Preprint articles, posted in advance of peer-reviewed versions.
27) Moura de Souza VH, Pellegrin C, Hanlon VCT, Xia C, Kranse OP, Sonawala U, Desikan P, Senatori B, Danchin EGJ*, Derevnina L, Eves-van den Akkers S. The host range paradox of Meloidogyne incognita: a physiological and transcriptomic analysis of nine susceptible interactions across six plant orders. BioRxiv 2025 (View Online).
26) Belliardo C*, Maurice N, Pere A, Mondy S, Franc A, Bailly-Bechet M*, Lemaitre C, Vicedomini R, Frigerio J-M, Salin F, Belmonte E, Sherman DJ, Abad P, Frioux C, Danchin EGJ*. Accurate MAG reconstruction from complex soil microbiome through combined short- and HiFi long-reads metagenomics. BioRxiv 2025 (View Online).
25) Zotta Mota AP*, Danchin EGJ*. Genomic characteristics of root-knot nematodes: a major group of crop pests. EcoEvoRxiv 2025 (View Online).
24) Bournaud C, Tollec A, Danchin EGJ, Coute Y, Eves-van den Akker S. DNA-protein interactions in Meloidogyne incognita. BioRxiv 2025 (View Online). [Accepted in Plant Methods].
23) Seçkin E., Colinet D., Sarti E., Danchin EGJ. Orphan and de novo Genes in Fungi and Animals: Identification, Origins and Functions. EcoEvoRxiv 2025 (View Online). [Accepted in Genome Biol. Evol.]
22) Shakya P, Maulana MI, Danchin EGJ, Voogt ML, van de Ruitenbeek SJS, Gimeno J, Taranto AP, Coomer Blundell A, Despot-Slade E, Meštrović N, Zotta Mota AP, Dai D, Williamson VM, Sterken MG, Siddique S. A Chromosome-scale Genome Assembly of Meloidogyne hapla Reveals Localized Recombination Hotspots Enriched with Effector Proteins. BioRxiv 2025 (View Online). –> Accepted in PLoS Pathogens.
21) Phan Thi N, Danchin EGJ, Koutsovoulos GD, Rancurel C, Vermeire M-L, Besnard G, Bellafiore S. Genomic rearrangements promote diversification of a facultative meiotic parthenogenetic nematode pest (Meloidogyne graminicola). BioRxiv 2025 (View Online).
20) Colinet D, Haon M, Drula E, Boyer M, Grisel S, Belliardo C, Koutsovoulos G, Berrin J-G, Danchin EGJ. Functional carbohydrate-active enzymes acquired by horizontal gene transfer from plants in the whitefly Bemisia tabaci. BioRxiv 2024 (View Online) –> Published in Genome Biol. Evol.
19) Poullet M, Gopal H, Rancurel C, Sallaberry M, Lopez-Roques C, Lledo J, Kiewnick S, Danchin EGJ. High-fidelity annotated genome of the polyploid and quarantine root-knot nematode, Meloidogyne enterolobii. BioRxiv 2024 (View Online) –> Published in Scientific Data.
18) Calia G, Porracciolo P, Chen Y, Kozlowski D, Schuler H, Cestaro A, Quentin M, Favery B, Danchin EGJ, Bottini S. Identification and characterization of specific motifs in effector proteins of plant parasites using MOnSTER. BioRxiv 2023 (View Online). –> Published in Communications Biology.
17) Moris V.C., Bruneau L., Berthe J., Heuskin A-C., Penninckx S., Ritter S., Weber U., Durante M., Danchin EGJ, Hespeels B, Van Doninck K. Ionizing radiation responses are incidental to desiccation responses in the bdelloid rotifer Adineta vaga. BioRxiv 2023 (View Online). –> Published in BMC Biology
16) Zotta Mota AP, Koutsovoulos GD, Perfus-Barbeoch L, Despot-Slade E, Labadie K, Aury JM, Robbe-Sermesant K, Bailly-Bechet M, Belser C, Pere A, Rancurel C, Kozlowski DK, Hassanaly-Goulamhoussen R, Da Rocha M, Noel B, Mestrovic-Radan N, Wincker P, Danchin EGJ. Unzipped assemblies of polyploid root-knot nematode genomes reveal new kinds of unilateral composite telomeric repeats. BioRxiv 2023 (View Online). –> Published in Nature Communications
15) Bovio E, Rancurel C, Seassau A, Magliano M, Gislard M, Loisier A, Kuchly C, Ponchet M, Danchin EGJ, Van Ghelder C. Genome sequence and annotation of Periconia digitata, a promising biocontrol agent of phytopathogenic oomycetes. BioRxiv 2023 (View Online). –> Published in Scientific Data.
