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Carpentier MC, Manfroi E, Wei FJ, Wu HP, Lasserre E, Llauro C, Debladis E, Akakpo R, Hsing YI, Panaud O. 2019. Retrotranspositional landscape of Asian rice revealed by 3000 genomes.. Nature Communications. 10(1)24.


Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, Chougule K, Gao D, Iwata A, Goicoechea JL, Wei S, Wang J, Liao Y, Wang M, Jacquemin J, Becker C, Kudrna D, Zhang J, Londono CEM, Song X, Lee S, Sanchez P, Zuccolo A, Ammiraju JSS, Talag J, Danowitz A, Rivera LF, Gschwend AR, Noutsos C, Wu CC, Kao SM, Zeng JW, Wei FJ, Zhao Q, Feng Q, El Baidouri M, Carpentier MC, Lasserre E, Cooke R, Rosa Farias DD, da Maia LC, Dos Santos RS, Nyberg KG, McNally KL, Mauleon R, Alexandrov N, Schmutz J, Flowers D, Fan C, Weigel D, Jena KK, Wicker T, Chen M, Han B, Henry R, Hsing YC, Kurata N, de Oliveira AC, Panaud O, Jackson SA, Machado CA, Sanderson MJ, Long M, Ware D, Wing RA.(2018). Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.. Nature Genetics. Jan 22. doi: 10.1038/s41588-018-0040-0.


Debladis E, Llauro C, Carpentier MC, Mirouze M, Panaud O (2017). Detection of active transposable elements in Arabidopsis thaliana using Oxford Nanopore Sequencing technology.. BMC genomics. Jul 17;18(1):537.

Lanciano S, Carpentier MC, 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 Genet. Feb 17;13(2):e1006630.


Wicker T, Yu Y, Haberer G, Mayer KF, Marri PR, Rounsley S, Chen M, Zuccolo A, Panaud O, Wing RA, Roffler S. (2016). DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses. Nat Commun. Sep 7;7:12790.

Panaud O. (2016). Horizontal transfers of transposable elements in eukaryotes: The flying genes. C R Biol. Jul-Aug;339(7-8):296-9.

Casacuberta JM, Jackson S, Panaud O, Purugganan M, Wendel J (2016). Evolution of Plant Phenotypes, from Genomes to Traits. G3 (Bethesda). Feb 11. pii: g3.115.025502.


Copetti D, Zhang J, El Baidouri M, Gao D, Wang J, Barghini E, Cossu RM, Angelova A, Maldonado L CE, Roffler S, Ohyanagi H, Wicker T, Fan C, Zuccolo A, Chen M, Costa de Oliveira A, Han B, Henry R, Hsing YI, Kurata N, Wang W, Jackson SA, Panaud O, Wing RA. BMC Genomics. Jul 22;16:538

El Baidouri M, Kim KD, Abernathy B, Arikit S, Maumus F, Panaud O, Meyers BC, Jackson SA. (2015). A new approach for annotation of transposable elements using small RNA mapping. Nucleic Acid Research. pii: gkv257. [Epub ahead of print].

Finatto T, de Oliveira AC, Chaparro C, da Maia LC, Farias DR, Woyann LG, