Publications

The PGTB must be cited in the acknowledgement section of every paper resulting from a project achieved at the facility. Here is a proposition:

"Part of the experiments (specify which ones) were performed at the Genome Transcriptome Facility of Bordeaux (grants from the Conseil Régional d’Aquitaine n°20030304002FA and 20040305003FA, from the European Union FEDER n°2003227 and from Investissements d'Avenir ANR-10-EQPX-16-01)".


2017

Co-authorship

 

Albertin, W., Chernova, M., Durrens, P., Guichoux, E., Sherman, D.J., Masneuf-Pomarede, I., Marullo, P., 2017. Many interspecific chromosomal introgressions are highly prevalent in Holarctic Saccharomyces uvarum strains found in human-related fermentations. Yeast. https://doi.org/10.1002/yea.3248

Blanc-Jolivet, C., Kersten, B., Bourland, N., Guichoux, E., Delcamp, A., Doucet, J.-L., Degen, B., 2017a. Development of nuclear SNP markers for the timber tracking of the African tree species Sapelli, Entandrophragma cylindricum. Conservation Genetics Resources 1–3. https://doi.org/10.1007/s12686-017-0872-4

Blanc-Jolivet, C., Kersten, B., Daïnou, K., Hardy, O., Guichoux, E., Delcamp, A., Degen, B., 2017b. Development of nuclear SNP markers for genetic tracking of Iroko, Milicia excelsa and Milicia regia. Conservation Genetics Resources 9, 531–533. https://doi.org/10.1007/s12686-017-0716-2

Desprez-Loustau, M.-L., Massot, M., Feau, N., Fort, T., de Vicente, A., Torés, J.A., Ortuño, D.F., 2017. Further Support of Conspecificity of Oak and Mango Powdery Mildew and First Report of Erysiphe quercicola and Erysiphe alphitoides on Mango in Mainland Europe. Plant Disease PDIS–01. https://doi.org/10.1094/PDIS-01-17-0116-RE

El Khoury, M., Campbell-Sills, H., Salin, F., Guichoux, E., Claisse, O., Lucas, P.M., 2017. Biogeography of Oenococcus oeni Reveals Distinctive but Nonspecific Populations in Wine-Producing Regions. Applied and environmental microbiology 83, e02322–16. https://doi.org/10.1128/AEM.02322-16

Merceron, N.R., Leroy, T., Chancerel, E., Romero-Severson, J., Borkowski, D.S., Ducousso, A., Monty, A., Porté, A.J., Kremer, A., 2017. Back to America: tracking the origin of European introduced populations of Quercus rubra L. Genome 60, 778–790. https://doi.org/10.1139/gen-2016-0187

Meyer-Sand, B.R., Blanc-Jolivet, C., Mader, M., Paredes-Villanueva, K., Tysklind, N., Sebbenn, A.M., Guichoux, E., Degen, B., 2017. Development of a set of SNP markers for population genetics studies of Ipe (Handroanthus sp.), a valuable tree genus from Latin America. Conservation Genetics Resources 1–3. https://doi.org/10.1007/s12686-017-0928-5

Truffaut, L., Chancerel, E., Ducousso, A., Dupouey, J.L., Badeau, V., Ehrenmann, F., Kremer, A., 2017. Fine-scale species distribution changes in a mixed oak stand over two successive generations. New Phytologist 215, 126–139. https://doi.org/10.1111/nph.14561

Wan, Q., Zheng, Z., Huang, K., Guichoux, E., Petit, R.J., 2017. Genetic divergence within the monotypic tree genus Platycarya (Juglandaceae) and its implications for species’ past dynamics in subtropical China. Tree Genetics & Genomes 13, 73. http://dx.doi.org/10.1007/s11295-017-1153-9

 

Acknowledgments

 

Kimuda, M.P., Noyes, H., Mulindwa, J., Enyaru, J., Alibu, V.P., Sidibe, I., Mumba, D., Hertz-Fowler, C., MacLeod, A., Bishop, O.T., Matovu, E., Grp, T.R., C, as members of T.H., 2017. No evidence for association with APOL1 kidney disease risk alleles and Human African Trypanosomiasis in two Ugandan populations. bioRxiv 180679. https://doi.org/10.1101/180679

Lepais, O., Manicki, A., Glise, S., Buoro, M., Bardonnet, A., 2017. Genetic architecture of threshold reaction norms for male alternative reproductive tactics in Atlantic salmon (Salmo salar L.). Scientific Reports 7, 43552.

