Résultats pour : "génomique"

Alternative double strand break repair pathways shape the evolution of high recombination in the honey bee, Apis mellifera. Fouks Bertrand, Miller Kathleen J., Ross Caitlin, Jones Corbin, Rueppell Olav. 2024. Insect Molecular Biology, 18 p.

Characterization of adaptation mechanisms in sorghum using a multireference back-cross nested association mapping design and envirotyping. Garin Vincent, Diallo Chiaka, Tekete Mohamed Lamine, Thera Mamoutou Korotimi, Guitton Baptiste, Dagno Karim, Diallo Abdoulaye, Kouressy Mamoutou, Leiser Willmar L., Rattunde Fred, Sissoko Ibrahima, Touré Aboubacar, Nébié Baloua, Samaké Moussa, Kholova Jana, Frouin Julien, Pot David, Vaksmann Michel, Weltzien Eva, Témé Niaba, Rami Jean-François. 2024. Genetics:iyae003, 17 p.

Continent-wide genomic analysis of the African buffalo (Syncerus caffer). Talenti Andrea, Wilkinson Toby, Cook Elizabeth A., Hemmink Johanneke D., Paxton Edith A., Mutinda Matthew, Ngulu Stephen D., Jayaraman Siddharth, Bishop Richard P., Obara Isaiah, Hourlier Thibaut, Garcia Giron Carlos, Martin Fergal J., Labuschagne Michel, Atimnedi Patrick, Nanteza Anne, Keyyu Julius, Mramba Furaha, Caron Alexandre, Cornelis Daniel, Chardonnet Philippe, Fyumagwa Robert, Lembo Tiziana, Auty Harriet K., Michaux Johan, Smitz Nathalie, Toye Philip, Robert Christelle, Prendergast James G.D., Morrison Liam. 2024. Communications Biology, 7:792, 14 p.

Estimation of contemporary effective population size in plant populations: Limitations of genomic datasets. Gargiulo Roberta, Decroocq Véronique, González-Martínez Santiago C., Paz-Vinas Ivan, Aury Jean-Marc, Lesur Kupin Isabelle, Plomion Christophe, Schmitt Sylvain, Scotti Ivan, Heuertz Myriam. 2024. Evolutionary Applications, 17 (5):e13691, 16 p.

Genome-wide association for agro-morphological traits in a triploid banana population with large chromosome rearrangements. Rio Simon, Toniutti Lucile, Salmon Frédéric, Hervouet Catherine, Cardi Céline, Mournet Pierre, Guiougou Chantal, Marius Franck, Mina Claude, Delos Jean-Marie Eric, Lambert Frédéric, Madec Camille, Efile Jean-Claude, Cruaud Corinne, Aury Jean-Marc, D'Hont Angélique, Hoarau Jean-Yves, Martin Guillaume. 2024. Horticulture Research:uhae307

Linking genetic markers and crop model parameters using neural networks to enhance genomic prediction of integrative traits. Larue Florian, Rouan Lauriane, Pot David, Rami Jean-François, Luquet Delphine, Beurier Grégory. 2024. Frontiers in Plant Science, 15:1393965, 13 p.

Low-frequency somatic mutations are heritable in tropical trees Dicorynia guianensis and Sextonia rubra. Schmitt Sylvain, Heuret Patrick, Troispoux Valérie, Beraud Mélmanie, Cazal Jocelyn, Chancerel Emilie, Cravero Charlotte, Guichoux Erwan, Lepais Olivier, Loureiro João, Marande William, Martin-Ducup Olivier, Vincent Grégoire, Chave Jérôme, Plomion Christophe, Leroy Thibault, Heuertz Myriam, Tysklind Niklas. 2024. Proceedings of the National Academy of Sciences of the United States of America, 121 (10):e2313312121, 7 p.

Revisiting superiority and stability metrics of cultivar performances using genomic data: Derivations of new estimators. Carvalho Fanelli Humberto, Rio Simon, García-Abadillo Julian, Isidro y Sánchez Julio. 2024. Plant Methods, 20:85, 16 p.

Screening of triploid banana population under natural and controlled black sigatoka disease for genomic selection. Mbo Nkoulou Luther Fort, Fifen Nkouandou Yacouba, Bille Ngalle Hermine, Cros David, Martin Guillaume, Molo Thierry, Ngombo Eya'a Clement, Essome Charles, Zandjanakou-Tachin Martine, Dégbey Hervé, Bell Joseph Martin, Achigan-Dako Enoch G.. 2024. Plant Disease, 108 (7) : 2006-2016.

Whole-genome sequencing and comparative genomics reveal candidate genes associated with quality traits in Dioscorea alata. Zotta Mota Ana, Dossa Komivi, Lechaudel Mathieu, Cornet Denis, Mournet Pierre, Santoni Sylvain, Lopez David, Chaïr Hâna. 2024. BMC Genomics, 25:248, 17 p.

The complex polyploid genome architecture of sugarcane. Healey Adam, Garsmeur Olivier, Lovell John, Shengquiang S., Sreedasyam Avinash, Jenkins Jerry, Plott C.B., Piperidis George, Pompidor Nicolas, Llaca V., Metcalfe Daniel J., Dolezel Jaroslav, Cápal P., Carlson J.E., Hoarau Jean-Yves, Hervouet Catherine, Zini Cyrille, Diévart Anne, Lipzen Anna, Williams M., Boston L.B., Webber J., Keymanesh K., Tejomurthula S., Rajasekar S., Suchecki R., Furtado Agnelo, May G., Parakkal P., Simmons B.A., Barry K., Henry Robert, Grimwood Jane, Aitken Karen S., Schmutz J., D'Hont Angélique. 2024. Nature, 628 : 804-810.

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Salojärvi Jarkko, Rambani Aditi, Yu Zhe, Guyot Romain, Strickler Susan R., Lepelley Maud, Wang Cui, Rajaraman Sitaram, Rastas Pasi, Zheng Chunfang, Santos Muñoz Daniella, Meidanis João, Rossi Paschoal Alexandre, Bawin Yves, Krabbenhoft Trevor J., Wang Zhen Qin, Fleck Steven J., Aussel Rudy, Bellanger Laurence, Charpagne Aline, Fournier Coralie, Kassam Mohamed, Lefebvre Gregory, Métairon Sylviane, Descombes Patrick, Rigoreau Michel, Stolte Jens, Hamon Perla, Couturon Emmanuel, Tranchant-Dubreuil Christine, Mukherjee Minakshi, Lan Tianying, Engelhardt Jan, Stadler Peter, De Lemos Samara Mireza Correia, Ivamoto Suzuki Suzana, Sumirat Ucu, Wai Ching Man, Dauchot Nicolas, Orozco-Arias Simon, Garavito Giovanny, Kiwuka Catherine, Musoli Pascal, Nalukenge Anne, Guichoux Erwan, Reinout Havinga, Smit Martin, Carretero-Paulet Lorenzo, Guerreiro Filho Oliveiro, Toma Braghini Masako, Padilha Lilian, Hiroshi Sera Gustavo, Ruttink Tom, Henry Robert, Marraccini Pierre, et al.. 2024. Nature Genetics, 56 : 721-731.

The invasive land flatworm Arthurdendyus triangulatus has repeated sequences in the mitogenome, extra-long cox2 gene and paralogous nuclear rRNA clusters. Gastineau Romain, Lemieux Claude, Turmel Monique, Otis Christian, Boyle Brian, Coulis Mathieu, Gouraud Clément, Boag Brian, Murchie Archie, Winsor Leigh, Justine Jean-Lou. 2024. Scientific Reports, 14:7840, 15 p.

Adaptive evolution in virulence effectors of the rice blast fungus Pyricularia oryzae. Le Naour-Vernet Marie, Charriat FLorian, Gracy Jérôme, Cros-Arteil Sandrine, Ravel Sébastien, Veillet Florian, Meusnier Isabelle, Padilla André, Kroj Thomas, Cesari Stella, Gladieux Pierre. 2023. PLoS Pathogens, 19 (9):e1011294, 29 p.

Combining fusion of cells with CRISPR-Cas9 editing for the cloning of large DNA fragments or complete bacterial genomes in yeast. Guesdon Gabrielle, Gourgues Géraldine, Rideau Fabien, Ipoutcha Thomas, Manso-Silvan Lucia, Jules Matthieu, Sirand-Pugnet Pascal, Blanchard Alain, Lartigue Carole. 2023. ACS Synthetic Biology, 12 (11) : 3252-3266.

Endogenous caulimovirids: Fossils, zombies, and living in plant genomes. Vassilieff Héléna, Geering Andrew D., Choisne Nathalie, Teycheney Pierre-Yves, Maumus Florian. 2023. Biomolecules, 13 (7):1069, 18 p.

Evolution of the cotton genus, Gossypium, and its domestication in the Americas. Viot Christopher, Wendel Jonathan F.. 2023. Critical Reviews in Plant Sciences, 42 (1) : 1-33.

First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini): Comparative models for mimicry genetic studies. Gauthier Jérémy, Meier Joana, Legeai Fabrice, McClure Melanie, Whibley Annabel, Bretaudeau Anthony, Boulain Hélène, Parrinello Hugues, Mugford Sam T., Durbin Richard, Zhou Chenxi, McCarthy Shane, Wheat Christopher W., Piron-Prunier Florence, Monsempès Christelle, François Marie-Christine, Jay Paul, Noûs Camille, Persyn Emma, Jacquin-Jolyb Emmanuelle, Meslin Camille, Montagné Nicolas, Lemaitre Claire, Elias Marianne. 2023. Molecular Ecology Resources, 23 (4) : 872-885.

