DIversité - Adaptation - DEveloppement des plantes

2019

Tranchant-Dubreuil C, Rouard M, Sabot F. Plant Pangenome: Impacts On Phenotypes And Evolution. Annual Plant Reviews, Wiley Online Library 2019, ⟨10.1002/9781119312994.apr0664⟩. ⟨hal-02053647⟩

Agnoun, Y., Yelome, I., Sie, M., Albar, L., Ghesquiere, A. & Silue, D. Resistance of selected Oryza glaberrima landraces and their intra-specific breeding lines to Beninese Rice yellow mottle virus isolates. Crop Protection 119, 172–176 (2019).

Atindehou, M., Adeoti, K., Loko, L. E. Y., Beule, T., Paradis, E., Djedatin, G., Tranchant-Dubreuil, C., Sabot, F., Lagnika, L. & Jaligot, E. MooSciTIC: Training of trainers in West African research and higher education. Plos Biology 17, e3000312 (2019).

Bertioli, D. J., Jenkins, J., Clevenger, J., Dudchenko, O., Gao, D., Seijo, G., Leal-Bertioli, S. C. M., Ren, L., Farmer, A. D., Pandey, M. K., Samoluk, S. S., Abernathy, B., Agarwal, G., Ballen-Taborda, C., Cameron, C., Campbell, J., Chavarro, C., Chitikineni, A., Chu, Y., Dash, S., El Baidouri, M., Guo, B., Huang, W., Do Kim, K., Korani, W., Lanciano, S., Lui, C. G., Mirouze, M., Moretzsohn, M. C., Pham, M., Shin, J. H., Shirasawa, K., Sinharoy, S., Sreedasyam, A., Weeks, N. T., Zhang, X., Zheng, Z., Sun, Z., Froenicke, L., Aiden, E. L., Michelmore, R., Varshney, R. K., Holbrook, C. C., Cannon, E. K. S., Scheffler, B. E., Grimwood, J., Ozias-Akins, P., Cannon, S. B., Jackson, S. A. & Schmutz, J. The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nature Genetics 51, 877-+ (2019).

Bethune, K., Mariac, C., Couderc, M., Scarcelli, N., Santoni, S., Ardisson, M., Martin, J.-F., Montufar, R., Klein, V., Sabot, F., Vigouroux, Y. & Couvreur, T. L. R. Long-fragment targeted capture for long-read sequencing of plastomes. Applications in Plant Sciences 7, e1243 (2019).

Juanillas, V., Dereeper, A., Beaume, N., Droc, G., Dizon, J., Mendoza, J. R., Perdon, J. P., Mansueto, L., Triplett, L., Lang, J., Zhou, G., Ratharanjan, K., Plale, B., Haga, J., Leach, J. E., Ruiz, M., Thomson, M., Alexandrov, N., Larmande, P., Kretzschmar, T. & Mauleon, R. P. Rice Galaxy: an open resource for plant science. Gigascience 8, giz028 (2019).

Merot-L’anthoene, V., Tournebize, R., Darracq, O., et al. (2019) Development and evaluation of a genome-wide Coffee 8.5K SNP array and its application for high-density genetic mapping and for investigating the origin of Coffea arabica L. PLANT BIOTECHNOLOGY JOURNAL, 17, 1418–1430.

Scheben, A., Chan, C.-K. K., Mansueto, L., Mauleon, R., Larmande, P., Alexandrov, N., Wing, R. A., McNally, K. L., Quesneville, H. & Edwards, D. Progress in single-access information systems for wheat and rice crop improvement. Briefings in Bioinformatics 20, 565–571 (2019).

Sempere, G., Petel, A., Rouard, M., Frouin, J., Hueber, Y., De Bellis, F. & Larmande, P. Gigwa v2-Extended and improved genotype investigator. Gigascience 8, giz051 (2019).

 

Larmande P, Huy Do, Yue Wang. OryzaGP: rice gene and protein dataset for named-entity recognition. Genomics Inform. 2019;17(2):e17. Published online June 26, 2019. 

