Etienne G.J. Danchin

evolutionary and comparative genomics

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Publications
Publications 2003-2007
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Publications in scientific journals


2017

*) Schiffer PH, Danchin EGJ, Burnell AM, Schiffer 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. bioRxiv. 2017 (View Online). *not peer-reviewed

57) Blanc-Mathieu R., Perfus-Babeoch 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 E.G.J. Hybridization and Polyploidy Enable Genomic Plasticity Without Sex in the Most Devastating Plant-Parasitic Nematodes. PLoS Genetics 2017 (View Online).

56) Arrais Guimaraes L., Zotta Mota A.P., Guerra Araujo A.C., de Alencar Figueiredo L.F., Medeiros Pereira B., de Passos Saraiva M.A., Bispo Silva R., Danchin E.G.J., Messenberg Guimaraes P., Brasileiro A.C.M. Genome-wide analysis of expansin superfamily in wild Arachis discloses a stress-responsive expansin-like B gene. Plant Mol. Biol. 2017 (View Online).

2016

*) Blanc-Mathieu R., Perfus-Babeoch L., Aury JM., Da Rocha M., Gouzy J., Sallet E., Martin-Jimenez C., Castagnone-Sereno P., Flot JF., Kozlowski D., Cazareth J., Couloux A., Da Silva C., Guy J., Rancurel C., Schiex T., Abad P., Wincker P., Danchin E.G.J. Peculiar hybrid genomes of devastating plant pests promote plasticity in the absence of sex and meiosis. bioRxiv. 2016 (View Online).*not peer-reviewed

55) Danchin E.G.J. Lateral gene transfer in eukaryotes: tip of the iceberg or of the ice cube? BMC Biology. 2016 (commentary, View Online)

54) Fatouros N., Cusumano A., Danchin E.G.J., Colazza S. Prospects of herbivore egg-killing plant defences for sustainable crop protection. Ecology and Evolution. 2016 (View Online).

53) Eves-van den Akker S., Laetsch D.R., Thorpe P., Lilley C.J., Danchin E.G.J, Da Rocha M., Rancurel C, Holroyd N.E., Cotton J.A., Szitenberg A, Grenier E., Montarry J., Mimee B., Duceppe M-O, Boyes I, Marvin JMC, Jones LM, ..., Koutsovoulos G., Blok V, Mantelin S, Cock PJA, Phillips W, Henrissat B, Urwin PE, Blaxter M, Jones JT. The genome of the yellow potato cyst nematode Globodera rostochiensis reveals insights into the basis of parasitism and virulence. Genome Biology. 2016 (View Online).

52) Shelomi M., Danchin E.G.J., Heckel D., Wipfler B., Bradler S., Zhou X., Pauchet Y. Horizontal Gene Transfer of Pectinases from Bacteria Preceded the Diversification of Stick and Leaf Insects. Scientific Reports. 2016 (View Online).

51) Damiani I., Drain A., Guichard M., Balzergue S., Boscari A., Boyer J-C, Brunaud V., Cottaz S., Rancurel C., Da Rocha M., Fizames C., Fort S., Gaillard I., Danchin E.G.J., Maillol V., Rouached H., Samain E., Su Y-H, Thouin J., Touraine B., Puppo A., Frachisse J-M, Pauly N., Sentenac H. Nod factor effects on root hair-specific transcriptome of Medicago truncatula: focus on plasma membrane transport systems and reactive oxygen species networks. Frontiers in Plant Science. 2016 (View Online).

50) Danchin E.G.J., Guzeeva E., Mantelin S., Berepiki A., Jones J.T. Horizontal gene transfer from bacteria has enabled nematodes to feed on plant-derived sucrose. Molecular Biology & Evolution. 2016; 33 (6): 1571-1579. (View Online).

2015

49) Bird D.M., Jones J.T., Opperman C.H., Kikuchi T., Danchin E.G.J. Signatures of adaptation to plant parasitism in nematode genomes. Parasitology. 2015 (View Online).

2014

48) Veneault-Fourrey C., Commun C., Kohler A., Morin E., Balestrini R., Plett J., Danchin E.G.J., Coutinho P., Wiebenga A., de Vries R., Henrissat B., Martin F. Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment. Fungal Genetics & Biology. 2014 (View Online).

