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Institut Sophia Agrobiotech

UMR INRA - Univ. Nice Sophia Antipolis - Cnrs

http://www.paca.inra.fr/institut-sophia-agrobiotech_eng/

Publications des membres de l'équipe

Publications dans des revues à comité de lecture

2022

Siddique S, Radakovic Z, Hiltl C, Pellegrin C, Baum T, Beasley H, Bent A, Chitambo O, Chopra D, Danchin E.G.J.*, Grenier E, Habash S, Shamim Hasan M, Helder J, Hewezi T, Holbein J, Holterman M, Janakowski S, Koutsovoulos G.D.*, Kranse O, Lozano-Torres J, Maier T, Masonbrink R, Mendy B, Reimer E, Sobczak M, USonawala U, Sterken M, Thorpe P, van Steenbrugge J, Zahid N, Grundler F, and Eves-van den Akker S. The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5. Nature Communications. 2022 (View Online).

Belliardo C*, Koutsovoulos G*, Rancurel C, Clement M, Lipuma J, Bailly-Bechet M*, Danchin EGJ*.  Improvement of Eukaryotic Proteins Prediction from Soil Metagenomes. Scientific Data. 2022 (View Online).

2021

Hassanaly-Goulamhoussen R., De Carvalho Augusto R., Marteu-Garello N., Péré A., Favery B., Da Rocha M., Danchin E.G.J.*, Abad P., Grunau C., Perfus-Barbeoch L. Chromatin Landscape Dynamics in Development of the Plant Parasitic Nematode Meloidogyne incognita. Frontiers in Cell and Developmental Biology. 2021 (View Online).

Cavigliasso F, Mathé-Hubert H, Gatti J-L, Colinet D*, Poirié M. Parasitic success and venom composition evolve upon specialization of parasitoid wasps to different host species. Peer Community Journal 1: e51. 2021 (View online)

Vieira P, Myers RY, Pellegrin C, Wram C, Hesse C, Maier TR, Shao J, Koutsovoulos GD*, Zasada I, Matsumoto T, Danchin EGJ*, Baum TJ, Eves-van den Akker S, Nemchinovet LG. Targeted transcriptomics reveals signatures of large-scale independent origins and concerted regulation of effector genes in Radopholus similis. PLoS Pathogens. 17(11): e1010036. 2021 (View online)

Simion P, Narayan J, Houtain A, Derzelle A, Baudry L, Nicolas E, Arora R, Cariou M, Cruaud C, Rodriguez Gaudray F, Gilbert C, Guiglielmoni N, Hespeels B, Kozlowski DKL*, Labadie K, Limasset A, Lliros M, Marbouty M, Terwagne M, Virgo J, Cordaux R, Danchin EGJ*, Hallet B, Koszul R, Lenormand T, Flot J-F, Van Doninck K. Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga. Science Advances. 2021 (View online).

Cavigliasso F, Gatti J-L, Colinet D*, Poirié M. Impact of temperature on the immune interaction between a parasitoid wasp and Drosophila host species. Insects 12: 647. 2021 (View online)

Da Rocha M., Bournaud C., Dazenière J.*, Thorpe P., Pellegrin C., Bailly-Bechet M.*, Péré A., Grynberg P., Perfus-Barbeoch L., Eves-van den Akker S., Danchin E.G.J.* Genome expression dynamics reveals parasitism regulatory landscape of the root-knot nematode Meloidogyne incognita and a promoter motif associated with effector genes. GENES. 2021 (View online).

Kozlowski DKL*, Hassanaly-Goulamhoussen R, Da Rocha M, Koutsovoulos GD*, Bailly-Bechet M*, Danchin  EGJ*. Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pest. Evolutionary Applications. 2021 (View online), recommended in PCI Evolutionary Biology. 2020 (Recommendation).

2020

Arraes F.B.M.*, Martins-de-Sa D., Noriega Vasquez D.D., Paes Melo B., Faheem M., Lima Pepino de Macedo L., Morgante C.V., Barbosa J.A.R.G., Coiti Togawa R., Moreira V.J.V, Danchin E.G.J.*, Grossi-de-Sa M.F. Dissecting Protein Domain Variability In The Core RNA Interference Machinery Of Five Insect Orders. RNA Biology. 2020. (View Online).