Marquet, S., Conte, I., Poudiougou, B., Argiro, L., Dessein, H., Couturier, C., Burté, F., Oumar, A.A., Brown, B.J., Traore, A., Afolabi, N.K., Barry, A., Omokhodion, S., Shokunbi, W.A., Sodeinde, O., Doumbo, O., Fernandez-Reyes, D., Dessein, A.J., 2017. A Functional IL22 Polymorphism (rs2227473) Is Associated with Predisposition to Childhood Cerebral Malaria. Scientific Reports 7, 41636.

 


2016

Co-authorship

 

Bartholomé, J., Van Heerwaarden, J., Isik, F., Boury, C., Vidal, M., Plomion, C., and Bouffier, L. (2016a). Performance of genomic prediction within and across generations in maritime pine. BMC Genomics 17, 604.

Bartholomé, J., Bink, M.C., van Heerwaarden, J., Chancerel, E., Boury, C., Lesur, I., Isik, F., Bouffier, L., and Plomion, C. (2016b). Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness. PLoS ONE 11, e0165323.

Bodénès, C., Chancerel, E., Ehrenmann, F., Kremer, A., and Plomion, C. (2016). High-density linkage mapping and distribution of segregation distortion regions in the oak genome. DNA Res. 23, 115–124.

Börlin, M., Venet, P., Claisse, O., Salin, F., Legras, J.-L., and Masneuf-Pomarede, I. (2016). Cellar-Associated Saccharomyces cerevisiae Population Structure Revealed High-Level Diversity and Perennial Persistence at Sauternes Wine Estates. Appl. Environ. Microbiol. 82, 2909–2918.

Gleize, Y., Mendisco, F., Pemonge, M.-H., Hubert, C., Groppi, A., Houix, B., Deguilloux, M.-F., and Breuil, J.-Y. (2016). Early Medieval Muslim Graves in France: First Archaeological, Anthropological and Palaeogenomic Evidence. PLoS ONE 11, e0148583.

Gourgues G, Barré A, Beaudoing E, Weber J, Magdelenat G, Barbe V, Schieck E, Jores J, Vashee S, Blanchard A, Lartigue C, Sirand-Pugnet P. Complete Genome Sequence of Mycoplasma mycoides subsp. mycoides T1/44, a Vaccine Strain against Contagious Bovine Pleuropneumonia. Genome Announc. 2016 Apr 14;4(2). pii: e00263-16. doi: 10.1128/genomeA.00263-16.

Isik, F., Bartholomé, J., Farjat, A., Chancerel, E., Raffin, A., Sanchez, L., Plomion, C., Bouffier, L., 2016. Genomic selection in maritime pine. Plant Science 242, 108–119. doi:10.1016/j.plantsci.2015.08.006

Masneuf-Pomarede, I., Salin, F., Börlin, M., Coton, E., Coton, M., Jeune, C.L., and Legras, J.-L. (2016). Microsatellite analysis of Saccharomyces uvarum diversity. FEMS Yeast Res. 16, fow002.

Moutton, S., Fergelot, P., Naudion, S., Cordier, M.-P., Solé, G., Guerineau, E., Hubert, C., Rooryck, C., Vuillaume, M.-L., Houcinat, N., et al. (2016). Otopalatodigital spectrum disorders: refinement of the phenotypic and mutational spectrum. J. Hum. Genet. 61, 693–699.