47) Eves-van den Akker S., Lilley C.,  Danchin E.G.J., Rancurel C., Cock P., Urwin P., Jones J.T. The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes. Genome Biol. Evol. 2014 (View Online).

46) Castagnone-Sereno P., Danchin E.G.J. Parasitic success without sex – the nematode experience. Journal of Evol. Biol. 2014 (View Online).

2013

45) Danchin EGJ, Arguel M-J, Campan-Fournier A, Perfus-Barbeoch L, Magliano M, Rosso M-N, Da Rocha M, Da Silva C, Nottet N, Labadie K, Guy J, Artiguenave F, Abad P. Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining. PLoS Pathogens 2013 (View Online, Pubmed).

44) Flot JF, Hespeels B, Li X, Noel B, Arkhipova I, Danchin EGJ, Hejnol A, Henrissat B,..., Pontarotti P, Weissenbach J, Wincker P, Jaillon O, Van Doninck K. Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature 2013 (View Online, PubMed).

43) Jones J. T., Haegeman A., Danchin E.G.J., Gaur H.S., Helder J., Jones M., Kikuchi T., Manzanilla-Lopez R., Palomares-Rius J., Wesemael W., Perry R.N. Top 10 plant parasitic nematodes in molecular plant pathology. Mol Plant Path 2013 (View Online, PubMed).

42) Castagnone-Sereno P., Danchin E.G.J., Perfus-Barbeoch L. and Abad P. Diversity and evolution of root-knot nematodes, genus Meloidogyne: new insights from the genomic era. Annual Review of Phytopathology 2013 (View Online, PubMed).

2012

41) Paganini J, Campan-Fournier A, Da Rocha M, Gouret P, Pontarotti P, Wajnberg E, Abad P, Danchin EGJ. Contribution of Lateral Gene Transfers to the Genome Composition and Parasitic Ability of Root-Knot Nematodes. PLoS One 2012 (View Online, PubMed).

40) Arias MC, Danchin EGJ, Coutinho PM, Henrissat B, Ball S. Eukaryote to gut bacteria transfer of a glycoside hydrolase gene essential for starch breakdown in plants. Mobile Genetic Elements 2012 (View Online, Pubmed).

39) Jaouannet M, Perfus-Barbeoch L, Deleury E, Magliano M, Engler G, Vieira P, Danchin EGJ, Da Rocha M, Coquillard P, Abad P, Rosso MN. A root-knot nematode secreted protein is injected into giant-cells and targeted to the nuclei. New Phytol. 2012 (View Online, PubMed).

38) Danchin E.G.J, Rosso MN. Lateral gene transfers have polished animal genomes: lessons from Nematodes. Front. Cell. Inf. Microbio. 2012 (View Online, Pubmed).

37) Coutard B, Danchin E.G.J, Oubelaid R, Canard B, Bignon CSingle pH buffer refolding screen for protein from inclusion bodies. Protein Expression and Purification 2012 (View Online, Pubmed).

2011

36) Danchin E.G.J. What Nematode genomes tell us about the importance of horizontal gene transfers in the evolutionary history of animals ? Mobile Genetic Elements 2011 Nov/Dec 1(4):1-5 (View Online, PubMed).

35) Amselem J., Cuomo C.A., van Kan J.A.L., Viaud M., Benito E.P., Couloux A., Coutinho P.M, de Vries R.P.,...,Danchin E.G., Da Silva C.,...,Rollins J.A., Lebrun MH, Dickman M. Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genetics 2011Aug;7(8):e1002230 (View Online).

34) Hok S., Danchin E.G.J., Allasia V., Panabières F., Attard A., Keller H. An Arabidopsis (malectin-like) leucine-rich repeat receptor-like kinase contributes to downy mildew disease. Plant, Cell & Environment 2011 Jun 28. doi: 10.1111/j.1365-3040.2011.02390.x. (View Online).

33) Haegeman A., Jones J., Danchin E.G.J. Horizontal gene transfer in nematodes: a catalyst for plant parasitism? MPMI 2011 Aug;24(8):879-87. (View Online).

32) Vens C., Rosso MN., Danchin E.G.J. Identifying discriminative classification-based motifs in biological sequences. Bioinformatics 2011; 27 (9): 1231-1238.(View Online) (Download the Software).