Grynberg P., Coiti Togawa R., Dias de Freitas L., Antonino J.D., Rancurel C., Mota do Carmo Costa M., Grossi-de-Sa M.F., Miller R.N.G., Brasileiro A.C.M., Messenberg Guimaraes P., Danchin E.G.J.* Comparative genomics reveals novel target genes towards specific control of plant-parasitic nematodes. Genes. 2020. (View Online).

Montarry J., Mimee B., Danchin EGJ*, Koutsovoulos G.D*, Ste-Croix DT and Grenier E. Recent advances in population genomics of plant-parasitic nematodes. Phytopathology. 2020 (View Online).

Koutsovoulos G.D*, Poullet M., El Ashry A., Kozlowski D.K*, Sallet E., Da Rocha M., Martin-Jimenez C., Perfus-Barbeoch L., Frey J-E, Ahrens C., Kiewnick S., Danchin E.G.J* Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode. Scientific Data. 2020 (View Online).

Dennis AB, Ballesteros GI, Robin S, Schrader L, Bast J, Berghöfer J, Beukeboom LW, Belghazi M, Bretaudeau A, Buellesbach J, Cash E, Colinet D* et al. Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum. BMC Genomics 21: 376. 2020 (View online)

Fouret J, Brunet FG., Binet M, Aurine N, Enchery F, Croze S, Guinier M, Goulaidi Abdelghafar, Perininger Doris, Volff Jean-Nicolas, Bailly-Bechet M*, Lachuer J, Horvat B, Legras-Lachuer C. Sequencing the Genome of Indian Flying Fox, Natural Reservoir of Nipah Virus, Using Hybrid Assembly and Conservative Secondary Scaffolding. Frontiers in Microbiology. 2020 (View Online).

Vinson CC, Zotta Mota AP*, Porto BN, Oliveira TN, Sampaio I, Lacerda AL, Danchin EGJ*, Guimaraes PM, Williams TCR, Brasileiro ACM. Characterization of raffinose metabolism genes uncovers a wild Arachis galactinol synthase conferring tolerance to abiotic stresses. Scientific Reports. 2020 (View online).

Phan NT, Orjuela J, Danchin EGJ*, Klopp C, Perfus-Barbeoch L, Kozlowski DK*, Koutsovoulos GD*, Lopez-Roques C, Bouchez O, Zahm M , Besnard G, Bellafiore S. Genome structure and content of the rice root-knot nematode (Meloidogyne graminicola). Ecology & Evolution. 2020 (View online).

Danel S, Troina G, Dufour V, Bailly-Bechet M*, Von Bayern A, Osiurak F. Social learning in great white pelicans (Pelecanus onocrotalus): A preliminary study. Learning and Behavior. 2020. (View Online)

Zotta Mota AP*; Fernandez D.; Arraes FBM; Petitot A-S; Paes de Melo B; Lisei de Sa ME; Grynberg P; Passos Saraiva MA; Messenberg Guimaraes P; Brasileiro ACM; Albuquerque EVS; Danchin EGJ*; Grossi–de–Sa MF. Evolutionarily conserved plant genes responsive to root-knot nematodes identified by comparative genomics. Molecular Genetics And Genomics 2020 (View Online).

Susič N, Koutsovoulos GD*, Riccio C, Danchin EGJ*, Blaxter ML, Lunt DH, Strajnar P, Širca S, Urek G, Gerič Stare B. Genome Sequence of the Root-Knot Nematode Meloidogyne luci. Journal of Nematology 2020 (View Online)

2019

Schiffer PH, Danchin EGJ*, Burnell AM, Creevey C, Wong S, Dix I,  O’Mahony G, Culleton BA, Rancurel C, Stier G, Martinez-Salazar EA, Marconi A, Trivedi U, Kroiher M, Thorne MAS, Schierenberg E, Wiehe T, Blaxter M. Signatures of the evolution of parthenogenesis and cryptobiosis in the genomes of panagrolaimid nematodes. iScience 2019 (View Online)

