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4. Full Text FrameDP: sensitive peptide detection on noisy matured sequences
by Gouzy, Jérôme and Carrere, Sébastien and Schiex, Thomas
Bioinformatics, ISSN 1367-4803, 3/2009, Volume 25, Issue 5, pp. 670 - 671
Transcriptome sequencing represents a fundamental source of information for genome-wide studies and transcriptome analysis and will become increasingly... 
GENOMES | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | PROGRAM | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Sequence Analysis, Protein - methods | Gene Expression Profiling | Software | Internet | Peptides - chemistry | Applications Note
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5. Full Text Multiple recent horizontal transfers of a large genomic region in cheese making fungi
by Cheeseman, K and Ropars, J and Renault, P and Dupont, J and Gouzy, J and Branca, A and Abraham, AL and Ceppi, M and Conseiller, E and Debuchy, R and Malagnac, F and Goarin, A and Silar, P and Lacoste, S and Sallet, E and Bensimon, A and Giraud, T and Brygoo, Y
NATURE COMMUNICATIONS, ISSN 2041-1723, 01/2014, Volume 5, Issue 1, p. 2876
While the extent and impact of horizontal transfers in prokaryotes are widely acknowledged, their importance to the eukaryotic kingdom is unclear and thought... 
ORIGIN | PATHOGEN | EVENTS | DNA | ANNOTATION | MULTIDISCIPLINARY SCIENCES | SEQUENCE | DISEASE | GENE-TRANSFER | EMERGENCE | Penicillium - genetics | Genomic Islands - genetics | DNA, Fungal - genetics | Base Sequence | Molecular Sequence Data | Cheese | Gene Transfer, Horizontal - genetics | Life Sciences | Microbiology and Parasitology | Biochemistry, Molecular Biology
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6. Full Text The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae
by Pieretti, Isabelle and Royer, Monique and Barbe, Valérie and Carrere, Sébastien and Koebnik, Ralf and Cociancich, Stéphane and Couloux, Arnaud and Darrasse, Armelle and Gouzy, Jérôme and Jacques, Marie-Agnès and Lauber, Emmanuelle and Manceau, Charles and Mangenot, Sophie and Poussier, Stéphane and Segurens, Béatrice and Szurek, Boris and Verdier, Valérie and Arlat, Matthieu and Rott, Philippe
BMC Genomics, ISSN 1471-2164, 12/2009, Volume 10, Issue 1, pp. 616 - 616
Background: The Xanthomonadaceae family contains two xylem-limited plant pathogenic bacterial species, Xanthomonas albilineans and Xylella fastidiosa. X.... 
MYCOBACTERIUM-TUBERCULOSIS | PLANT | PATHOGEN | GENE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | ESCHERICHIA-COLI | GENETICS & HEREDITY | DNA GYRASE | ANTIBIOTIC-RESISTANCE | ALBICIDIN | DRUG-RESISTANCE | DIFFERING HOST SPECIFICITIES | Genome, Bacterial - genetics | Xanthomonas - classification | Molecular Sequence Data | RNA, Bacterial - genetics | Xanthomonadaceae - classification | Xylem - microbiology | Models, Genetic | Phylogeny | Xanthomonadaceae - genetics | RNA, Ribosomal - genetics | Evolution, Molecular | Xanthomonas - genetics | Proteobacteria | Genetic aspects | Research | Nucleotide sequence | Bacterial genetics | Adaptations | Pathogens | Xylem | Secretion | rRNA | Symbionts | Stem cells | Evolution | genomics | Toxins | Niches | Genome, Bacterial | Xanthomonadaceae | Xanthomonas | Life Sciences | Phytopathology and phytopharmacy | RNA, Ribosomal | RNA, Bacterial | Vegetal Biology
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7. Full Text Chaos of rearrangements in the mating-type chromosomes of the anther-smut fungus Microbotryum lychnidis-dioicae
by Badouin, Hélène and Hood, Michael E and Gouzy, Jérôme and Aguileta, Gabriela and Siguenza, Sophie and Perlin, Michael H and Cuomo, Christina A and Fairhead, Cécile and Branca, Antoine and Giraudtatiana, Tatiana
Genetics, ISSN 0016-6731, 08/2015, Volume 200, Issue 4, pp. 1275 - 1284
Sex chromosomes in plants and animals and fungal mating-type chromosomes often show exceptional genome features, with extensive suppression of homologous... 