Genome assembly of Musa beccarii shows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes. Wang Zheng-Feng, Rouard Mathieu, Droc Gaëtan, Heslop Harrison Pat, Ge Xue-Jun. 2023. GigaScience, 12, 20 p.

Genome-wide admixture mapping identifies wild ancestry-of-origin segments in cultivated Robusta coffee. Vi Tram, Vigouroux Yves, Cubry Philippe, Marraccini Pierre, Phan Viet Ha, Khong Ngan Giang, Poncet Valérie. 2023. Genome Biology and Evolution, 15 (5):evad065, 12 p.

Genomes of the cosmopolitan fruit pest Bactrocera dorsalis (Diptera: Tephritidae) reveal its global invasion history and thermal adaptation. Zhang Yue, Liu Shanlin, De Meyer Marc, Liao Zuxing, Zhao Yan, Virgilio Massimiliano, Feng Shiqian, Qin Yujia, Singh Sandeep, Wee Suk Ling, Jiang Fan, Guo Shaokun, Li Hu, Deschepper Pablo, Vanbergen Sam, Delatte Hélène, Van Sauers-Muller Aliès, Syamsudin Tati Suryati, Kawi Anastasia Priscilla, Kasina Muo, Badji Kemo, Said Fazal, Liu Lijun, Zhao Zihua, Li Zhihong. 2023. Journal of Advanced Research, 53 : 61-74.

Genomic prediction in a multi-generation Eucalyptus globulus breeding population. Haristoy Geoffrey, Bouffier Laurent, Fontes Luis, Leal Luis, Paiva Jorge A. P., Pina João Pedro, Gion Jean-Marc. 2023. Tree Genetics and Genomes, 19:8, 17 p.

Genomic selection for salinity tolerance in japonica rice. Bartholome Jérôme, Frouin Julien, Brottier Laurent, Cao Tuong-Vi, Boisnard Arnaud, Ahmadi Nourollah, Courtois Brigitte. 2023. PloS One, 18 (9):e0291833, 22 p.

Global transcriptome profiling reveals differential regulatory, metabolic and hormonal networks during somatic embryogenesis in Coffea arabica. Awada Rayan, Lepelley Maud, Breton David, Charpagne Aline, Campa Claudine, Berry Victoria, Georget Frederic, Breitler Jean-Christophe, Leran Sophie, Djerrab Doaa, Martinez-Seidel Federico, Descombes Patrick, Crouzillat Dominique, Bertrand Benoît, Etienne Hervé. 2023. BMC Genomics, 24:41, 19 p.

Mate selection: A useful approach to maximize genetic gain and control inbreeding in genomic and conventional oil palm (Elaeis guineensis Jacq.) hybrid breeding. Tchounke Billy, Sanchez Leopoldo, Bell Joseph Martin, Cros David. 2023. PLoS Computational Biology, 19 (9):e1010290, 27 p.

Multi-environment genomic selection in rice elite breeding lines. Nguyen Van Hieu, Morantte Rose Imee Zhella, Lopena Vitaliano, Verdeprado Holden, Murori Rosemary, Ndayiragije Alexis, Kumar Katiyar Sanjay, Islam Md Rafiqul, Juma Roselyne Uside, Flandez-Galvez Hayde, Glaszmann Jean-Christophe, Cobb Joshua N., Bartholome Jérôme. 2023. Rice, 16 (1), 17 p.

Phylogeny, ecology, and gene families covariation shaped the olfactory subgenome of rodents. Courcelle Maxime, Fabre Pierre-Henri, Douzery Emmanuel. 2023. Genome Biology and Evolution, 15 (11):evad197, 15 p.

Suspicions of two bridgehead invasions of Xylella fastidiosa subsp. multiplex in France. Dupas Enora, Durand Karine, Rieux Adrien, Briand Martial, Pruvost Olivier, Cunty Amandine, Denancé Nicolas, Donnadieu Cecile, Legendre Bruno, Lopez-Roques Céline, Cesbron Sophie, Ravigné Virginie, Jacques Marie Agnès. 2023. Communications Biology, 6:103, 13 p.

Whole-genome sequences of Bipolaris bicolor, Curvularia hawaiiensis, Curvularia spicifera, and Exserohilum rostratum isolated from rice in Burkina Faso, France, Mali, and Pakistan. Kaboré Kouka Hilaire, Kassankogno Abalo Itolou, Adreit Henri, Ravel Sébastien, Charriat Florian, Diagne Diariatou, Lebrun Marc-Henri, Tharreau Didier. 2023. Mycology, 12 (11), 4 p.

A quantitative theory for genomic offset statistics. Gain Clément, Rhone Bénédicte, Cubry Philippe, Salazar Israfel, Forbes Florence, Vigouroux Yves, Jay Flora, François Olivier. 2023. Molecular Biology and Evolution, 40 (6):msad140, 10 p.

Across-population genomic prediction in grapevine opens up promising prospects for breeding. Brault Charlotte, Segura Vincent, This Patrice, Le Cunff Loïc, Flutre Timothée, François Pierre, Pons Thierry, Péros Jean-Pierre, Doligez Agnès. 2022. Horticulture Research, 9:uhac041, 13 p.

Adaptive potential of Coffea canephora from Uganda in response to climate change. Oliveira de Aquino Sinara, Kiwuka Catherine, Tournebize Rémi, Gain Clément, Marraccini Pierre, Mariac Cédric, Bethume Kévin, Couderc Marie, Cubry Philippe, Andrade Alan Carvalho, Lepelley Maud, Darracq Olivier, Crouzillat Dominique, Anten Niels P.R., Musoli Pascal, Vigouroux Yves, De Kochko Alexandre, Manel Stéphanie, François Olivier, Poncet Valérie. 2022. Molecular Ecology, 31 (6) : 1800-1819.

The Banana Genome Hub: A community database for genomics in the Musaceae. Droc Gaëtan, Martin Guillaume, Guignon Valentin, Summo Marilyne, Sempere Guilhem, Durant Eloi, Soriano Alexandre, Baurens Franc-Christophe, Cenci Alberto, Breton Catherine, Shah Trushar, Aury Jean-Marc, Ge Xue-Jun, Harrison Pat Heslop, Yahiaoui Nabila, D'Hont Angélique, Rouard Mathieu. 2022. Horticulture Research, 9:uhac221, 10 p.

Complete genome sequence of a novel marafivirus infecting pearl millet in Burkina Faso. Palanga Essowé, Tibiri Ezechiel Bionimian, Bangratz Martine, Filloux Denis, Julian Charlotte, Pinel-Galzi Agnès, Koala Moustapha, Bouma Neya James, Brugidou Christophe, Tiendrebeogo Fidèle, Roumagnac Philippe, Hebrard Eugénie. 2022. Archives of Virology, 167 : 145-148.

CulebrONT: A streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes. Orjuela Castellanos Julie, Comte Aurore, Ravel Sébastien, Charriat Florian, Vi Tram, Sabot François, Cunnac Sébastien. 2022. Peer Community Journal, 2:e46, 9 p.

EggLib 3: A python package for population genetics and genomics. Siol Mathieu, Coudoux Thomas, Ravel Sébastien, De Mita Stéphane. 2022. Molecular Ecology Resources, 22 (8) : 3176-3187.

Genome characterization and complete sequence of a new badnavirus from Pandanus amaryllifolius. Alvarez-Quinto Robert A., Grinstead Samuel, Rott Philippe, Mollow Dimitre. 2022. Archives of Virology, 167 : 1717-1720.

Genome-wide association studies and genomic selection assays made in a large sample of cacao (Theobroma cacao L.) germplasm reveal significant marker-trait associations and good predictive value for improving yield potential. Bekele Frances L., Bidaisee Gillian, Allegre Mathilde, Argout Xavier, Fouet Olivier, Boccara Michel, Saravanakumar Duraisamy, Bekele Isaac, Lanaud Claire. 2022. PloS One, 17 (10):e0260907, 35 p.

Genomic instability in somatic hybridization between Poncirus and Citrus species aiming to create new rootstocks. Dambier Dominique, Barantin Pascal, Boulard Gabriel, Costantino Gilles, Mournet Pierre, Perdereau Aude, Morillon Raphaël, Ollitrault Patrick. 2022. Agriculture (Basel), 12 (2):134, 26 p.

Genomic prediction of complex traits : methods and protocols. Ahmadi Nourollah (ed.), Bartholome Jérôme (ed.). 2022. New-York : Humana Press-Springer, 659 p. (Methods in Molecular Biology, 2467) ISBN 978-1-0716-2204-9

Genomic selection in tropical perennial crops and plantation trees: A review. Seyum Essubalew Getachew, Bille Ngalle Hermine, Abtew Wosene Gebreselassie, Munyengwa Norman, Bell Joseph Martin, Cros David. 2022. Molecular Breeding, 42:58, 23 p.

Genomicus in 2022: Comparative tools for thousands of genomes and reconstructed ancestors. Nguyen Nga Thi Thuy, Vincens Pierre, Dufayard Jean François, Roest Crollius Hugues, Louis Alexandra. 2022. Nucleic Acids Research, 50 (1) : 1025-1031.