Bresso E., Fernandez D., Amora D.X., Noel P., Petitot A-S., Lisei de Sa M-E., Albuquerque E.V.S, Danchin E.G.J*, Maigret B., Martins N.F. A chemosensory GPCR as a potential target to control the root-knot nematode Meloidogyne incognita parasitism in plants. Molecules 2019 (View Online)

Koutsovoulos G.D*, Marques E., Arguel M-J, Duret L., Machado A.C.Z., Carneiro R.M.D.G., Kozlowski D.K*, Bailly-Bechet M*, Castagnone-Sereno, Albuquerque E.V.S, Danchin E.G.J* Population genomics supports clonal reproduction and multiple independent gains and losses of parasitic abilities in the most devastating nematode pest. Evolutionary Applications 2019 (View Online) *Peer-reviewed and recommended in PCI Evolutionary Biology 2019 (View Online)

Michelet C., Danchin E.G.J*, Jaouannet M., Bernhagen J., Panstruga R., Kogel K-H., Keller H., Coustau C. Cross-Kingdom Analysis of Diversity, Evolutionary History, and Site Selection within the Eukaryotic Macrophage Migration Inhibitory Factor Superfamily. Genes 2019 (View Online)

Busch A., Danchin E.G.J*, Pauchet Y. Functional diversification of horizontally acquired glycoside hydrolase family 45 (GH45) proteins in Phytophaga beetles. BMC Evolutionary Biology 2019 (View Online)

Cavigliasso F, Mathé-Hubert H, Kremmer L, Rebuf C, Gatti J-L, Malausa T, Colinet D*, Poirié M. Rapid and differential evolution of the venom composition of a parasitoid wasp depending on the host strain. Toxins 11: 629. 2019 (View online)

Mathé-Hubert H, Kremmer L, Colinet D*, Gatti J-L, Van Baaren J, Delava E, Poirié M. Variation in the venom of parasitic wasps, drift or selection ? Insights from a multivariate QST analysis. Front Ecol Evol 7: 156. 2019 (View online)

Zotta Mota A.P*, Nicolini Oliveira T., Cleo Vinson C., Rhys Williams T.C., Mota do Carmo Costa M., Guerra Araujo A.C., Danchin E.G.J*, Grossi-De-Sa M.F., Messenberg Guimaraes P., Miranda Brasileiro A.C. Contrasting effects of wild Arachis dehydrin under abiotic and biotic stresses. Frontiers In Plant Science 2019 (View Online)

Castagnone-Sereno P., Mulet K., Danchin E.G.J*, Koutsovoulos G.D*, Karaulic M., Da Rocha M., Bailly-Bechet M*, Pratx L., Perfus-Barbeoch L., Abad P. Gene copy number variations as signatures of adaptive evolution in the parthenogenetic, plant-parasitic nematode Meloidogyne incognita. Molecular Ecology 2019 (View Online)

Djian-Caporalino C, Navarrete M, Fazari A, Bailly-Bechet M*, Marteu N, Dufils A, Tchamitchian M, Lefevre A, Pares L, Mateille T, Tavoillot J, Palloix A, Sage-Palloix A-M, Védie H, Goillon C, Castagnone-Sereno P. Conception et évaluation de systèmes de culture maraîchers méditerranéens innovants pour gérer les nématodes à galles. Biotechnologie, Agronomie, Société et Environnement. 2019 (View Online)

Djian-Caporalino C, Mateille T, Bailly-Bechet M*, Marteu N, Fazari A, Bautheac P, Raptopoulo A, Van Luan D, Tavoillot J, Martiny B, Goillon C, Castagnone-Sereno P. Evaluating sorghums as green manure against root-knot nematodes. Crop Protection. 2019 (View Online)

Sultana T, Van Essen D, Siol O, Bailly-Bechet M*, Philippe C, El Aabidine Amal Z, Pioger L, Nigumann P, Saccani S, Andrau J-C, Gilbert N, Cristofari G. The Landscape of L1 Retrotransposons in the Human Genome Is Shaped by Pre-insertion Sequence Biases and Post-insertion Selection. Molecular Cell. 2019 (View Online).