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  1/ Oak genome pre-submission paper

  • Plomion C, Aury JM, Amselem J, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Boudet N, Boury C, Canaguier A, Couloux A, Da Silva C, Duplessis S, Ehrenmann F, Estrada-Mairey B, Fouteau S, Francillonne N, Gaspin C, Guichard C, Klopp C, Labadie K, Lalanne C, Le Clainche I, Leplé JC, Le Provost G, Leroy T, Lesur I, Martin F, Mercier J, Michotey C, Murat F, Salin F, Steinbach D, Faivre-Rampant P, Wincker P, Salse S, Quesneville H, Kremer A (2016) Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Mol Ecol Res. 16: 254-265

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  2/ Other publications on Fagaceae genomics from our group


  • Song J, Brendel O, Bodénès C, Plomion C, Kremer A, Colin F (2017)  X-ray computed tomography to decipher the genetic architecture of tree branching traits: oak as a case study. Tree Genet Genomes 13: 5
  • Holliday J, Aitken S, Cooke J, Fady B,González-Martínez S,Heuertz M, Jaramillo-Correa J, Lexer C, Staton M, Whetten R, Plomion C (2017) Advances in ecological genomics in forest trees and applications to genetic resources conservation and breeding. Mol Ecol 26: 706-717
  • Leroy T, Roux C, Villate L, Bodénès C, Romiguier J, Paiva J, Azema Dossat C, Aury JM, Plomion C, Kremer A (2017)  Extensive recent secondary contacts between four European white oak species. New Phytol 214: 865-878



  •  Bodénès C, Chancerel E, Ehrenmann F, Kremer A, Plomion C (2016) High-density linkage mapping and distribution of segregation distortion regions in the oak genome. DNA Res 23:115-24.
  •  Plomion C, Bastien C, Bogeat-Triboulot MB, Bouffier L, Déjardin A, Duplessis S, Fady B, Heuertz M, Le Gac AL, Le Provost G, Legué V, Lelu-Walter MA, Leplé JC, Maury S, Morel A, Oddou-Muratorio S, Pilate G, Sanchez L, Scotti I, Scotti-Saintagne C, V, Trontin JF, Vacher C (2016) Forest tree genomics: 10 achievements from the past 10 years and future prospects. Ann For Sci 73: 77-103
  • Rellstab C, Zoller S,Walthert L, Lesur I, Pluess AR, Graf T, Bodénès C, Sperisen C, Kremer A, Gugerli F (2016) Signatures of local adaptation in candidate genes of oaks (Quercus spp.) with respect to present and future climatic conditions. Mol Ecol (doi: 10.1111/mec.13889)
  • Le Provost G, Lesur I, Lalanne C , Da Silva C, Labadie K, Aury JM, Leplé JC, Plomion C (2016) Implication of the suberin pathway in adaptation to waterlogging and hypertrophied lenticels formation in pedunculate oak (Quercus robur L.). Tree Physiol (doi: 10.1093/treephys/tpw056)
  • Lesur I, Köller A, Martin F, Kremer A, Plomion C, Le Provost G (2016) Transcriptomic resources for Hazelnut tree (Corylus avellana L.) in Genomic Resources Notes. Dryad Digital Repository. Mol Ecol Res 16: 377



  • Goicoechea PG, Herrán A, Durand J, Bodénès C, Plomion C, Kremer A (2015) A linkage disequilibrium perspective on the genetic mosaic of speciation in two hybridizing Mediterranean white oaks. Heredity 114: 373-86
  • Lesur I, Le Provost G, Bento P, Da Silva C, , Leplé JC, Murat F, Ueno S, Bartholomé J, Lalanne C, Ehrenmann F, Noirot C, Burban C, Loustau ML, Léger V, Amselem J, Belser C, Quesneville H, Stierschneider M, Fluch S, Feldhahn L, Tarkka M, Herrmann S, Buscot F, Klopp C, Kremer A, Salse J, Aury JM, Plomion C (2015) The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. BMC Genomics 16:112
  • Lesur I, Bechade A, Lalanne C, Klopp C, Noirot C, Leplé JC, Kremer A, Plomion C, Le Provost G (2015) A unigene set for European beech (Fagus sylvatica L.) and its use to decipher the molecular mechanisms involved in dormancy regulation. Mol Ecol Res 15:1192-1204
  • Lepoittevin C, Bodénès C, Chancerel E, Villate L, Lang T, Lesur I, Boury C, Ehrenmann F, Zelenica D, Boland A, Besse C, Garnier-Géré P, Plomion C, Kremer A (2015) Single-nucleotide polymorphism discovery and validation in high density SNP array for genetic analysis in European white oaks. Mol Ecol Res 15:1446-59