Incipient speciation between host-plant strains in the fall armyworm. Durand Karine, Yainna Kumarihami Sudeeptha, Nam Kiwoong. 2022. BMC Ecology and Evolution, 22 (1), 8 p.

Interest of phenomic prediction as an alternative to genomic prediction in grapevine. Brault Charlotte, Lazerges Juliette, Doligez Agnès, Thomas Miguel, Ecarnot Martin, Roumet Pierre, Bertrand Yves, Berger Gilles, Pons Thierry, François Pierre, Le Cunff Loïc, This Patrice, Segura Vincent. 2022. Plant Methods, 18 (1):108, 13 p.

Mapping for males: Sustainable sex control in nile tilapia. D'Cotta Helena, Triay Cécile, Sissao Rokyatou, Bezault Etienne, Conte Matthieu, Courcelle Maxime, Caminade Pierre, Toguyeni Aboubacar, Kocher Thomas D., Baroiller Jean-François. 2022. Aquaculture Journal, 2 (2), p. 95 Genomics in Aquaculture (GIA). 6, Grenade, Espagne, 4 Mai 2022/6 Mai 2022.

Towards smart and sustainable development of modern berry cultivars in Europe. Senger Elisa, Osorio Sonia, Olbricht Klaus, Shaw Paul, Denoyes Béatrice, Davik Jahn, Predieri Stefano, Karhu Saila, Raubach Sebastian, Lippi Nico, Höfer Monika, Cockerton Helen, Pradal Christophe, Kafkas Ebru, Litthauer Suzanne, Usadel Björn, Mezzetti Bruno. 2022. Plant Journal, 11 (5) : 1238-1251.

Virion-associated nucleic acid-based metagenomics: A decade of advances in molecular characterization of plant viruses. Moubset Oumaima, François Sarah, Maclot François, Palanga Essowé, Julian Charlotte, Claude Lisa, Fernandez Emmanuel, Rott Philippe, Daugrois Jean-Heinrich, Antoine-Lorquin Aymeric, Bernardo Pauline, Blouin Arnaud G., Temple Coline, Kraberger Simona, Fontenele Rafaela S, Harkins Gordon William, Ma Yuxin, Marais Armelle, Candresse Thierry, Ben Chehida Sélim, Lefeuvre Pierre, Lett Jean-Michel, Varsani Arvind, Massart Sébastien, Ogliastro Mylène, Martin Darren Patrick, Filloux Denis, Roumagnac Philippe. 2022. Phytopathology, 112 (11) : 2253-2272.

A divide-and-conquer approach for genomic prediction in rubber tree using machine learning. Hild Aono Alexandre, Francisco Felipe Roberto, Moura Souza Livia, De Souza Gonçalves Paulo, Scaloppi Junior Erivaldo José, Le Guen Vincent, Fritsche-Neto Roberto, Gorjanc Gregor, Gonçalves Quiles Marcos, Pereira de Souza Anete. 2022. Scientific Reports, 12:18023, 14 p.

The highly repeat-diverse (Peri) centromeres of white lupin (Lupinus albus L.). Marques André, Hufnagel Maciel Bárbara, Soriano Alexandre, Péret Benjamin. 2022. Frontiers in Plant Science, 13:862079, 10 p.

Association mapping and genomic selection for sorghum adaptation to tropical soils of Brazil in a sorghum multiparental random mating population. Bernardino Karine C., de Menezes Cícero B., de Sousa Sylvia M., Guimaraes Claudia Teixeira, Carneiro Pedro C.S., Schaffert Robert E., Kochian Leon V., Hufnagel Maciel Bárbara, Pastina Maria Marta, Magalhaes Jurandir V.. 2021. Theoretical and Applied Genetics, 134 (1) : 295-312.

Contribution à l'étude génomique des histoires démographique et adaptative des bovins et ovins de l'Océan Indien. Magnier Jessica. 2021. Montpellier : Montpellier SupAgro, 314 p. Thèse de doctorat : Génétique et génomique : Montpellier SupAgro

DILS: Demographic inferences with linked selection by using ABC. Fraïsse Christelle, Popovic Iva, Mazoyer Clément, Spataro Bruno, Delmotte Stéphane, Romiguier Jonathan, Loire Etienne, Simon Alexis, Galtier Nicolas, Duret Laurent, Bierne Nicolas, Vekemans Xavier, Roux Camille. 2021. Molecular Ecology Resources, 21 (8), n.spéc. : 2629-2644.

Genomic prediction of arsenic tolerance and grain yield in rice: Contribution of trait-specific markers and multi-environment models. Ahmadi Nourollah, Cao Tuong-Vi, Frouin Julien, Norton Gareth J., Price Adam H.. 2021. Rice Science, 28 (3) : 268-278.

Grapevine breeding optimization with genomic and phenomic predictions. Brault Charlotte. 2021. Montpellier : Montpellier SupAgro, 264 p. Thèse de doctorat : Génétique et amélioration des plantes : Montpellier SupAgro

GreenPhylDB v5: A comparative pangenomic database for plant genomes. Guignon Valentin, Toure Abdel, Droc Gaëtan, Dufayard Jean François, Conte Matthieu, Rouard Mathieu. 2021. Nucleic Acids Research, 49 (D1) : D1464-D1471.

High genomic diversity of novel phages infecting the plant pathogen Ralstonia solanacearum, isolated in Mauritius and Reunion islands. Trotereau Angélina, Boyer Claudine, Bonnard Isabelle, Pécheur Max Jean Bernard, Schouler Catherine, Torres-Barceló Clara. 2021. Scientific Reports, 11 (1):5382, 10 p.

Mitochondrial genomes reveal diverse lineages of Diaphorina citri Kuwayama (Hemiptera: Sternorrhyncha: Psyllidae) in Kenya and La Réunion. Wang Yanjing, Halbert Susan, Mohamed Samira A., Delatte Hélène, Reynaud Bernard, Beattie George A.C., Holford Paul, Lu Jinming, Cen Yijing. 2021. Biological Invasions, 23 : 3109-3117.

Nanopore sequencing is a credible alternative to recover complete genomes of geminiviruses. Ben Chehida Sélim, Filloux Denis, Fernandez Emmanuel, Moubset Oumaima, Hoareau Murielle, Julian Charlotte, Blondin Laurence, Lett Jean-Michel, Roumagnac Philippe, Lefeuvre Pierre. 2021. Microorganisms, 9:903, 15 p.

On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo. Rabier Charles-Elie, Berry Vinvent, Stoltz Marnus, Santos João D., Wang Wensheng, Glaszmann Jean-Christophe, Pardi Fabio, Scornavacca Céline. 2021. PLoS Computational Biology, 17 (9):e1008380, 39 p.

Sélection bayésienne de variables pour données longitudinales avec effets différentiels dans le temps : application à l'amélioration génétique. Heuclin Benjamin. 2021. Montpellier : Université de Montpellier, 138 p. Thèse de doctorat : Biostatistique : Université de Montpellier

Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing. Belser Caroline, Baurens Franc-Christophe, Noël Benjamin, Martin Guillaume, Cruaud Corinne, Istace Benjamin, Yahiaoui Nabila, Labadie Karine, Hribova Eva, Dolezel Jaroslav, Lemainque Arnaud, Wincker Patrick, D'Hont Angélique, Aury Jean-Marc. 2021. Communications Biology, 4:1047, 12 p.

A genomics resource for genetics, physiology, and breeding of West African sorghum. Faye Jacques, Maina Fanna, Akata Eyanawa, Sine Bassirou, Diatta Cyril, Mamadou Aïssata, Marla Sandeep R., Bouchet Sophie, Témé Niaba, Rami Jean-François, Foncéka Daniel, Cissé Ndiaga, Morris Geoffrey P.. 2021. Plant Genome, 14 (2):e20075, 18 p.

A high-resolution genome-wide association study of the grain ionome and agronomic traits in rice Oryza sativa subsp. indica. Cu Suong T., Warnock Nicholas I., Pasuquin Julie, Dingkuhn Michael, Stangoulis James. 2021. Scientific Reports, 11:19230, 17 p.

A library preparation optimized for metagenomics of RNA viruses. Gil Patricia, Dupuy Virginie, Koual Rachid, Exbrayat Antoni, Loire Etienne, Fall Assane Gueye, Gimonneau Geoffrey, Biteye Biram, Talla Seck Monar, Rakotoarivony Ignace, Marie Albane, Francés Benoit, Lambert Grégory, Reveillaud Julie, Balenghien Thomas, Garros Claire, Albina Emmanuel, Eloit Marc, Gutierrez Serafin. 2021. Molecular Ecology Resources, 21 (6) : 1788-1807.

metaXplor: An interactive viral and microbial metagenomic data manager. Sempere Guilhem, Petel Adrien, Abbé Magsen, Lefeuvre Pierre, Roumagnac Philippe, Mahé Frédéric, Baurens Gaël, Filloux Denis. 2021. GigaScience, 10 (2):giab001 : 1-8.