Abbeloos R, Backlund JE, Basterrechea Salido M, Bauchet .... Larmande P, .... Muller. M. BrAPI - an Application Programming Interface for Plant Breeding Applications. Bioinformatics. 2019 Mar 23. pii: btz190. 

Yaw Nti-Addae, Dave Matthews, Victor Jun Ulat, Raza Syed, Guilhem Sempere, Adrien Petel, Jon Renner, Pierre Larmande, Valentin Guignon, Elizabeth Jones, Kelly Robbins. Benchmarking Database Systems for Genomic Selection Implementation. Database, Volume 2019, 2019, baz096.

Gnacadja, C., Berthouly-Salazar, C., Nourou Sall, S.N., Zekraoui, L., Sabot, F., Pegalepo, E., Manneh, B., Vieira-Dalode, G., Moreira, J., Soumanou, M.M., Azokpota, P., and Sie, M. 2018. Caractérisation phénotypique et génétique du riz africain (Oryza glaberrima Steud). International Journal of Advanced Research 6(2): 1389-1398

 

 

2018

 

Barckmann, B., El-Barouk, M., Pelisson, A., Mugat, B., Li, B., Franckhauser, C., Lavier, A.-S. F., Mirouze, M., Fablet, M. & Chambeyron, S. The somatic piRNA pathway controls germline transposition over generations. Nucleic Acids Research 46, 9524–9536 (2018).

 

Cubry, P., Tranchant-Dubreuil, C., Thuillet, A.-C., Monat, C., Ndjiondjop, M.-N., Labadie, K., Cruaud, C., Engelen, S., Scarcelli, N., Rhone, B., Burgarella, C., Dupuy, C., Larmande, P., Wincker, P., Francois, O., Sabot, F. & Vigouroux, Y. The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes. Current Biology 28, 2274-+ (2018).

 

Esposito, S., Aversano, R., D’Amelia, V., Villano, C., Alioto, D., Mirouze, M. & Carputo, D. Dicer-like and RNA-dependent RNA polymerase gene family identification and annotation in the cultivated Solanum tuberosum and its wild relative S-commersonii. Planta 248, 729–743 (2018).

 

Gallusci, P., Bucher, E. & Mirouze, M. in Plant Epigenetics Coming of Age for Breeding Applications (eds. Mirouze, M., Bucher, E. & Gallusci, P.) 88, XV–XVIII (2018).

 

Harper, L., Campbell, J., Cannon, E. K. S., Jung, S., Poelchau, M., Walls, R., Andorf, C., Arnaud, E., Berardini, T. Z., Birkett, C., Cannon, S., Carson, J., Condon, B., Cooper, L., Dunn, N., Elsik, C. G., Farmer, A., Ficklin, S. P., Grant, D., Grau, E., Herndon, N., Hu, Z.-L., Humann, J., Jaiswal, P., Jonquet, C., Laporte, M.-A., Larmande, P., Lazo, G., McCarthy, F., Menda, N., Mungall, C. J., Munoz-Torres, M. C., Naithani, S., Nelson, R., Nesdill, D., Park, C., Reecy, J., Reiser, L., Sanderson, L.-A., Sen, T. Z., Staton, M., Subramaniam, S., Tello-Ruiz, M. K., Unda, V., Unni, D., Wang, L., Ware, D., Wegrzyn, J., Williams, J., Woodhouse, M., Yu, J. & Main, D. AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database-the Journal of Biological Databases and Curation bay088 (2018). doi:10.1093/database/bay088

 

Hebrard, E., Pinel-Galzi, A., Oludare, A., Poulicard, N., Aribi, J., Fabre, S., Issaka, S., Mariac, C., Dereeper, A., Albar, L., Silue, D. & Fargette, D. Identification of a Hypervirulent Pathotype of Rice yellow mottle virus: A Threat to Genetic Resistance Deployment in West-Central Africa. Phytopathology 108, 299–307 (2018).

 

Jonquet, C., Toulet, A., Arnaud, E., Aubin, S., Yeumo, E. D., Emonet, V., Graybeal, J., Laporte, M.-A., Musen, M. A., Pesce, V. & Larmande, P. AgroPortal: A vocabulary and ontology repository for agronomy. Computers and Electronics in Agriculture 144, 126–143 (2018).