  • Gailing O, Bodénès C, Finkeldey R, Kremer A, Plomion C (2013) Genetic mapping of EST-derived Simple Sequence Repeats (EST-SSRs) to identify QTL for leaf morphological characters in a Quercus robur full-sib family. Trees Genetics & Genomes 9: 1361-1367
  • Petit RJ, Carlson J, Curtu L, Loustau ML, Plomion C, Rodriguez AG, Sork V, Ducousso A (2013). Fagaceae trees as models to integrate ecology, evolution and genomics. New Phytol 197: 369-371
  • Ueno S, Klopp C, Noirot C, Léger V, Prince E, Kremer A, Plomion C, Le Provost G (2013) Transcriptional profiling of bud dormancy induction and release in oak by next-generation sequencing. BMC Genomics 14:236
  • Plomion C, Fievet V (2013) Oak genomics takes off and enters the ecological genomics era. New Phytol 199: 308-31



  • Bodénès C, Chancerel E, Murat F, Bagnoli F, Gailing O, Durand J, Koelewijn HP, Goicoechea P, Villani F, Roussel G, Salse S, Vendramin GG, Soularue JP, Boury C, Alberto F, Kremer A, Plomion C (2012) Comparative mapping in the Fagaceae and beyond using EST-SSRs. BMC Plant Biol 12:153
  • Kremer A, Abbott AG, Carlson JE, Manos PS, Plomion C, Sisco P, Staton ME, Ueno S, Vendramin GG (2012) Genomics of Fagaceae. Trees Genet Genomes 8:583-610
  • Le Provost G, Sulmon C, Frigério JM, Bodénès C, Kremer A, Plomion C (2012) The role of water-logging responsive genes in shapping inter-specific differentiation between two sympatric oak species. Tree Physiol 32: 19-134



  • Lesur I, Durand J, Sebastiani F, Gyllenstrand N, Bodénès C, Lascoux M, Kremer K, Vendramin GG, Plomion C (2011) A sample view of the pedunculate oak (Quercus robur) genome from the sequencing of hypomethylated and random genomic libraries. Trees Genet Genomes  7: 1277-1285
  • Vornam B, Gailing O, Dérory J, Plomion C, Kremer A, Finkeldey R (2011) Characterization and allelic variation of a dehydrin gene in Quercus petraea (Matt.) Liebl. Plant Biol 13: 881-887
  • Faivre-Rampant P, Lesur I, Boussardon C, Bitton F, Bodénès C, Le Provost G, Bergès H, Fluch S, Kremer A, Plomion C (2011). Analysis of BAC end sequences in oak, providing insights into the composition of the genome of this keystone species. BMC Genomics 12: 292



  • Durand J, Bodénès C, Chancerel E, Frigerio JM, Vendramin G, Sebastiani F, Buonamici A, Gailing O, Koelewijn HP, Villani F, Mattioni C, Cherubini M, Goicoechea PG, Herrán A, Ikaran Z, Cabané C, Ueno S, Alberto F, Dumoulin P-Y, Guichoux E, de Daruvar A, Kremer A, Plomion C (2010) A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study. BMC Genomics 11: 570
  • Ueno S, Le Provost G, Léger V, Klopp C, Noirot C, Frigerio J-M, Salin F, Salse J, Abrouk M, Murat F, Brendel O, Derory J, Abadie P, Léger P, Cabane C, Barré A, de Daruvar A, Couloux A, Wincker P, Reviron M-P, Kremer A, Plomion C (2010) Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak. BMC Genomics 11: 650

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