Bartonella gabonensis sp. nov., a new Bartonella species from savannah rodent Lophuromys sp. in Franceville, Gabon. Mangombi-Pambou J.B., N'Dilimabaka Nadine, Medkour H., Banga O.L., Tall M.L., Ben Khedher M., Terras J., Abdi S., Bourgarel Mathieu, Leroy E., Fenollar Florence, Mediannikov Oleg. 2020. New Microbes and New Infections, 38:100796, 9 p.

Complete genome sequence reveals evolutionary and comparative genomic features of Xanthomonas albilineans causing sugarcane leaf scald. Zhang Hui-Li, Ntambo Mbuya Sylvain, Rott Philippe, Chen Gongyou, Chen Li-Lan, Huang Mei-Ting, Gao San-Ji. 2020. Microorganisms, 8 (2):182, 16 p.

Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate. Abrouk Michael, Ibrahim Ahmed Hanin, Cubry Philippe, Simoníková Denisa, Cauet Stéphane, Pailles Yveline, Bettgenhaeuser Jan, Gapa Liubov, Scarcelli Nora, Couderc Marie, Zekraoui Leïla, Kathiresan Nagarajan, Cizkova Jana, Hribova Eva, Dolozel Jaroslav, Arribat Sandrine, Berges Hélène, Wieringa Jan J., Gueye Mathieu, Kane Ndjido Ardo, Leclerc Christian, Causse Sandrine, Vancoppenolle Sylvie, Billot Claire, Wicker Thomas, Vigouroux Yves, Barnaud Adeline, Krattinger Simon G.. 2020. Nature Communications, 11:4488, 13 p.

Genome resource of two potato strains of Ralstonia solanacearum biovar 2 (Phylotype IIB Sequevar 1) and biovar 2T (Phylotype IIB Sequevar 25) isolated from lowlands in Iran. Sedighian Nasim, Krijger Marjon, Taparia Tanvi, Taghavi S. Mohsen, Wicker Emmanuel, van der Wolf Jan M., Osdaghi Ebrahim. 2020. Molecular Plant-Microbe Interactions, 33 (7) : 872-875.

Genomic acquisitions in emerging populations of Xanthomonas vasicola pv. vasculorum infecting corn in the United States and Argentina. Pérez-Quintero Alvaro L., Ortiz-Castro Mary, Lang Jillian M., Rieux Adrien, Wu Guangxi, Liu Sanzhen, Chapman Toni A., Chang Christine, Ziegle Janet, Peng Zhao, White Frank F., Plazas Maria Cristina, Leach Jan E., Broders Kirk. 2020. Phytopathology, 110 (6) : 1161-1173.

Genomic signatures of domestication in Old World camels. Fitak Robert Rodgers, Mohandesan Elmira, Corander Jukka, Yadamsuren Adiya, Chuluunbat Battsetseg, Abdelhadi Omer M.A., Raziq Abdul, Nagy Peter, Walzer Chris, Faye Bernard, Burger Pamela A.. 2020. Communications Biology, 3 (1):316, 10 p.

High-quality genome sequence of white lupin provides insight into soil exploration and seed quality. Hufnagel Maciel Bárbara, Marques André, Soriano Alexandre, Marquès Laurence, Divol Fanchon, Doumas Patrick, Sallet Erika, Mancinotti Davide, Carrère Sébastien, Marande William, Arribat Sandrine, Keller Jean, Huneau Cécile, Blein Thomas, Aimé Delphine, Laguerre Malika, Taylor Jemma, Schubert Veit, Nelson Matthew, Geu-Flores Fernando, Crespi Martin, Gallardo Karine, Delaux Pierre-Marc, Salse Jérôme, Berges Hélène, Guyot Romain, Gouzy Jérôme, Péret Benjamin. 2020. Nature Communications, 11:492, 12 p.

Neurospora from natural populations: Population genomics insights into the Life history of a model microbial Eukaryote. Gladieux Pierre, De Bellis Fabien, Hann-Soden Christopher, Svedberg Jesper, Johannesson Hanna, Taylor John W.. 2020. In : Statistical population genomics. Dutheil Julien Y. (ed.). Cham : Springer, 313-336. (Method in Molecular Biology, 2090) ISBN 978-1-07-160199-0

A PCR, qPCR, and LAMP toolkit for the detection of the wheat blast pathogen in seeds. Thierry Maud, Chatet Axel, Fournier Elisabeth, Tharreau Didier, Ioos Renaud. 2020. Plants, 9:227, 14 p.

Pearl millet genomic vulnerability to climate change in West Africa highlights the need for regional collaboration. Rhone Bénédicte, Defrance Dimitri, Berthouly-Salazar Cécile, Mariac Cédric, Cubry Philippe, Couderc Marie, Dequincey Anaïs, Assoumane Aichatou, Kane Ndjido Ardo, Sultan Benjamin, Barnaud Adeline, Vigouroux Yves. 2020. Nature Communications, 11:5274, 9 p.

Ploidy manipulation for citrus breeding, genetics and genomics. Ollitrault Patrick, Germanà Maria Antonietta, Froelicher Yann, Cuenca José, Aleza Pablo, Morillon Raphaël, Grosser Jude W., Guo Wenwu. 2020. In : The citrus genome. Gentile Alesssandra (ed.), La Malfa Stefano (ed.), Deng Ziniu (ed.). Cham : Springer, 75-105. (Compendium of Plant Genomes) ISBN 978-3-030-10799-4

Transcriptional regulation of sorghum stem composition: Key players identified through co-expression gene network and comparative genomics analyses. Hennet Lauriane, Berger Angélique, Trabanco Noemi, Ricciuti Emeline, Dufayard Jean François, Bocs Stéphanie, Bastianelli Denis, Bonnal Laurent, Roques Sandrine, Rossini Laura, Luquet Delphine, Terrier Nancy, Pot David. 2020. Frontiers in Plant Science, 11:224, 29 p.

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Crop plants with improved culture and quality traits for food, feed and other uses. Nogue Fabien, Vergne Philippe, Chèvre Anne-Marie, Chauvin Jean-Eric, Bouchabke-Coussa Oumaya, Déjardin Annabelle, Chevreau Elisabeth, Hibrand-Saint Oyant Laurence, Mazier Marianne, Barret Pierre, Guiderdoni Emmanuel, Sallaud Christophe, Foucrier Séverine, Devaux Pierre, Rogowsky Peter. 2019. Transgenic Research, 28 (2), suppl. : 65-73. OECD Conference on Genome Editing: Applications in Agriculture – Implications for Health, Environment and Regulation, Paris, France, 28 Juin 2018/29 Juin 2018.

Development of the automated primer design workflow uniqprimer and diagnostic primers for the broad-host-range plant pathogen Dickeya dianthicola. Karim Shaista, McNally R. Ryan, Nasaruddin Afnan S., Dereeper Alexis, Mauleon Ramil P., Charkowski Amy O., Leach Jan E., Ben-Hur Asa, Triplett Lindsay R.. 2019. Plant Disease, 103 (11) : 2893-2902.

Diversity of dromedary camel coronavirus HKU23 in African camels revealed multiple recombination events among closely related betacoronaviruses of the subgenus embecovirus. So Ray T.Y., Chu Daniel K.W., Miguel Eve, Perera Ranawaka A.P.M., Oladipo Jamiu O., Fassi-Fihri Ouafaa, Aylet Gelagay, Ko Ronald L. W., Zhou Ziqi, Cheng Mo-Sheung, Kuranga Sulyman A., Roger François, Chevalier Véronique, Webby Richard J., Woo Patrick C. Y., Poon Leo L.M., Peiris Malik. 2019. Journal of Virology, 93 (23):e01236-19, 18 p.

Evolution and ecology of plant viruses. Lefeuvre Pierre, Martin Darren Patrick, Elena Santiago F., Shepherd Dionne Natalie, Roumagnac Philippe, Varsani Arvind. 2019. Nature Reviews. Microbiology, 13 p.

Gigwa v2—Extended and improved genotype investigator. Sempere Guilhem, Petel Adrien, Rouard Mathieu, Frouin Julien, Hueber Yann, De Bellis Fabien, Larmande Pierre. 2019. GigaScience, 8 (5), 9 p.

Pervasive hybridizations in the history of wheat relatives. Glemin Sylvain, Scornavacca Céline, Dainat Jacques, Burgarella Concetta, Viader Véronique, Ardisson Morgane, Sarah Gautier, Santoni Sylvain, David Jacques, Ranwez Vincent. 2019. Science Advances, 5 (5), 10 p.

Seed comparative genomics in three coffee species identify desiccation tolerance mechanisms in intermediate seeds. Stavrinides Anna K., Dussert Stéphane, Combes Marie-Christine, Fock-Bastide Isabelle, Severac Dany, Minier Jérôme, Bastos-Siqueira Aldecinei, Demolombe Vincent, Hem Sonia, Lashermes Philippe, Joët Thierry. 2019. Journal of Experimental Botany, 71 (4) : 1418-1433.

Selection of trait-specific markers and multi-environment models improve genomic predictive ability in rice. Bhandari Aditi, Bartholome Jérôme, Cao-Hamadou Tuong-Vi, Kumari Nilima, Frouin Julien, Kumar Arvind, Ahmadi Nourollah. 2019. PloS One, 14 (5), e0208871, 21 p.