Basidiomycete | MAT | Intratetrad mating | Selfing | Microbotryum violaceum | Bipolarity | Finished genome assembly | basidiomycete | VIOLACEUM | bipolarity | SEX-DETERMINING REGIONS | GENOME | DEGENERATION | selfing | LINKAGE RELATIONSHIPS | Y-CHROMOSOME | NEUROSPORA-TETRASPERMA | MUTATION | GENETICS & HEREDITY | finished genome assembly | EVOLUTIONARY STRATA | GENUS MICROBOTRYUM | intratetrad mating | Chromosomes, Fungal - genetics | Centromere - genetics | Gene Rearrangement | Genomics | Genes, Mating Type, Fungal - genetics | Basidiomycota - genetics | Recombination, Genetic - genetics | Evolution, Molecular | Telomere - genetics | Sex chromosomes | Genomes | Research | Courtship of animals | Centromeres | Fungi | Genetics | Chromosomes | Life Sciences | Investigations
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8. Full Text RNA-Seq analysis of rye-grass transcriptomic response to an herbicide inhibiting acetolactate-synthase identifies transcripts linked to non-target-site-based resistance
by Duhoux, Arnaud and Carrère, Sébastien and Gouzy, Jérôme and Bonin, Ludovic and Délye, Christophe
Plant Molecular Biology, ISSN 0167-4412, 3/2015, Volume 87, Issue 4, pp. 473 - 487
Non-target-site resistance (NTSR) to herbicides that disrupts agricultural weed control is a worldwide concern for food security. NTSR is considered a... 
Life Sciences | Biochemistry, general | Plant Pathology | RNA-Seq | Transcriptomics | Lolium | Non-target-site resistance | Acetolactate synthase | Plant Sciences | Herbicide | ARABIDOPSIS-THALIANA | PROTEIN | BIOCHEMISTRY & MOLECULAR BIOLOGY | WEEDS | LOLIUM-RIGIDUM | PLANT SCIENCES | EVOLUTION | BLACK-GRASS | GENES | PLANTS | STRESS | Gene Expression Regulation, Plant - drug effects | Lolium - drug effects | Lolium - genetics | Lolium - enzymology | Gene Expression Regulation, Plant - genetics | Herbicides - pharmacology | Transcriptome - drug effects | Transcriptome - genetics | Acetolactate Synthase - antagonists & inhibitors | Herbicides | Herbicide resistance | RNA | Glutathione transferase | Analysis | Amyotrophic lateral sclerosis | Plants | Gene expression | Food supply | Ribonucleic acid--RNA | Plant resistance | Weeds
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9. Full Text Transcription reprogramming during root nodule development in Medicago truncatula
by Moreau, Sandra and Verdenaud, Marion and Ott, Thomas and Letort, Sébastien and de Billy, Françoise and Niebel, Andreas and Gouzy, Jérôme and de Carvalho-Niebel, Fernanda and Gamas, Pascal
PLoS ONE, ISSN 1932-6203, 2011, Volume 6, Issue 1, p. e16463
Many genes which are associated with root nodule development and activity in the model legume Medicago truncatula have been described. However information on... 
FALSE DISCOVERY RATE | FACTOR SIGNAL-TRANSDUCTION | LOTUS-JAPONICUS | ARABIDOPSIS-THALIANA | SINORHIZOBIUM-MELILOTI | MULTIDISCIPLINARY SCIENCES | GENE-EXPRESSION | SUBTRACTIVE HYBRIDIZATION APPROACH | ARBUSCULAR MYCORRHIZA | POTENTIAL REGULATORS | RHIZOBIUM-MELILOTI | Symbiosis | Medicago truncatula - genetics | Medicago truncatula - growth & development | Root Nodules, Plant - genetics | Gene Expression Profiling | Medicago truncatula - microbiology | Plant Roots - microbiology | Gene Expression Regulation, Plant | Transcription, Genetic | Transcription Factors | Root Nodules, Plant - growth & development | Sinorhizobium meliloti | Nitrogen Fixation | Legumes | Beans | DNA microarrays | Bacterial infections | Fixation | Analysis | Physiological aspects | Genetic aspects | Genetic transcription | Cell differentiation | Nitrogen | Mimosaceae | Cell culture | Regulators | Senescence | Transcription factors | Transcription | Genes | Genomics | Differentiation (biology) | Handbooks | Infections | Activation | Genomes | Biosynthesis | Kinases | Information sources | Signal transduction | Annotations | Transcription activation | Nitrogen fixation | Bacteria | Jasmonic acid | Statistical analysis | Alfalfa | Metabolism | Gene expression | Nodules | Polymerase chain reaction | Signaling
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10. Full Text A Resource Allocation Trade-Off between Virulence and Proliferation Drives Metabolic Versatility in the Plant Pathogen Ralstonia solanacearum
by Peyraud, Rémi and Cottret, Ludovic and Marmiesse, Lucas and Gouzy, Jérôme and Genin, Stéphane
PLoS Pathogens, ISSN 1553-7366, 10/2016, Volume 12, Issue 10, p. e1005939
Bacterial pathogenicity relies on a proficient metabolism and there is increasing evidence that metabolic adaptation to exploit host resources is a key... 