Naudion, S., Moutton, S., Coupry, I., Sole, G., Deforges, J., Guerineau, E., Hubert, C., Deves, S., Pilliod, J., Rooryck, C., et al. (2016). Fetal phenotypes in otopalatodigital spectrum disorders. Clin. Genet. 89, 371–377.

Plomion, C., Aury, J.-M., Amselem, J., Alaeitabar, T., Barbe, V., Belser, C., Bergès, H., Bodénès, C., Boudet, N., Boury, C., et al. (2016). Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Mol Ecol Resour 16, 254–265.

Rimet, F., Chaumeil, P., Keck, F., Kermarrec, L., Vasselon, V., Kahlert, M., Franc, A., and Bouchez, A. (2016). R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring. Database (Oxford) 2016.

Sampaio, T., Branco, M., Guichoux, E., Petit, R. J., Pereira, J. S., Varela, M. C., Almeida, M. H. (2016). Does the geography of cork oak origin influence budburst and leaf pest damage?. Forest Ecology and Management, 373, 33-43. DOI : 10.1016/j.foreco.2016.04.019

Verdu, C.F., Guichoux, E., Quevauvillers, S., De Thier, O., Laizet, Y. ’han, Delcamp, A., Gévaudant, F., Monty, A., Porté, A.J., Lejeune, P., et al. (2016). Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L. Ecology and Evolution 6, 7323–7333.

Yacoub, E., Sirand-Pugnet, P., Barré, A., Blanchard, A., Hubert, C., Maurier, F., Bouilhol, E., and Ben Abdelmoumen Mardassi, B. (2016). Genome Sequences of Two Tunisian Field Strains of Avian Mycoplasma, M. meleagridis and M. gallinarum. Genome Announc 4.

 

Acknowledgements

 

Fraïsse, C., Belkhir, K., Welch, J.J., and Bierne, N. (2016). Local interspecies introgression is the main cause of extreme levels of intraspecific differentiation in mussels. Mol. Ecol. 25, 269–286.

Marchal, A., Prida, A., and Dubourdieu, D. (2016). New Approach for Differentiating Sessile and Pedunculate Oak: Development of a LC-HRMS Method To Quantitate Triterpenoids in Wood. J. Agric. Food Chem.

 

Communication orales

 

Sirand-Pugnet, P. Quoi de neuf à propos du NGS ? Séminaire lors du Club B’nB (communauté santé CHU), 2016

Sirand-Pugnet, P. What’s new about NGS ? Conférence invitée, Presented at Genomics and Forest Tree Genetics Conference, Arcachon, FRA (2016-05-30 - 2016-06-03).

Guichoux, E. Traçabilité génétiques des bois de chêne de tonnellerie : vers une meilleure prédiction des propriétés organoleptiques – Rencontre annuelle du GDR Bois, Novembre 2016

Salse, J., Aury, J. M., Murat, F., Faye, S., Labadie, K., Dossat, C., d’Agata, L., Da Silva, C., Barbe, V., Wincker, P., Klopp, C., Faivre-Rampant, P., Berges, H., Amselem, J., Quesneville, H., Francillonne, N., Bodénès, C., Le Provost, G., Lalanne, C., Salin, F., Ehrenmann, F., Leroy, T., Lesur, I., Kremer, A., Plomion, C. (2016). Oak genome sequencing and evolution. In: Book of abstracts (p. 36). Presented at Genomics and Forest Tree Genetics Conference, Arcachon, FRA (2016-05-30 - 2016-06-03).

 

Posters

 

Bartholome, J., De Vega, M., Lesur, I., Salin, F., Chancerel, E., Lamy, J.-B., Bohlmann, J., Plomion, C. (2016). Genetic analysis of oleoresin terpenoid content in maritime pine. In: Book of abstracts (p. 55-56). Presented at Genomics and Forest Tree Genetics Conference, Arcachon, FRA (2016-05-30 - 2016-06-03).