Sunflower resistance to multiple downy mildew pathotypes revealed by recognition of conserved effectors of the oomycete Plasmopara halstedii. Pecrix Yann, Buendia Luis, Penouilh-Suzette Charlotte, Maréchaux Maude, Legrand Ludovic, Bouchez Olivier, Rengel David, Gouzy Jérôme, Cottret Ludovic, Vear Felicity, Godiard Laurence. 2019. Plant Journal, 97 (4) : 730-748.

Taxonomic Study of French Guiana Fungi to Identify and Isolate Pure Cultured Fungi for Oleoresin Production in Aquilaria: Use of Sequences from the Small Ribosomal DNA (R) Subunit (SSU) and the Two Primer Pairs SR6/SR10R and SR7/SR1R. Zaremski Clara, Ducousso-Détrez Amandine, Amusant Nadine, Zaremski Alba. 2019. Pro Ligno, 15 (3) : 3-16.

Variations structurales chez le bananier : Caractérisation et impact sur les ségrégations chromosomiques de deux translocations réciproques originaires du groupe M. acuminata burmannica. Dupouy Marion. 2019. Montpellier : Montpellier SupAgro, 148 p. Thèse de doctorat : Génétique et amélioration des plantes : Montpellier SupAgro

Within-family genomic selection in rubber tree (Hevea brasiliensis) increases genetic gain for rubber production. Cros David, Mbo-Nkoulou Luther, Bell Joseph Martin, Oum Jean, Masson Aurélien, Soumahoro Mouman, Tran Dinh Minh, Achour Zeineb, Le Guen Vincent, Clément-Demange André. 2019. Industrial Crops and Products, 138:111464, 13 p.

Yam genomics supports West Africa as a major cradle of crop domestication. Scarcelli Nora, Cubry Philippe, Akakpo Roland, Thuillet Anne-Céline, Obidiegwu Jude, Baco Mohamed N., Otoo Emmanuel, Sonké Bonaventure, Dansi Alexandre, Djedatin Gustave, Mariac Cédric, Couderc Marie, Causse Sandrine, Alix Karine, Chaïr Hâna, François Olivier, Vigouroux Yves. 2019. Science Advances, 5 (5):eaaw1947, 7 p.

Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps. Belser Caroline, Istace Benjamin, Denis Erwan, Dubarry Marion, Baurens Franc-Christophe, Falentin Cyril, Genete Mathieu, Berrabah Wahiba, Chèvre Anne-Marie, Delourme Régine, Deniot Gwenaëlle, Denoeud France, Duffé Philippe, Engelen Stefan, Lemainque Arnaud, Manzanares-Dauleux Maria J., Martin Guillaume, Morice Jérôme, Noël Benjamin, Vekemans Xavier, D'Hont Angélique, Rousseau-Gueutin Mathieu, Barbe Valérie, Cruaud Corinne, Wincker Patrick, Aury Jean-Marc. 2018. Nature Plants, 4 (11) : 879-887.

Complete genome sequence of a lineage II Peste des Petits Ruminants virus from Sierra Leone. Dundon William G., Adombi Caroline Mélanie, Kanu Saidu, Loitsch Angelika, Cattoli Giovanni, Diallo Adama. 2018. Genome Announcements, 6 (1):e01417-17, 2 p.

Genome sequence and effectorome of Moniliophthora perniciosa and Moniliophthora roreri subpopulations. Barbosa Ceslaine Santos, Da Fonseca Rute R., Batista Thiago Mafra, Barreto Mariana Araújo, Argolo Caio Suzart, de Carvalho Mariana Rocha, Do Amaral Daniel Oliveira Jordão, De Andrade Silva Edson Mario, Arévalo-Gardini Enrique, Hidalgo Karina Solis, Franco Glória Regina, Pirovani Carlos Priminho, Micheli Fabienne, Gramacho Karina Peres. 2018. BMC Genomics, 19 (509), 12 p.

Genome-wide analysis of Corynespora cassiicola leaf fall disease putative effectors. Lopez David, Ribeiro Sébastien, Label Philippe, Fumanal Boris, Venisse Jean-Stéphane, Kohler Annegret, de Oliveira Ricardo R., Labutti Kurt, Lipzen Anna, Lail Kathleen, Bauer Diane, Ohm Robin, Barry Kerrie W., Spatafora Joseph W., Grigoriev Igor, Martin Francis, Pujade-Renaud Valérie. 2018. Frontiers in Microbiology, 9:276, 21 p.

Genomics of the origin and evolution of Citrus. Wu Guohong Albert, Terol Javier F., Ibáñez Victoria, López-García Antonio, Pérez-Román Estela, Borredá Carles, Domingo Concha, Tadeo Francisco, Carbonell-Caballero Jose, Alonso Roberto, Curk Franck, Du Dongliang, Ollitrault Patrick, Roose Mikeal L., Dopazo Joaquin, Gmitter Frederick G., Rokhsar Daniel S., Talon Manuel. 2018. Nature, 554 (7692) : 311-136.

Liste des clones de cacaoyers spontanés de Guyane (Theobroma cacao L.) pré-sélectionnés " candidats-élites ". Clément Didier, Lachenaud Philippe. 2018. Montpellier : CIRAD, 4 p.

Liste des clones de cacaoyers spontanés de Guyane (Theobroma cacao L.) pré-sélectionnés " candidats-élites ". Annexe au dossier Cacao. Clément Didier, Lachenaud Philippe. 2018. La Lettre du Conseil Scientifique du Parc Naturel Régional de Guyane (2), 4 p.

Nanovirus‐alphasatellite complex identi ed in Vicia cracca in the Rhône delta region of France. Gallet Romain, Kraberger Simona, Filloux Denis, Galzi Serge, Fontes Hugo, Martin Darren Patrick, Varsani Arvind, Roumagnac Philippe. 2018. Archives of Virology, 163 (3) : 695-700.

Performance of multi-trait genomic selection for Eucalyptus robusta breeding program. Rambolarimanana Herintahina, Ramamonjisoa Lolona, Verhaegen Daniel, Leong Pock Tsy Jean-Michel, Jacquin Laval, Cao-Hamadou Tuong-Vi, Makouanzi Chrissy Garel, Bouvet Jean-Marc. 2018. Tree Genetics and Genomes, 14 (5):71, 13 p.

Recent progress in understanding three major bacterial diseases of sugarcane: gumming, leaf scald and ratoon stunting. Royer Monique, Pieretti Isabelle, Cociancich Stéphane, Rott Philippe. 2018. In : Achieving sustainable cultivation of sugarcane. Volume 2: Breeding, pests and diseases. Rott Philippe (ed.). Cambridge : Burleigh Dodds Science Publishing, 311-336. ISBN 978-1-78676-148-4

Ten broad spectrum resistances to downy mildew physically mapped on the sunflower genome. Pecrix Yann, Penouilh-Suzette Charlotte, Muños Stéphane, Vear Felicity, Godiard Laurence. 2018. Frontiers in Plant Science, 9:1780, 15 p.

Whole-genome prediction of reaction norms to environmental stress in bread wheat (Triticum aestivum L.) by genomic random regression. Ly Delphine, Huet Sylvie, Gauffreteau Arnaud, Rincent Renaud, Touzy Gaëtan, Mini Agathe, Jannink Jean-Luc, Cormier Fabien, Paux Etienne, Lafarge Stéphane, Le Gouis Jacques, Charmet Gilles. 2018. Field Crops Research, 216 : 32-41.

The structure and function of the global citrus rhizosphere microbiome. Xu Jin, Zhang Yunzeng, Zhang Pengfan, Trivedi Pankaj, Riera Nadia, Wang Yayu, Liu Xin, Fan Guangyi, Tang Jiliang, Coletta-Filho Helvécio D, Cubero Jaime, Deng Xiaoling, Ancona Veronica, Lu Zhanjun, Zhong Balian, Roper Caroline, Capote Nieves, Catara Vittoria, Pietersen Gerhard, Vernière Christian, Al-Sadi Abdullah M., Li Lei, Yang Fan, Xu Xun, Wang Jian, Yang Huanming, Jin Tao, Wang Nian. 2018. Nature Communications, 9:4894, 10 p.

Comparative genomics of the zoonotic pathogen Ehrlichia chaffeensis reveals candidate type IV effectors and putative host cell targets. Noroy Christophe, Meyer Damien. 2017. Frontiers in Cellular and Infection Microbiology, 6 (204), 15 p.

Deciphering the Theobroma cacao self-incompatibility system: from genomics to diagnostic markers for self-compatibility. Lanaud Claire, Fouet Olivier, Legavre Thierry, Lopes Uilson Vanderlei, Sounigo Olivier, Eyango Marie Claire, Mermaz Benoit, da Silva Marcos Ramos, Loor Solorzano Rey Gaston, Argout Xavier, Gyapay Gabor, Ebaiarrey Herman Ebai, Colonges Kelly, Sanier Christine, Rivallan Ronan, Mastin Géraldine, Cryer Nicholas, Boccara Michel, Verdeil Jean-Luc, Efombagn Mousseni Ives Bruno, Peres Gramacho Karina, Clément Didier. 2017. Journal of Experimental Botany, 68 (17) : 4775-4790.

Development of highly informative genome-wide single sequence repeat markers for breeding applications in sesame and construction of a web resource: SisatBase. Dossa Komivi, Yu Jingyin, Liao Boshou, Cissé Ndiaga, Zhang Xiurong. 2017. Frontiers in Plant Science, 8:1470, 10 p.