14) Koutsovoulos G, Granjeon Noriot S, Bailly-Bechet M, Danchin EGJ and Rancurel C. AvP: a software package for automatic phylogenetic detection of candidate horizontal gene transfers. BioRxiv 2022 (View Online). ->Published in PLoS Computational Biology.
13) Belliardo C, Koutsovoulos G, Rancurel C, Clement M, Lipuma J, Bailly-Bechet M, Danchin EGJ. Improvement of Eukaryotic Proteins Prediction from Soil Metagenomes. BioRxiv 2021 (View Online). –> Published in Scientific Data.
12) Siddique S., Radakovic Z.S., Hiltl C., Pellegrin C., Baum T.J., Beasley H., Chitambo O., Chopra D., Danchin E.G.J, Grenier E., Habash S.S., Shamim Hasan M., Helder J., Hewezi T., Holbein J., Holterman M., Janakowski S. , Koutsovoulos G.D., Kranse O.P., Lozano-Torres J.L., Maier T.R., Masonbrink R.E., Mendy B., Riemer E., Sobczak M., Sonawala U., Sterken M.G., Thorpe P., van Steenbrugge J.J.M., Zahid N., Grundler F., 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. BioRxiv 2021. (View Online). -> Published in Nature communications.
11) 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. BioRxiv 2021. (View Online). -> Published in Frontiers in Cell and Developmental Biology (Link)
10) 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. BioRxiv 2021. (View Online).-> Published in Genes
9) 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. Preprints 2020. (View Online).-> Published in Genes
8) Simion P., Narayan J., Houtain A., Derzelle A., Baudry L., Nicolas E., Cariou M., Guiglielmoni N., Kozlowski DKL., Rodriguez Gaudray F., Terwagne M., Virgo J., Noel B., Wincker P., Danchin EGJ., Marbouty M., Hallet B., Koszul R., Limasset A., Flot J-F.,Van Doninck K. Homologous chromosomes in the asexual rotifer Adineta vaga suggest automixis. bioRxiv. 2020 (View Online). –> Published in Science Advances
7) Kozlowski DKL , Hassanaly-Goulamhoussen R, Da Rocha M, Koutsovoulos GD, Bailly-Bechet M, Danchin EGJ. Transposable Elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognita. bioRxiv. 2020 (View Online). -> Now peer-reviewed and recommended in PCI Evolutionary Biology.-> Published in Evolutionary Applications
6) 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.* The polyploid genome of the mitotic parthenogenetic root knot nematode Meloidogyne enterolobii. bioRxiv. 2019 (View Online). *co-last authors -> Published in Scientific Data
5) Busch A., Danchin E.G.J., Pauchet Y. Functional analyses of the horizontally acquired Phytophaga glycoside hydrolase family 45 (GH45) proteins reveal distinct functional characteristics. bioRxiv. 2018 (View Online). -> Published in BMC Evolutionary Biology
4) G.D. Koutsovoulos, E. Marques, M.-J. Arguel, L. Duret, A.C.Z. Machado, R.M.D.G. Carneiro, D.K. Kozlowski, M. Bailly-Bechet, P. Castagnone-Sereno, E.V.S. Albuquerque*, E.G.J. Danchin*. Population genomics supports clonal reproduction and multiple gains and losses of parasitic abilities in the most devastating nematode pest. bioRxiv. 2018 (View Online). *equal contribution. -> Now peer-reviewed and recommended in PCI Evolutionary Biology –> Published in Evolutionary Applications
3) Rancurel, C., Legrand, L., Danchin, E.G.J. Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life. Preprints 2017, 2017080107 (doi: 10.20944/preprints201708.0107.v1). (View Online). –> Published in Genes
2) 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). –> Published in iScience
1) 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). -> Published in PLoS Genetics
Etienne GJ Danchin 