Gourgues, G., Barré, A., Beaudoing, E., Weber, J., Magdelenat, G., Barbe, V., Schieck, E., Jores, J., Vashee, S., Blanchard, A., Lartigue, C., Sirand-Pugnet, P. Complete Genome sequence of Mycoplasma mycoides subsp. mycoides T1/44, vaccine strain against contagious bovine pleuropneumonia

Le Provost, G., Guichoux, E., Prida, A., Marchal, A., Salin, F., Plomion, C. (2016). An RNAseq approach to decipher the molecular mechanisms involved in the biosynthesis of the aromatic compounds in European white oaks wood. In: Book of abstracts (p. 109). Presented at Genomics and Forest Tree Genetics Conference, Arcachon, FRA (2016-05-30 - 2016-06-03).

Verdu, C., Guichoux, E., Monty, A., Porté, A., Mariette, S., Lassois, L. (2016). SNP development and genetic diversity of the non-native tree Robinia Pseudoacacia in Belgium. In: Book of abstracts (p. 93-94). Presented at Genomics and Forest Tree Genetics Conference, Arcachon, FRA (2016-05-30 - 2016-06-03).

Truffaut, L., Chancerel, E., Ducousso, A., Dencausse, B., Reynet, P., Lagane, F., Kremer, A. (2016). Reproductive success and species occupancy changes during natural regeneration in a mixed oak stand (Quercus petraea and Quercus robur). Presented at Genomics and Forest Tree Genetics Conference, Arcachon, FRA (2016-05-30 - 2016-06-03).

 


2015

Co-authorship

 

Almeida J, da Silva Azevedo M, Spicher L, Glauser G, vom Dorp K, Guyer L, del Valle Carranza A, Asis R, Pereira de Souza A, Buckeridge M, Demarco D, Bres C, Rothan C, Pereira Peres LE, Hörtensteiner S, Kessler F, Dörmann P, Carrari F, Rossi M, 2015. Down-regulation of tomato PHYTOL KINASE strongly impairs tocopherol biosynthesis and affects prenyllipid metabolism in an organ-specific manner. J. Exp. Bot. doi:10.1093/jxb/erv504.

Cabezas, J.A., González-Martínez, S.C., Collada, C., Guevara, M.A., Boury, C., de María, N., Eveno, E., Aranda, I., Garnier-Géré, P.H., Brach, J., et al. (2015). Nucleotide polymorphisms in a pine ortholog of the Arabidopsis degrading enzyme cellulase KORRIGAN are associated with early growth performance in Pinus pinaster. Tree Physiol. 35, 1000–1006.

Freyburger, G., Labrouche, S., Hubert, C., and Bauduer, F. (2015). Haemostaseome-associated SNPs: has the thrombotic phenotype a greater influence than ethnicity? GMT study from Aquitaine including Basque individuals. Thromb. Haemost. 113, 66–76.

Guichoux, E. (2015). Le génotypage par spectrométrie de masse MALDI-TOF : principe et applications biologiques. Journal de Mycologie Médicale / Journal of Medical Mycology 25, 218.

Lepoittevin, C., Bodénès, C., Chancerel, E., Villate, L., Lang, T., Lesur, I., Boury, C., Ehrenmann, F., Zelenica, D., Boland, A., et al. (2015). Single-nucleotide polymorphism discovery and validation in high-density SNP array for genetic analysis in European white oaks. Mol Ecol Resour 15, 1446–1459.

Masneuf-Pomarede, I., Juquin, E., Miot-Sertier, C., Renault, P., Laizet, Y. ’han, Salin, F., Alexandre, H., Capozzi, V., Cocolin, L., Colonna-Ceccaldi, B., et al. (2015). The yeast Starmerella bacillaris (synonym Candida zemplinina) shows high genetic diversity in winemaking environments. FEMS Yeast Res. 15, fov045.

Naudion, S., Moutton, S., Coupry, I., Sole, G., Deforges, J., Guerineau, E., Hubert, C., Deves, S., Pilliod, J., Rooryck, C., et al. (2015). Fetal phenotypes in otopalatodigital spectrum disorders. Clin. Genet.

Philippe G, Gaillard C, Petit J, Geneix N, Dalgalarrondo M, Bres C, Mauxion JP, Franke, Rothan C, Schreiber L, Marion D, Bakan B. 2015. Ester-crosslink Profiling of the Cutin Polymer of Wild Type and Cutin Synthase Tomato (Solanum lycopersicum L.) Mutants Highlights Different Mechanisms of Polymerization. Plant Physiol.

Pilliod, J., Moutton, S., Lavie, J., Maurat, E., Hubert, C., Bellance, N., Anheim, M., Forlani, S., Mochel, F., N’Guyen, K., et al. (2015). New practical definitions for the diagnosis of autosomal recessive spastic ataxia of Charlevoix-Saguenay. Ann. Neurol.

Plomion, C., Aury, J.-M., Amselem, J., Alaeitabar, T., Barbe, V., Belser, C., Bergès, H., Bodénès, C., Boudet, N., Boury, C., et al. (2015a). Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Mol Ecol Resour.

Plomion, C., Bartholomé, J., Lesur, I., Boury, C., Rodríguez-Quilón, I., Lagraulet, H., Ehrenmann, F., Bouffier, L., Gion, J.M., Grivet, D., et al. (2015b). High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster). Mol Ecol Resour.

Vidal, M., Plomion, C., Harvengt, L., Raffin, A., Boury, C., and Bouffier, L. (2015). Paternity recovery in two maritime pine polycross mating designs and consequences for breeding. Tree Genetics & Genomes 11, 1–13.

Yacoub, E., Sirand-Pugnet, P., Blanchard, A., and Ben Abdelmoumen Mardassi, B. (2015). Genome Sequence of Mycoplasma meleagridis Type Strain 17529. Genome Announc 3.

 

Acknowledgements

 

Antonecchia, G., Fortini, P., Lepais, O., Gerber, S., Legér, P., Scippa, G.S., and Viscosi, V. (2015). Genetic structure of a natural oak community in central Italy: Evidence of gene flow between three sympatric white oak species (Quercus, Fagaceae). Annals of Forest Research 58, 205–216.

Castède, S., Campoy, J.A., Le Dantec, L., Quero-García, J., Barreneche, T., Wenden, B., and Dirlewanger, E. (2015). Mapping of Candidate Genes Involved in Bud Dormancy and Flowering Time in Sweet Cherry (Prunus avium). PLoS ONE 10, e0143250.

Le Morvan, V., Litière, S., Laroche-Clary, A., Ait-ouferoukh, S., Bellott, R., Messina, C., Cameron, D., Bonnefoi, H., and Robert, J. (2015). Identification of SNPs associated with response of breast cancer patients to neoadjuvant chemotherapy in the EORTC-10994 randomized phase III trial. Pharmacogenomics J 15, 63–68.

Lesur, I., Bechade, A., Lalanne, C., Klopp, C., Noirot, C., Leplé, J.-C., Kremer, A., Plomion, C., and Le Provost, G. (2015a). A unigene set for European beech (Fagus sylvatica L.) and its use to decipher the molecular mechanisms involved in dormancy regulation. Mol Ecol Resour 15, 1192–1204.

Lesur, I., Le Provost, G., Bento, P., Da Silva, C., Leplé, J.-C., Murat, F., Ueno, S., Bartholomé, J., Lalanne, C., Ehrenmann, F., et al. (2015b). The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. BMC Genomics 16, 112.

Mbatchi, L.C., Schmitt, A., Thomas, F., Cazaubon, Y., Robert, J., Lumbroso, S., Brouillet, J.-P., Pourquier, P., Chatelut, E., Boyer, J.-C., et al. (2015). Polymorphisms in SLCO1B3 and NR1I2 as genetic determinants of hematotoxicity of carboplatin and paclitaxel combination. Pharmacogenomics 16, 1439–1450.