Epidémiologie moléculaire des géminivirus responsables de maladies émergentes sur les cultures maraîchères au Burkina Faso. Ouattara Alassane. 2017. Saint-Denis : Université de la Réunion, 292 p. Thèse de doctorat : Sciences : Université de la Réunion

Evolutionary forces affecting synonymous variations in plant genomes. Clément Yves, Sarah Gautier, Holtz Yan, Homa Félix, Pointet Stéphanie, Contreras Sandy, Nabholz Benoit, Sabot François, Sauné Laure, Ardisson Morgane, Bacilieri Roberto, Besnard Guillaume, Berger Angélique, Cardi Céline, De Bellis Fabien, Fouet Olivier, Jourda Cyril, Khadari Bouchaib, Lanaud Claire, Leroy Thierry, Pot David, Sauvage Christopher, Scarcelli Nora, Tregear James, Vigouroux Yves, Yahiaoui Nabila, Ruiz Manuel, Santoni Sylvain, Labouisse Jean-Pierre, Pham Jean Louis, David Jacques, Glemin Sylvain. 2017. PLoS Genetics, 13 (5):e1006799, 28 p.

Experimental evaluation of faecal Escherichia coli and hepatitis E virus as biological indicators of contacts between domestic pigs and Eurasian wild boar. Barth S., Geue L., Hinsching A., Jenckel M., Schlosser J., Eiden Martin, Pietschmann J., Menge Christian, Beer Martin, Groschup Martin, Jori Ferran, Etter Eric, Blome S.. 2017. Transboundary and Emerging Diseases, 64 (2) : 487-494.

Functional genes of microorganisms, comprehending the dynamics of agricultural ecosystems. Reali Catiusca, Pilz Júnior Harry Luiz, Meile Jean-Christophe, Shorr Galindo Sabine, Fiuza Lidia Mariana. 2017. Brazilian Archives of Biology and Technology, 60:e17160370, 18 p.

Genome sequencing of the sweetpotato whitefly Bemisia tabaci MED/Q. Xie Wen, Chen Chunhai, Yang Zezhong, Guo Litao, Yang Xin, Wang Dan, Chen Ming, Huang Jinqun, Wen Yanan, Zeng Yang, Liu Yating, Xia Jixing, Tian Lixia, Cui Hongying, Wu Qingjun, Wang Shaoli, Wu Baoyun, Li Xianchiun, Tan Xinqiu, Ghanim Murad, Qiu Baoli, Pan Huipeng, Chu Dong, Delatte Hélène, Maruthi M.N., Ge Feng, Zhou Xueping, Wang Xiaowei, Wan Fang-Hao, Du Yuzhou, Luo Chen, Yan Fengming, Preisser Evan L., Jiao Xiaoguo, Coates Brad S., Zhao Jinyang, Gao Qiang, Xia Jinquan, Yin Ye, Liu Yong, Brown Judith, Zhou Xuguo-Joe, Zhang Youjun. 2017. GigaScience, 6 (5), 7 p.

Genomic preselection with genotyping-bysequencing increases performance of commercial oil palm hybrid crosses. Cros David, Bocs Stéphanie, Riou Virginie, Ortega Abboud Enrique, Tisne Sébastien, Argout Xavier, Pomies Virginie, Nodichao Leifi, Lubis Zulkifli, Cochard Benoît, Durand-Gasselin Tristan. 2017. BMC Genomics, 18:839, 17 p.

Genotypic, size and morphological diversity of virioplankton in a deep oligomesotrophic freshwater lake (Lac Pavin, France). Colombet Jonathan, Robin Agnès, Sime-Ngando Télesphore. 2017. Journal of Environmental Sciences, 53 : 48-59.

Improving transcriptome de novo assembly by using a reference genome of a related species: Translational genomics from oil palm to coconut. Armero Villanueva Alix Augusto, Baudouin Luc, Bocs Stéphanie, This Dominique. 2017. PloS One, 12 (3):e0173300, 22 p.

Las biotecnologías como impulsadoras de la producción de aceite de palma sostenible. Rival Alain. 2017. Palmas, 37, n.spéc. Tomo 1 : 175-182.

Molecular genetics and breeding. Soh Aik Chin, Mayes Sean, Roberts Jeremy, Zaki Noorhariza Mohd, Madon Maria, Schwarzacher Trude, Heslop-Harrison Pat, Ithnin Maizura Bint, Din Amiruddin Mohd, Ramli Umi Salamah, Othman Abrizah, Zulkifli Yaakub, Low Eng Ti Leslie, Ong-Abdullah Meilina, Singh Rajinder, Teh Chee Keng, Kwong Qi Bin, Ong Ail Ling, Mohamed Mohaimi, Apparow Sukganah, Chew Fook Tim, Appleton David Ross, Kulaveerasingam Harikrishna, Teh Huey Fang, Mebus Katharina, Neoh Bee Keat, Ooi Tony Eng Keong, Wong Yick Ching, Cros David. 2017. In : Oil palm breeding : genetics and genomics. Soh Aik Chin (ed.), Mayes Sean (ed.) , Roberts Jeremy A. (ed.). Boca Raton : CRC Press, 225-281. ISBN 978-1-4987-1544-7

Occurrence of a novel mastrevirus in sugarcane germplasm collections in Florida, Guadeloupe and Réunion. Boukari Wardatou, Alcala-Briseño Ricardo I., Kraberger Simona, Fernandez Emmanuel, Filloux Denis, Daugrois Jean-Heinrich, Comstock Jack C., Lett Jean-Michel, Martin Darren Patrick, Varsani Arvind, Roumagnac Philippe, Polston Jane E., Rott Philippe. 2017. Virology Journal, 14:146, 8 p.

QTL mapping and candidate gene analysis of ferrous iron and zinc toxicity tolerance at seedling stage in rice by genome-wide association study. Zhang Jian, Chen Kay, Pang Yunlong, Naveed Shahzad Amir, Zhao Xiuqin, Wang Xiaoqian, Wang Yun, Dingkuhn Michael, Pasuquin Julie, Li Zhikang, Xu Jianlong. 2017. BMC Genomics, 18 (1):828, 15 p.

Two novel Alphaflexiviridae members revealed by deep sequencing of the Vanilla (Orchidaceae) virome. Grisoni Michel, Marais Armelle, Filloux Denis, Saison Anne, Faure Chantal, Julian Charlotte, Theil Sébastien, Contreras Sandy, Teycheney Pierre-Yves, Roumagnac Philippe, Candresse Thierry. 2017. Archives of Virology, 162 (12) : 3855-3861.

A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives. Sarah Gautier, Homa Félix, Pointet Stéphanie, Contreras Sandy, Sabot François, Nabholz Benoit, Santoni Sylvain, Sauné Laure, Ardisson Morgane, Chantret Nathalie, Sauvage Christopher, Tregear James, Jourda Cyril, Pot David, Vigouroux Yves, Chaïr Hâna, Scarcelli Nora, Billot Claire, Yahiaoui Nabila, Bacilieri Roberto, Khadari Bouchaib, Boccara Michel, Barnaud Adeline, Péros Jean-Pierre, Labouisse Jean-Pierre, Pham Jean Louis, David Jacques, Glemin Sylvain, Ruiz Manuel. 2017. Molecular Ecology Resources, 17 (3) : 565-580.

Applications of metagenomics to fermented foods. Bigot Céline, Meile Jean-Christophe, Remize Fabienne, Strub Caroline. 2016. In : Fermented foods. Part I: biochemistry and biotechnology. Montet Didier (ed.), Ray Ramesh C. (ed.). Boca Raton : CRC Press, 333-346. (Food Biology Series) ISBN 978-1-4987-4079-1

DArT whole genome profiling provides insights on the evolution and taxonomy of edible Banana (Musa spp.). Sardos Julie, Perrier Xavier, Dolezel Jaroslav, Hribova Eva, Christelová Pavla, Van Den Houwe Ines, Kilian Andrzej, Roux Nicolas. 2016. Annals of Botany, 118 (7) : 1269-1278.

Distribution patterns of microbial communities in ultramafic landscape: A metagenetic approach highlights the strong relationships between diversity and environmental traits. Bordez Laurent, Jourand Philippe, Ducousso Marc, Carriconde Fabian, Cavaloc Yvon, Santini Sébastien, Claverie Jean-Michel, Wantiez L., Leveau Antoine, Amir Hamid. 2016. Molecular Ecology, 25 (10) : 2258-2272.

Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae. Islam M. Totazzal, Croll Daniel, Gladieux Pierre, Soanes Darren M., Persoons Antoine, Bhattacharjee Pallab, Hossain Md. Shaid, Gupta Dipali Rani, Rahman Md Mahbubur, Mahboob M. Golam, Cook Nicola, Salam Moin U., Surovy Musrat Zahan, Sancho Vanessa Bueno, Maciel João Leodato Nunes, NhaniJúnior Antonio, Castroagudín Vanina Lilián, de Assis Reges Juliana T., Ceresini Paulo Cezar, Ravel Sébastien, Kellner Ronny, Fournier Elisabeth, Tharreau Didier, Lebrun Marc-Henri, McDonald Bruce A., Stitt Timothy, Swan Daniel, Talbot Nicholas J., Saunders Diane G.O., Win Joe, Kamoun Sophien. 2016. BMC Biology, 14 (84), 11 p.