31) Marino D., Andrio E., Danchin E.G.J., Oger E., Gucciardo S., Lambert A., Puppo A., Pauly N. A Medicago truncatula NADPH oxidase is involved in symbiotic nodule functioning. New Phytol. 2011; Jan;189(2):580-92. 13(Open access).

30) Arguel M-J, Campan-Fournier A, Perfus-Barbeoch L, Danchin EGJ, Rosso M-N, Da Silva C, Labadie K, Marteu N, Artiguenave F, Abad P. Identification of plant-parasitism genes in nematodes in silico screening and in vivo validation in Meloidogyne incognita. Commun Agric Appl Biol Sci. 2011;76(3):409-12. (PubMed).

2010

29) Vieira P., Danchin E.G.J., Neveu C., Crozat C., Jaubert S., Hussey R.S., Engler G., Abad P., de Almeida-Engler J., Castagnone-Sereno P., Rosso M.N. The plant apoplasm is an important recipient compartment for nematode secreted proteins . J Exp Bot. 2011 Jan;62(3):1241-53. (Open access).

28) Castagnone-Sereno P., Deleury E., Perfus-Barbeoch L., Danchin E.G.J., Abad P. Data-mining of the Meloidogyne incognita degradome and comparative analysis of proteases in nematode. Genomics 2011; Jan;97(1):29-36. (View Online)

27) Castagnone-Sereno P, Danchin E.G.J., Deleury E, Guillemaud T, Malausa T, Abad P. Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita. BMC Genomics. 2010 Oct 25; 11:598. (Open access)

26) Danchin E.G.J., Rosso M-N., Vieira P., de Almeida-Engler J., Coutinho P, Henrissat B., Abad P. Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes. PNAS 2010; Oct 12;107(41):17651-6. (Open access)

25) Ma L., van der Does C., Borkovich K.A., Coleman J.J., ... , Danchin E.G.J., ... , Galagan J., Cuomo C.A., Kistler H.C., Rep M. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 2010; Mar 18;464(7287):367-73. (View Online)

2009

24) Lopez-Rascol V, Levasseur A, Chabrol O, Gruseas S, Gouret P, Danchin EGJ, Pontarotti P. CASSIOPE: an expert system for conserved regions searches. BMC Bioinformatics. 2009 Sep 10;10(1):284. (Open Access)

23) Coleman J.J, Rounsley S.D, Rodriguez-Carres M, Kuo A, ... , Danchin EGJ, Henrissat B, Coutinho P.M, ... , Covert S.F, Temporini E,  VanEtten H.D. The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. Plos Genetics. 2009, Aug;5(8):e1000618. (Open access)

22) Bird D.M, Williamson V.M, Abad P, McCarter J,  Danchin EGJ, Castagnone-Sereno P, Opperman C.H.. The genomes of root-knot nematodes. Annu. Rev. Phytopatol. 2009, online on May 4, 2009. (View Online).

2008

21) Abad P, Gouzy J, Aury JM, Castagnone-Sereno P, Danchin EGJ,..., Rosso MN, Schiex T, Smant G, Weissenbach J, Wincker P. Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotechnol. Advance online 2008 July 28. (View Online).

20) Darbo E, Danchin EGJ, Mc Dermott MF, Pontarotti P. Evolution of major histocompatibility complex by "en bloc" duplication before mammalian radiation. Immunogenetics. 2008 June 17. (View Online).

19) Espagne E, Lespinet O, Malagnac F, ... , de Vries RP, Battaglia E, Coutinho PM, Danchin EGJ, Henrissat B, ... , Debuchy R, Wincker P, Weissenbach J, Silar P. The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biol. 2008 May 6;9(5):R77. (Open Access).

18) Martinez D, Berka RM, Henrissat B, Saloheimo M, ... , Coutinho PM, Cullen D, Danchin EGJ, Grigoriev IV, ... , Rokhsar DS, Lucas SM, Rubin EM, Dunn-Coleman N, Ward M, Brettin TS. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol. 2008, May;26(5):553-60. (View Online).

17) Martin F, Aerts A, Ahrén D, Brun A, Danchin E.G.J,...,Coutinho P.M,..., Henrissat B,...,Tuskan G & Grigoriev I. V. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 2008, Mar 6;452(7183):88-92. (View Online).



 

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