SPECIES COMPLEX | ESCHERICHIA-COLI | BACTERIAL VIRULENCE | MICROBIOLOGY | TRANSCRIPTIONAL REGULATOR | GENOME-SCALE RECONSTRUCTION | VIROLOGY | GENE | AMINO-ACIDS | GROWTH | PSEUDOMONAS-SOLANACEARUM | PARASITOLOGY | III SECRETION SYSTEM | Metabolic Networks and Pathways | Ralstonia solanacearum - metabolism | Cell Proliferation - physiology | Nuclear Magnetic Resonance, Biomolecular | Virulence - physiology | Plant Diseases - microbiology | Ralstonia solanacearum - pathogenicity | Virulence Factors - metabolism | Gram-Negative Bacterial Infections - metabolism | Cell proliferation | Microbial metabolism | Analysis | Physiological aspects | Bacteria, Phytopathogenic | Research | Virulence (Microbiology) | Pathogens | Genotype & phenotype | Algorithms | Growth rate | Funding | Genes | Infections | Genomes | Metabolism | Life Sciences
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11. Full Text High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development
by Daccord, Nicolas and Celton, Jean-Marc and Linsmith, Gareth and Becker, Claude and Choisne, Nathalie and Schijlen, Elio and Geest, van de, Henri and Bianco, Luca and Micheletti, Diego and Velasco, Riccardo and Pierro, Di, Erica Adele and Gouzy, Jérôme and Rees, D.J.G and Guérif, Philippe and Muranty, Hélène and Durel, Charles Eric and Laurens, François and Lespinasse, Yves and Gaillard, Sylvain and Aubourg, Sébastien and Quesneville, Hadi and Weigel, Detlef and Weg, van de, Eric and Troggio, Michela and Bucher, Etienne
Nature Genetics, ISSN 1061-4036, 2017, Volume 49, Issue 7, pp. 1099 - 1106
Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome.... 
PBR Biodiversity and genetic variation | PE&RC | WUR PB Biodiversiteit en Genetische Variatie | BIOS Applied Bioinformatics | EPS | PBR Biodiversiteit en Genetische Variatie | PRI BIOS Applied Bioinformatics | MALUS-X-DOMESTICA | DIRECTED DNA METHYLATION | RNA GENES | EVOLUTION | SEQUENCES | ANNOTATION | GENETICS & HEREDITY | TRANSPOSABLE ELEMENTS | FLOWERING PLANTS | EPIGENETIC MUTATION | ARABIDOPSIS | Genes, Plant | Molecular Sequence Annotation | Synteny | Genotype | Genome, Plant | Malus - growth & development | Sequence Analysis, DNA | DNA Transposable Elements | Malus - genetics | Linkage Disequilibrium | Fruit - growth & development | DNA Methylation | DNA, Plant - chemistry | Chromosomes, Plant - genetics | DNA, Plant - genetics | Divergence | Nucleotide sequence | Genomes | Gene expression | Uplift | Fruits | Gene sequencing | Mountains | Studies | Annotations | Agronomy | DNA methylation | Epigenetics | Methylation | Gene mapping | Bioinformatics | Assembly | Deoxyribonucleic acid--DNA | Transfer RNA | Life Sciences | Agricultural sciences | Vegetal Biology
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12. Full Text An integrated analysis of plant and bacterial gene expression in symbiotic root nodules using laser‐capture microdissection coupled to RNA sequencing
by Roux, Brice and Rodde, Nathalie and Jardinaud, Marie‐Françoise and Timmers, Ton and Sauviac, Laurent and Cottret, Ludovic and Carrère, Sébastien and Sallet, Erika and Courcelle, Emmanuel and Moreau, Sandra and Debellé, Frédéric and Capela, Delphine and Carvalho‐Niebel, Fernanda and Gouzy, Jérôme and Bruand, Claude and Gamas, Pascal
The Plant Journal, ISSN 0960-7412, 03/2014, Volume 77, Issue 6, pp. 817 - 837
Summary Rhizobium‐induced root nodules are specialized organs for symbiotic nitrogen fixation. Indeterminate‐type nodules are formed from an apical meristem... 
model legume | Medicago truncatula | nitrogen‐fixing symbiosis | regulators | transcriptome | Sinorhizobium meliloti | nitrogen-fixing symbiosis | ANAPHASE-PROMOTING COMPLEX | SINORHIZOBIUM-MELILOTI | POTENTIAL REGULATORS | PLANT SCIENCES | NITROGEN-FIXATION | LOTUS-JAPONICUS | MEDICAGO-TRUNCATULA | NITRIC-OXIDE | ERF TRANSCRIPTION FACTOR | RHIZOBIUM-MELILOTI | Symbiosis | Sinorhizobium meliloti - genetics | Gene Expression | Medicago truncatula - genetics | Genes, Bacterial - genetics | Plant Roots - genetics | Root Nodules, Plant - genetics | Gene Expression Profiling | Laser Capture Microdissection - methods | Sequence Analysis, RNA - methods | Sinorhizobium meliloti - cytology | Medicago truncatula - cytology | Meristem - genetics | Gene Expression Regulation, Plant | Nitrogen Fixation | Plant biology | Bacteria | Gene expression | Ribonucleic acid--RNA
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