 

Lanciano, S. & Mirouze, M. Transposable elements: all mobile, all different, some stress responsive, some adaptive? Current Opinion in Genetics & Development 49, 106–114 (2018).

 

Oltehua-Lopez, O., Dorantes-Acosta, A. E., Ingouff, M., Lanciano, S., Leblanc, O., Grimanelli, D., Mirouze, M. & Arteaga-Vazquez, M. A. in Plant Epigenetics Coming of Age for Breeding Applications (eds. Mirouze, M., Bucher, E. & Gallusci, P.) 88, 361–386 (2018).

 

Phan, N. T., De Waele, D., Lorieux, M., Xiong, L. & Bellafiore, S. A Hypersensitivity-Like Response to Meloidogyne graminicola in Rice (Oryza sativa). Phytopathology 108, 521–528 (2018).

 

Pinel-Galzi, A., Hebrard, E., Traore, O., Silue, D. & Albar, L. Protocol for RYMV Inoculation and Resistance Evaluation in Rice Seedlings. Bio-Protocol 8, e2863 (2018).

 

Poirier, E. Z., Goic, B., Tome-Poderti, L., Frangeul, L., Boussier, J., Gausson, V., Blanc, H., Vallet, T., Loyd, H., Levi, L. I., Lanciano, S., Baron, C., Merkling, S. H., Lambrechts, L., Mirouze, M., Carpenter, S., Vignuzzi, M. & Saleh, M.-C. Dicer-2-Dependent Generation of Viral DNA from Defective Genomes of RNA Viruses Modulates Antiviral Immunity in Insects. Cell Host & Microbe 23, 353-+ (2018).

 

Sow, M. D., Le Gac, A., Lafon-Placette, C., Delaunay, A., Le Jan, I., Fichot, R., Maury, S., Mirouze, M., Lanciano, S., Tost, J., Segura, V., Chaparro, C., Grunau, C., Allona, I., Le Provost, G., Plomion, C., Salse, J., Ambroise, C., Gribkova, S. & Strauss, S. H. Clarifying the role of DNA methylation in tree phenotypic plasticity. Febs Open Bio 8, 138–138 (2018).

 

Venkatesan, A., Ngompe, G. T., El Hassouni, N., Chentli, I., Guignon, V., Jonquet, C., Ruiz, M. & Larmande, P. Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy. Plos One 13, e0198270 (2018).

 

 

Jonquet C, Toulet A, Arnaud E, Aubin S, Yeumo ED, Emonet V, Graybeal J, Laporte M-A, Musen MA, Pesce V, Larmande P (2018) AgroPortal: A vocabulary and ontology repository for agronomy. Computers and Electronics in Agriculture 144:126–143. doi: https://doi.org/10.1016/j.compag.2017.10.012

Pinel-Galzi A, Hébrard E, Traoré O, Silué D, Albar L (2018) Protocol for RYMV Inoculation and Resistance Evaluation in Rice Seedlings. Bio-protocol 8:1–13. doi: 10.21769/BioProtoc.2863

Scheben A, Chan C-KK, Mansueto L, Mauleon R, Larmande P, Alexandrov N, Wing RA, McNally KL, Quesneville H, Edwards D (2018) Progress in single-access information systems for wheat and rice crop improvement. Briefings in Bioinformatics bby016-bby016.

 

2017

Clément Y, Sarah G, Holtz Y, Homa F, Pointet S, Contreras S, Nabholz B, Sabot F, Sauné L, Ardisson M, et al (2017) Evolutionary forces affecting synonymous variations in plant genomes. PLOS Genetics 13:1–28. doi: 10.1371/journal.pgen.1006799

Cohen-Boulakia S, Belhajjame K, Collin O, Chopard J, Froidevaux C, Gaignard A, Hinsen K, Larmande P, Le Brass Y, Lemoine F, Mareuil F, Menager H, Pradal C, Blanchet C (2017) Scientific workflows for computational reproducibility in the life sciences : status, challenges and opportunities. Future Generation Computer Systems : the International Journal of E-science 75:284–298. doi: 10.1016/j.future.2017.01.012

Djedatin G, Monat C, Engelen S, Sabot F (2017) DuplicationDetector, a light weight tool for duplication detection using NGS data. Current Plant Biology 9–10:23–28. doi: 10.1016/j.cpb.2017.07.001

Dzale Yeumo E, Alaux M, Arnaud E, Aubin S, Baumann U, Buche P, Cooper L, Cwiek-Kupczynska H, Davey RP, Fulss RA, et al (2017) Developing data interoperability using standards: A wheat community use case [version 2; referees: 2 approved]. F1000Research. doi: 10.12688/f1000research.12234.1

Fragoso CA, Moreno M, Wang Z, Heffelfinger C, Arbelaez LJ, Aguirre JA, Franco N, Romero LE, Labadie K, Zhao H, Dellaporta SL, Lorieux M (2017) Genetic architecture of a rice nested association mapping population. G3: Genes|Genomes|Genetics. doi: 10.1534/g3.117.041608

Heffelfinger C, Fragoso CA, Lorieux M (2017) Constructing linkage maps in the genomics era with MapDisto 2.0. Bioinformatics 33:2224–2225. doi: 10.1093/bioinformatics/btx177

Lanciano S, Carpentier M-C, Llauro C, Jobet E, Robakowska-Hyzorek D, Lasserre E, Ghesquière A, Panaud O, Mirouze M (2017) Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants. PLOS Genetics 13:1–20. doi: 10.1371/journal.pgen.1006630

Lanciano S, Mirouze M (2017) DNA methylation in rice and relevance for breeding. Epigenomes 1:10. doi:10.3390/epigenomes1020010

Monat C, Pera B, Ndjiondjop M-N, Sow M, Tranchant-Dubreuil C, Bastianelli L, Ghesquière A, Sabot F (2017) De novo assemblies of three Oryza glaberrima accessions provide first insights about pan-genome of African rices. Genome Biology and Evolution 9:1–6. doi: 10.1093/gbe/evw253

Pidon H, Ghesquière A, Chéron S, Issaka S, Hébrard E, Sabot F, Kolade O, Silué D, Albar L (2017) Fine mapping of RYMV3: a new resistance gene to Rice yellow mottle virus from Oryza glaberrima. Theoretical and Applied Genetics 130:807–818. doi: 10.1007/s00122-017-2853-0

Richards CL, Alonso C, Becker C, Bossdorf O, Bucher E, Colome-Tatche M, Durka W, Engelhardt J, Gaspar B, Gogol-Doring A, et al (2017) Ecological plant epigenetics: Evidence from model and non-model species, and the way forward. bioRxiv. doi: 10.1101/130708

Sarah G, Homa F, Pointet S, Contreras S, Sabot F, Nabholz B, Santoni S, Sauné L, Ardisson M, Chantret N, et al (2017) A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives. Molecular Ecology Resources 17:565–580. doi: 10.1111/1755-0998.12587

Thieme M, Lanciano S, Balzergue S, Daccord N, Mirouze M, Bucher E (2017) Inhibition of RNA polymerase II allows controlled mobilisation of retrotransposons for plant breeding. Genome Biology 18:134. doi: 10.1186/s13059-017-1265-4

2016-

Djedatin G, Ndjiondjop M-N, Sanni A, Lorieux M, Verdier V, Ghesquiere A (2016) Identification of novel major and minor QTLs associated with Xanthomonas oryzae pv. oryzae (African strains) resistance in rice (Oryza sativa L.). Rice 9:18. doi: 10.1186/s12284-016-0090-9

Luyen LEN, Tireau A, Venkatesan A, Neveu P, Larmande P (2016) Development of a Knowledge System for Big Data: Case Study to Plant Phenotyping Data. In: Proceedings of the 6th International Conference on Web Intelligence, Mining and Semantics. ACM, New York, NY, USA, p 27:1--27:9

