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Publications

  1/ Oak genome paper

  • Plomion C, Aury JM, Amselem J, Leroy T, Murat F, Duplessis S, Faye S, Francillonne N, Labadie K, Le Provost G, Lesur I, Bartholomé B, Faivre-Rampant P, Kohler A, Leplé JC, Chantret N, Chen J, Diévart A, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Bogeat-Triboulot MB, Bouffaud ML, Brachi B, Chancerel E, Cohen D, Couloux A, Da Silva C, Dossat C, Ehrenmann F, Gaspin C, Grima-Pettenati J, Guichoux E, Hecker A, Herrmann S, Hugueney P, Hummel I, Klopp C, Lalanne C, Lascoux M, Lasserre E, Lemainque A, Desprez-Loustau ML, Luyten I, Madoui MA, Mangenot S, Marchal C, Maumus F, Mercier J, Michotey C, Panaud O, Picault N, Rouhier N, Rué O, Rustenholz C, Salin F, Soler M, Tarkka M, Velt A, Zanne A, Martin F, Wincker P, Quesneville H, Kremer A, Salse J. Oak genome reveals facets of long lifespan. Nature Plants 4 : 440-452

 

  2/ Other publications on Fagaceae genomics from our group

2023

  • Le Provost G, Lalanne C, Lesur I, Louvet JM, Delzon S, Kremer A, Labadie K, Aury JM, Da Silva C, Moritz T, Plomion C. Oak stands along an elevation gradient have different molecular strategies for regulating bud phenology. BMC Plant Biol 23: 108 10.1186/s12870-023-04069-2
  • Wagner S, Seguin-Orlando A, Leplé JC, Leroy T, Lalanne C; Labadie K, Aury JM, Poirier S, Wincker P, Plomion C, Kremer A, Orlando L. Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood. Mol Ecol. 10.1111/mec.16859

2022

  • Le Provost G, Gerardin T, Plomion C, Brendel O. Molecular plasticity to soil water deficit differs between sessile oak (Quercus Petraea (Matt.) Liebl.) high- and low-water use efficiency genotypes. Tree Physiol. 42: 2546-2562 10.1093/treephys/tpac087/6648420
  • Schmitt, Sylvain; Leroy, Thibault; Heuertz, Myriam; Tysklind, Niklas. Somatic mutation detection: a critical evaluation through simulations and reanalyses in oaks. Peer Community Journal, Volume 2 (2022), article no. e68. DOI : 10.24072/pcjournal.187
  • Le Provost G, Brachi B, Lesur I, Lalanne C, Labadie K, Aury JM, Da Silva C, Postolache D, Leroy T, Plomion C. Gene expression and genetic divergence in two sympatric oak species highlights adaptive genes to soil water constraints. Plant Phys. 190: 2466-2483. DOI : 10.1093/plphys/kiac420/6692722
  • R Fu, Y Zhu, Y Liu, Y Feng, RS Lu, Y Li, P Li, A Kremer, M Lascoux, J Chen. Genome-wide analyses of introgression between two sympatric Asian oak species. Nat Ecol Evol 6, 924–935 (2022). https://doi.org/10.1038/s41559-022-01754-7
  • Liang YY, Yuan S, Shi Y, Zhou BF, Chen XC, QQ, Ingvarsson PK, Plomion C, Wang B. Linked selection shapes the landscape of genomic variation in three oak species. New Phytol 233: 555-568 https://doi.org/10.1111/nph.17793
  • Saleh D, Chen J, Leplé JC, Leroy T, Truffaut L, Dencausse B, Lalanne C, Labadie K, Lesur I, Bert D, Lagane F, Morneau F, Aury JM, Plomion C, Lascoux M, Kremer A. Genome-wide evolutionary response of oaks since the Little Ice Age. Ecology Letters 6 (1), 4-20 https://doi.org/10.1002/evl3.269

2020

  • Bartholomé J, Brachi B, Marçais B, Mougou-Hamdane A, Bodénès C, Plomion C, Robin C, Desprez-Loustau ML. The genetics of exapted resistance to two exotic pathogens in pedunculate oak. New Phytol doi: 10.1111/NPH.16319
  • Leroy T, Louvet JM, Lalanne C, Le Provost G, Labadie K, Aury JM, Delzon S, Plomion C, Kremer A. Adaptive introgression as a driver of local adaptation to climate in European white oaks. New Phytol doi :10.1111/nph.16095
  • Leroy T, Rougemont Q, Dupouey JL, Bodénès C, Lalanne C, Belser C, Labadie K, Le Provost G, Aury JM, Kremer A, Plomion C. Massive postglacial gene flow between European white oaks uncovered genes underlying species barriers. New Phytol doi : 10.1111/nph.16039
  • Leroy T, Kremer A, Plomion C. Oak tree symbolism in the light of genomics. New Phytol doi: 10.1111/nph.15987
  • Hipp AL, Manos PS, Hahn M, Avishai M, Bodénès C, Cavender-Bares J, Crowl A, Deng M, Denk T, Fitz-Gibbon S, Gailing O, González-Elizondo MS, González-Rodríguez A, Grimm GW, Jiang XL, Kremer A, Lesur I, McVay JD, Plomion C, Rodríguez-Correa H, Schulze ED, Simeone MC, Sork VL, Valencia-Avalos S. Genomic landscape of the global oak phylogeny. New Phytol doi: 10.1111/nph.16162

 

Series of papers in a New Phytol special issue (see cover page)

  • Plomion C, Martin F. Oak genomics is proving its worth. New Phytol 226: 943-946
  • Kremer A, Hipp AL.. Oaks: an evolutionary success story. New Phyto 226 : 987-1011
  • Cannon CH, Petit RJ. The oak syngameon: more than the sum of it. New Phytol 226: 978-983
  • Bartholomé J, Brachi B, Marçais B, Mougou-Hamdane A, Bodénès C, Plomion C, Robin C, Desprez-Loustau ML. The genetics of exapted resistance to two exotic pathogens in pedunculate oak. New Phytol 226: 1088-1103
  • Hipp AL, Manos PS, Hahn M, Avishai M, Bodénès C, Cavender-Bares J, Crowl A, Deng M, Denk T, Fitz-Gibbon S, Gailing O, González-Elizondo MS, González-Rodríguez A, Grimm GW, Jiang XL, Kremer A, Lesur I, McVay JD, Plomion C, Rodríguez-Correa H, Schulze ED, Simeone MC, Sork VL, Valencia-Avalos S. Genomic landscape of the global oak phylogeny. New Phytol 226: 1198-1212
  • Leroy T, Louvet JM, Lalanne C, Le Provost G, Labadie K, Aury JM, Delzon S, Plomion C, Kremer A. Adaptive introgression as a driver of local adaptation to climate in European white oaks. New Phytol 226: 1171-1182
  • Leroy T, Rougemont Q, Dupouey JL, Bodénès C, Lalanne C, Belser C, Labadie K, Le Provost G, Aury JM, Kremer A, Plomion C. Massive postglacial gene flow between European white oaks uncovered genes underlying species barriers. New Phytol 226: 1183-1197
  • Leroy T, Kremer A, Plomion C. Oak tree symbolism in the light of genomics. New Phytol 226: 1012-1017

New Phytologist special issue

 

2019

  • Pont C, Wagner S, Kremer A, Orlando L, Plomion C, Salse J. 2019. Paleogenomics : reconstruction of plant evolutionary trajectories from modern and ancient DNA. Genome Biol 20:29.
  • T Caignard, S Delzon, C Bodénès, B Dencausse, A Kremer (2019) Heritability and genetic architecture of reproduction-related traits in a temperate oak species. Tree genetics & genomes 15 (1), 1

 

2018

  • Tuskan GA, Groover A, Schmutz J, DiFazio S, Myburg A, Grattapaglia D, Smart L, Yin T, Aury J-M, Kremer A, Leroy T, Le Provost G, Plomion C, Carlson J, Randall J, Westbrook J, Grimwood J, Muchero W, Jacobson D, Mitchener J. Hardwood tree genomics: Unlocking woody plant biology. Front. Plant. Sci. 9: 1799.
  • Cannon CH, Brendel O, Hipp AL, Kremer A, Kua C-H, Min D, Plomion C, Romero-Severson J, Sork VL. Building a global genomic perspective on Fagaceae diversity. New Phytol. 218: 894-897
  • Lesur I, Alexandre H, Boury C, Chancerel E, Plomion C, Kremer A. Development of target sequence capture and estimation of genomic relatedness in a mixed oak stand. Front. Plant Sci. 9: 996
  • Wagner S, Lagane F, Seguin-Orlando A, Schubert M, Leroy T, Guichoux R, Chancerel E, Bech-Hebelstrup I, Bernard V, Billard C, Billaud Y, Bolliger M, Croutsch C, Čufar K, Eynaud F, Heussner KU, Köninger J, Langenegger F, Leroy F, Lima C, Martinelli N, Momber G, Billamboz A,  Nelle O, Palomo A, Piqué R, Ramstein M, Schweichel R, Stäuble H, Tegel W, Terradas X, Verdin F, Plomion C, Kremer A, Orlando L. High-Throughput DNA sequencing of ancient wood. Mol Ecol 27: 1138-1154

 

2017

  • 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
  • L Truffaut, E Chancerel, A Ducousso, JL Dupouey, V Badeau (2017) Fine‐scale species distribution changes in a mixed oak stand over two successive generations. New Phytologist 215 (1), 126-139

 

2016

  • 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
  • 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

 

2015

  • 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

 

2013

  • 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

 

2012

  • 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

 

2011

  • 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

 

2010

  • 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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