Wagner, S., Liepelt, S., Gerber, S., and Petit, R.J. (2015). Within-range translocations and their consequences in European larch. PLoS ONE 10, e0127516.

 

Communications orales

 

Kahlert, M., Bouchez, A., Chaumeil, P., Franc, A., Frigerio, J.-M., Rimet, F., Salin, F., Vasselon, V. (2015). Gaps to fill when analyzing freshwater diatom diversity with DNA barcoding – notes from a boreal region. European Journal of Phycology, Volume 50, Supplément 1. Presented at 6. European Phycological Congress, Londres, GBR (2015-08-23 - 2015-09-28). DOI : 10.1080/09670262.2015.1069489.

Erwan Guichoux : Le génotypage par spectrométrie de masse MALDI-TOF : principe et applications biologiques - Congrès des Sociétés Françaises de Parasitologie et de Mycologie Médicale 2015

 

Posters

 

Elisabeth Fitzek, Erwan Guichoux, Remy Petit, Andrew Hipp - Oakcoding: a nuclear DNA barcode for evolutionary studies in oaks - New Phytologist Symposium 2015

Maximiliano Estravis Barcala, María Verónica Arana, Erwan Guichoux, Katrin Heer, Birgit Ziegenhagen, Paula Marchelli - Transcriptome sequencing of the southernmost Patagonian tree species, Nothofagus pumilio - International Congress of Plant Molecular Biology 2015

El Mujtar Veronica, Guichoux Erwan, Boury Christophe, Pilliet Myriam, Delcamp Adline, Salin Frank, Garnier Géré Pauline - Validating the use of Genotyping-By-Sequencing approach for population genomics studies in non-model species - Colloque de Génomique Environnementale 2015

Grégoire Le Provost, Céline Lalanne, Erwan Guichoux, Christophe Plomion, Jean-Marc Gion - Field experiment to identify the molecular mechanisms involved in drought stress adaptation in maritime pine (Pinus pinaster Ait) - Plant and Animal Genome 2015

S.Brun, P.Gueguen, L.ElKhattabi, N.Chatron, J.Nectoux, S.Schutz2, J.Pipoli da Fonseca, E.Guichoux, A.Sorlin, M.Quere, J.Boudjarane, C.Bonnet, F.Letourneur, C.Schluth-Bolard, P.Jonveaux, C.Bardel, V.Paquis-Fluckinger, S.Bannwarth, B.Arveiler, M.Goossens, C.Badens, J.Dupont, C.Rooryck, D.Sanlaville, C.Ferec, M.Vidaud - Non-invasive prenatal testing for the most common aneuploidies (trisomies 13, 18, 21) using a semiconductor sequencing platform : a French multicenter pilot study - European Society of Human Genetics Conference 2015

Nectoux J, Schutz S, Chatron N, Brun S, Gueguen P, El Khattabi L, Pipoli Da Fonseca J, Dumont F, Sorlin A, Quere M, Boudjarane J, Bonnet C, Letourneur F, Lagarde A, Schluth Bolard C, Guichoux E, Campan-Fournier A, Arveiler B, Jonveaux P, Goossens M, Badens C, Dupont JM, Sanlaville D, Ferec C, Bardel C, Vidaud M, Rooryck C - Comparison of two academic software (WISECONDOR and RAPIDR) for aneuploidies detection using semiconductor sequencing data in a NIPT process - European Society of Human Genetics Conference 2015

Sirand-Pugnet, P., Fergelot, P., Bres, C., Hubert, C., Salin, F. Centre de Génomique Fonctionnelle de Bordeaux (CGFB) PLATEFORME Génome-Transcriptome (PGTB). Journée scientifique TransBioMed, Hôpital Xavier Arnozan, FRA (2015-10-12)