Ogawa S, Valencia MO, Lorieux M, Arbelaez JD, McCouch S, Ishitani M, Selvaraj MG (2016) Identification of QTLs associated with agronomic performance under nitrogen-deficient conditions using chromosome segment substitution lines of a wild rice relative, Oryza rufipogon. Acta Physiologiae Plantarum 38:103. doi: 10.1007/s11738-016-2119-5

Pinel-Galzi A, Dubreuil-Tranchant C, Hébrard E, Mariac C, Ghesquière A, Albar L (2016) Mutations in Rice yellow mottle virus polyprotein P2a involved in RYMV2 gene resistance breakdown. Frontiers in Plant Science 7:1–11. doi: 10.3389/fpls.2016.01779

Rey O, Danchin E, Mirouze M, Loot C, Blanchet S (2016) Adaptation to Global Change: A Transposable Element-Epigenetics Perspective. Trends in Ecology and Evolution 31:514–526. doi: 10.1016/j.tree.2016.03.013

Sempéré G, Philippe F, Dereeper A, Ruiz M, Sarah G, Larmande P (2016) Gigwa—Genotype investigator for genome-wide analyses. GigaScience 5:1–9. doi: 10.1186/s13742-016-0131-8

South Green collaborators (2016) The South Green portal: a comprehensive resource for tropical and Mediterranean crop genomics. Current Plant Biology 7–8:6–9. doi: https://doi.org/10.1016/j.cpb.2016.12.002

2015-

Arbelaez JD, Moreno LT, Singh N, Tung C-W, Maron LG, Ospina Y, Martinez CP, Grenier C, Lorieux M, McCouch S (2015) Development and GBS-genotyping of introgression lines (ILs) using two wild species of rice, O. meridionalis and O. rufipogon, in a common recurrent parent, O. sativa cv. Curinga. MOLECULAR BREEDING. doi: 10.1007/s11032-015-0276-7

Dufey I, Draye X, Lutts S, Lorieux M, Martinez C, Bertin P (2015) Novel QTLs in an interspecific backcross Oryza sativa x Oryza glaberrima for resistance to iron toxicity in rice. EUPHYTICA 204:609–625. doi: 10.1007/s10681-014-1342-7

Duitama J, Silva A, Sanabria Y, Felipe Cruz D, Quintero C, Ballen C, Lorieux M, Scheffler B, Farmer A, Torres E, Oard J, Tohme J (2015) Whole Genome Sequencing of Elite Rice Cultivars as a Comprehensive Information Resource for Marker Assisted Selection. PLOS ONE. doi: 10.1371/journal.pone.0124617

Hutin M, Sabot F, Ghesquiere A, Koebnik R, Szurek B (2015) A knowledge-based molecular screen uncovers a broad-spectrum OsSWEET14 resistance allele to bacterial blight from wild rice. PLANT JOURNAL 84:694–703. doi: 10.1111/tpj.13042

Monat C, Tranchant-Dubreuil C, Kougbeadjo A, Farcy C, Ortega-Abboud E, Amanzougarene S, Ravel S, Agbessi M, Orjuela-Bouniol J, Summo M, Sabot F (2015) TOGGLE: toolbox for generic NGS analyses. BMC BIOINFORMATICS. doi: 10.1186/s12859-015-0795-6

Pariasca-Tanaka J, Lorieux M, He C, McCouch S, Thomson MJ, Wissuwa M (2015) Development of a SNP genotyping panel for detecting polymorphisms in Oryza glaberrima/O. sativa interspecific crosses. EUPHYTICA 201:67–78. doi: 10.1007/s10681-014-1183-4

Rebolledo MC, Dingkuhn M, Courtois B, Gibon Y, Clément-Vidal A, Cruz DF, Duitama J, Lorieux M, Luquet D (2015) Phenotypic and genetic dissection of component traits for early vigour in rice using plant growth modelling, sugar content analyses and association mapping. Journal of Experimental Botany 66:5555–5566. doi: 10.1093/jxb/erv258

Rubin BP, Brockes J, Galliot B, Grossniklaus U, Lobo D, Mainardi M, Mirouze M, Prochiantz A, Steger A (2015) A dynamic architecture of life. F1000Research 1–17. doi: 10.12688/f1000research.7315.1