Evaluation of hierarchical models for integrative genomic analyses. Denis Marie, Tadesse Mahlet. 2016. Bioinformatics, 32 (5) : 738-746.

Expression profiles, characterization and function of HbTCTP in rubber tree (Hevea brasiliensis). Deng Zhi, Chen Jiangshu, Leclercq Julie, Zhou Zhuangzhi, Liu Changren, Liu Hui, Yang Hong, Montoro Pascal, Xia Zhihui, Li Dejun. 2016. Frontiers in Plant Science, 7 (789), 10 p.

Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species. Prior Philippe, Ailloud Florent, Dalsing Beth, Remenant Benoit, Sanchez Borja, Allen Caitilyn. 2016. BMC Genomics, 17 (1), 11 p.

High-quality draft genome sequences of two Xanthomonas pathotype strains infecting aroid plants. Robène Isabelle, Bolot Stéphanie, Pruvost Olivier, Arlat Mathieu, Noel Laurent D., Carrère Sébastien, Jacques Marie Agnès, Koebnik Ralf, Gagnevin Lionel. 2016. Genome Announcements, 4 (5):e00902-16, 2 p.

Le riz, une plante modèle à croquer. Cunnac Sébastien, Gantet Pascal, Ghesquière Alain, Guiderdoni Emmanuel, Trung Luu Doan. 2016. Biofutur (380) : 30-34.

Modeling additive and non-additive effects in a hybrid population using genome-wide genotyping: Prediction accuracy implications. Bouvet Jean-Marc, Makouanzi Garel, Cros David, Vigneron Philippe. 2016. Heredity, 116 : 146-157.

Multivariate genomic model improves analysis of oil palm (Elaeis guineensis Jacq.) progeny tests. Marchal Alexandre, Legarra Andrés, Tisne Sébastien, Carasco-Lacombe Catherine, Manez Aurore, Suryana Edyana, Omoré Alphonse, Nouy Bruno, Durand-Gasselin Tristan, Sanchez Leopoldo, Bouvet Jean-Marc, Cros David. 2016. Molecular Breeding, 36 (1):2, 13 p.

Placental genetic variations in circadian clock-related genes increase the risk of placental abruption. Qiu Chunfang, Gelaye Bizu, Denis Marie, Tadesse Mahlet G., Enquobahrie Daniel A., Ananth Cande V., Pacora Percy N., Salazar Manuel, Sanchez Sixto E., Williams Michelle A.. 2016. International Journal of Molecular Epidemiology and Genetics, 7 (1) : 32-40.

The South Green portal: A comprehensive resource for tropical and Mediterranean crop genomics. Guignon Valentin, Hueber Yann, Rouard Mathieu, Bocs Stéphanie, Couvin David, De Lamotte Frédéric, Droc Gaëtan, Dufayard Jean François, El Hassouni Nordine, Farcy Cédric, Gkanogiannis Anestis, Hamelin Chantal, Larivière Delphine, Martin Guillaume, Ortega Enrique, Pitollat Bertrand, Pointet Stéphanie, Ruiz Manuel, Gautier Sarah, Summo Marilyne, This Dominique, Ravel Sébastien, Larmande Pierre, Monat Cécile, Sabot François, Tando Ndomassi, Tranchant-Dubreuil Christine, Sempere Guilhem, Dereeper Alexis. 2016. Current Plant Biology, 7-8 : 6-9.

Subtelomere organization in the genome of the microsporidian Encephalitozoon cuniculi: Patterns of repeated sequences and physicochemical signatures. Dia Ndongo, Lavie Laurence, Faye Ngor, Méténier Guy, Yeramian Edouard, Duroure Christophe, Toguebaye B.S., Frutos Roger, Niang Mbayame N., Vivares Christian, Ben Mamoun Choukri, Cornillot Emmanuel. 2016. BMC Genomics, 17 (34), 20 p.

Using ecology, physiology, and genomics to understand host specificity in Xanthomonas. Jacques Marie Agnès, Arlat Mathieu, Boulanger Alice, Boureau Tristan, Carrère Sébastien, Cesbron Sophie, Chen Nicolas W.G., Cociancich Stéphane, Darrasse Armelle, Denancé Nicolas, Fischer-Le-Caux Marion, Gagnevin Lionel, Koebnik Ralf, Lauber Emmanuelle, Noel Laurent D., Pieretti Isabelle, Portier Perrine, Pruvost Olivier, Rieux Adrien, Robène Isabelle, Royer Monique, Szurek Boris, Verdier Valérie, Vernière Christian. 2016. Annual Review of Phytopathology, 54 : 163-187.

Whole genome expression and hydraulic architecture of diploid and doubled diploid citrus seedlings in intra and interspecific contexts. de Souza Joadson Dutra, Rodrigues Valérie, Barigah Têté Sévérien, Ollitrault Patrick, Da Silva Gesteira Abelmon, Morillon Raphaël. 2016. Citrus Research and Technology, 37 (2) : 206-210.

Whole-genome sequences of Xanthomonas euvesicatoria strains clarify taxonomy and reveal a stepwise erosion of type 3 effectors. Barak Jeri D., Vancheva Taca, Lefeuvre Pierre, Jones Jeffrey B., Timilsina Sujan, Minsavage Gerald V., Vallad Gary E., Koebnik Ralf. 2016. Frontiers in Plant Science, 7 (1805), 12 p.

The rubber tree genome reveals new insights into rubber production and species adaptation. Tang Chaorong, Yang Meng, Fang Yongjun, Luo Yingfeng, Gao Shenghan, Xiao Xiaohu, An Zewei, Zhou Binhui, Zhang Bing, Tan Xinyu, Yeang Hoong Yeet, Qin Yunxia, Yang Jianghua, Lin Qiang, Mei Hailiang, Montoro Pascal, Long Xiangyu, Qi Jiyan, Hua Yuwei, He Zilong, Sun Min, Li Wenjie, Zeng Xia, Cheng Han, Liu Ying, Yang Jin, Tian Weimin, Zhuang Nansheng, Zeng Rizhong, Li Dejun, He Peng, Li Zhe, Zou Zhi, Li Shuangli, Li Chenji, Wang Jixiang, Wei Dong, Lai Chao-Qiang, Luo Wei, Yu Jun, Hu Songnian, Huang Huasun. 2016. Nature Plants, 10 p.

A unified and comprehensible view of parametric and kernel methods for genomic prediction with application to rice. Jacquin Laval, Cao Tuong-Vi, Ahmadi Nourollah. 2016. Frontiers in Genetics, 7 (145), 16 p.

Assessment of genetic and epigenetic changes during cell culture ageing and relations with somaclonal variation in Coffea arabica. Bobadilla Landey Roberto, Cenci Alberto, Guyot Romain, Bertrand Benoît, Georget Frederic, Dechamp Eveline, Herrera Juan Carlos, Aribi Jamel, Lashermes Philippe, Etienne Hervé. 2015. Plant Cell, Tissue and Organ Culture, 122 (3) : 517-531.

Clade- and species-specific features of genome evolution in the Saccharomycetaceae. Wolfe Kenneth H., Armisén David, Proux-Wera Estelle, ÓhÉigeartaigh Seán S., Azam Haleema, Gordon Jonathan, Byrne Kevin P.. 2015. FEMS Yeast Research, 15 (5), 12 p.

Comparative genomic analysis of Ralstonia solanacearum reveals candidate genes for host specificity. Ailloud Florent, Lowe Tiffany, Cellier Gilles, Roche David, Allen Caitilyn, Prior Philippe. 2015. BMC Genomics, 16 (270), 11 p.

DHOEM: a statistical simulation software for simulating new markers in real SNP marker data. Jacquin Laval, Cao Tuong-Vi, Grenier Cécile, Ahmadi Nourollah. 2015. BMC Bioinformatics, 16 (404), 8 p.

Development of a 63K SNP array for cotton and high-density mapping of intraspecific and interspecific populations of Gossypium spp. Hulse-Kemp Amanda M., Lemm Jana, Plieske Joerg, Ashrafi Hamid, Buyyarapu Ramesh, Fang David D., Frelichowski James, Giband Marc, Hague Steve, Hinze Lori L., Kochan Kelli J., Riggs Penny K., Scheffler Jodi, Udall Joshua, Ulloa Mauricio, Wang Shirley S., Zhu Qian-Hao, Bag Sumit K., Bhardwaj Archana, Burke John, Byers Robert L., Claverie Michel, Gore Michael A., Harker David B., Islam Md S., Jenkins Johnie N., Jones Don C., Lacape Jean-Marc, Llewellyn Danny, Percy Richard, Pepper Alan, Poland Jesse A., Mohan Rai Krishan, Sawant Samir V., Singh Sunil Kumar, Spriggs Andrew, Taylor Jen M., Wang Fei, Yourstone Scott M., Zheng Xiuting, Lawley Cindy T., Ganal Martin W., Van Deynze Allen, Wilson Iain W., Stelly David M.. 2015. G3 - Genes Genomes Genetics, 5 (6) : 1187-1209.

Draft genome sequence of an alphaproteobacterium associated with the Mediterranean sponge Oscarella lobularis. Jourda Cyril, Santini Sébastien, Rocher Caroline, Le Bivic André, Claverie Jean-Michel. 2015. Genome Announcements, 3 (5):e00977-15, 2 p.

Genomic selection prediction accuracy in a perennial crop: case study of oil palm (Elaeis guineensis Jacq.). Cros David, Denis Marie, Sanchez Leopoldo, Cochard Benoît, Flori Albert, Durand-Gasselin Tristan, Nouy Bruno, Omoré Alphonse, Pomies Virginie, Riou Virginie, Suryana Edyana, Bouvet Jean-Marc. 2015. Theoretical and Applied Genetics, 128 (3) : 397-410.

Genomics and transcriptomics of Xanthomonas campestris species challenge the concept of core type III effectome. Roux Brice, Bolot Stéphanie, Guy Endrick, Denancé Nicolas, Lautier Martine, Jardinaud Marie-Françoise, Fischer-Le-Caux Marion, Portier Perrine, Jacques Marie Agnès, Gagnevin Lionel, Pruvost Olivier, Lauber Emmanuelle, Arlat Mathieu, Carrère Sébastien, Koebnik Ralf, Noel Laurent D.. 2015. BMC Genomics, 16 (975), 19 p.

Identification of novel Bromus- and Trifolium-associated circular DNA viruses. Kraberger Simona, Farkas Kata, Bernardo Pauline, Booker Cameron, Argüello-Astorga Gerardo, Mesleard François, Martin Darren Patrick, Roumagnac Philippe, Varsani Arvind. 2015. Archives of Virology, 160 (5) : 1303-1311.

Long-term genomic selection for heterosis without dominance in multiplicative traits: Case study of bunch production in oil palm. Cros David, Denis Marie, Bouvet Jean-Marc, Sanchez Leopoldo. 2015. BMC Genomics, 16 (651), 16 p.

Next generation variety development for sustainable production of arabica coffee (Coffea arabica L.): A review. van der Vossen Herbert, Bertrand Benoît, Charrier André. 2015. Euphytica, 204 (2) : 243-256.

Nuclear species-diagnostic SNP markers mined from 454 amplicon sequencing reveal admixture genomic structure of modern Citrus varieties. Curk Franck, Ancillo Gema, Ollitrault Frédérique, Perrier Xavier, Jacquemoud-Collet Jean-Pierre, Garcia-Lor Andrés, Navarro Luis, Ollitrault Patrick. 2015. PloS One, 10 (5):e0125628, 25 p.

Spots on pot: Comparative genomics of two cannabis pathogens reveals insight into the evolution of Xanthomonas pathogenicity. Jacobs Jonathan M., Pesce Céline, Lefeuvre Pierre, Koebnik Ralf. 2015. Phytopathology, 105 (11S), Résumé : S4.64. 2015 APS Annual Meeting, Pasadena, États-Unis, 1 Août 2015/5 Août 2015.

U6 snRNA pseudogenes: Markers of retrotransposition dynamics in mammals. Doucet Aurélien, Droc Gaëtan, Siol Olivier, Audoux Jérôme, Gilbert Nicolas. 2015. Molecular Biology and Evolution, 32 (7) : 1815-1832.

Visacane: An innovative quarantine tool for the exchange of pest and disease-free sugarcane germplasm. Guinet-Brial Isabelle, Girard Jean-Claude, Roumagnac Philippe, Daugrois Jean-Heinrich, Fernandez Emmanuel, Rott Philippe. 2015. International Sugar Journal : 890-896.

The coffee genome hub: a resource for coffee genomes. Dereeper Alexis, Bocs Stéphanie, Rouard Mathieu, Guignon Valentin, Ravel Sébastien, Tranchant-Dubreuil Christine, Poncet Valérie, Garsmeur Olivier, Lashermes Philippe, Droc Gaëtan. 2015. Nucleic Acids Research, 43 (D1), D1028-D1035

The genome sequence of the orchid Phalaenopsis equestris. Cai Jing, Vanneste Kevin, Proost Sebastian, Tsai Wen-Chieh, Liu Ke-Wei, Chen Li-Jun, He Ying, Xu Qing, Bian Chao, Zheng Zhijun, Sun Fengming, Liu Weiqing, Hsiao Yu-Yun, Pan Zhao-Jun, Hsu Chia-Chi, Yang Ya-Ping, Hsu Yi-Chin, Chuang Yu-Chen, Diévart Anne, Dufayard Jean-François, Xu Xun, Wang Juhui, Wang Jung, Xiao Xin-Ju, Zhao Xue-Min, Du Rong, Zhang Guo-Qiang, Wang Meina, Su Yong-Yu, Xie Gao-Chang, Liu Guo-Hui, Li Li-Qiang, Huang Lai-Qiang, Luo Yi-Bo, Chen Hong-Hwa, Van de Peer Yves, Liu Zhong-Jian. 2015. Nature Genetics, 47 (1) : 65-74.

Etude des facteurs contrôlant l'efficacité de la sélection génomique chez le palmier à huile (Elaeis guineensis Jacq.). Cros David. 2014. Montpellier : Montpellier SupAgro, 204 p. Thèse de doctorat : Systèmes intégrés en biologie, agronomie, géosciences, hydrosciences, environnement (SIBAGHE). Biologie intégrative des plantes (BIP) : Montpellier SupAgro Centre international d'études supérieures en sciences agronomiques

Placental genome and maternal-placental genetic interactions: A genome-wide and candidate gene association study of placental abruption. Denis Marie, Salazar M., Williams M.A., Enquobahrie Daniel A., Tadesse Mahlet G., Sanchez Sixto E., Ananth Cande V.. 2014. PloS One, 9 (12):e116346, 24 p.

Reference-free population genomics from next-generation transcriptome data and the vertebrate–invertebrate gap. Gayral Philippe, Melo-Ferreira José, Glemin Sylvain, Bierne Nicolas, Carneiro Miguel, Nabholz Benoit, Lourenco Joao M., Alves Paulo, Ballenghien Marion, Faivre Nicolas, Belkhir Khalid, Cahais Vincent, Loire Etienne, Bernard Aurélien, Galtier Nicolas. 2013. PLoS Genetics, 9 (4):e1003457, 15 p.

Sélection assistée par marqueurs pour l'amélioration variétale de la canne à sucre : diversité génétique et phénotypique du germplasm cultivé, association mapping et sélection génomique. Gouy Matthieu. 2013. Saint Denis : Université de la Réunion, 179 p. Thèse de doctorat : Sciences : Université de la Réunion

What the genomics of arbuscular mycorrhizal symbiosis teaches us about root development. Formey Damien, Jourda Cyril, Roux Christophe, Delaux Pierre-Marc. 2013. In : Root Genomics and Soil Interactions. Crespi Martin (ed.). Oxford : Wiley-Blackwell, 171-188. ISBN 978-0-4709-6043-1

Matita, a new retroelement from peanut : Characterization and evolutionary context in the light of the Arachis A-B genome divergence. Nielen Stephan, Vidigal Bruna S., Leal-Bertioli Soraya C.M., Ratnaparkhe Milind B., Paterson Andrew H., Garsmeur Olivier, D'Hont Angélique, Guimarães Patricia Messenberg, Bertioli David J.. 2012. Molecular Genetics and Genomics, 287 (1) : 21-38.

A genetic map of pineapple (Ananas comosus (L.) Merr.) including SCAR, CAPS, SSR and EST-SSR markers. Carlier Jorge Dias, Sousa Nelson Horta, Santo Tatiana Espirito, Coppens D'Eeckenbrugge Géo, Leitão José Manuel. 2012. Molecular Breeding, 29 (1) : 245-260.

Genomic approach to study floral development genes in Rosa sp. Dubois Annick, Remay Arnaud, Raymond Olivier, Balzergue Sandrine, Chauvet Aurélie, Maene Marion, Pecrix Yann, Yang Shu-Hua, Jeauffre julien, Thouroude Tatiana, Boltz Véronique, Martin-Magniette Marie-Laure, Janczarski Stéphane, Legeai Fabrice, Renou Jean-Pierre, Vergne Philippe, Le Bris Manuel, Foucher Fabrice, Bendahmane Mohammed. 2011. PloS One, 6 (12):e28455, 14 p.

Clonal origin of emerging populations of Ehrlichia ruminantium in Burkina Faso. Adakal Hassane, Gavotte Laurent, Stachurski Frédéric, Konkobo Maurice, Henri Hélène, Zoungrana Sébastien, Huber Karine, Vachiery Nathalie, Martinez Dominique, Morand Serge, Frutos Roger. 2010. Infection, Genetics and Evolution, 10 (7) : 903-912.

Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus). Soler Lucile, Conte Matthew A., Katagiri Takayuki, Howe Aimée E., Lee Bo-Young, Amemiya Chris, Stuart Andrew, Dossat Carole, Poulain Julie, Johnson Jeremy, Di Palma Frederica, Lindblad-Toh Kerstin, Baroiller Jean-François, D'Cotta Helena, Ozouf-Costaz Catherine, Kocher Thomas D.. 2010. BMC Genomics, 11 (636), 8 p.

Etude des déséquilibres de liaison dans une collection de cacaoyers (Theobroma cacao L.) appartenant au groupe Criollo/Trinitario et application au marquage génétique des caractères d'intérêt. Pugh-Moreno Tatiana. 2005. Montpellier : ENSAM, 158 p. Thèse de doctorat : Sciences agronomiques (Amélioration des plantes) : Ecole nationale supérieure agronomique de Montpellier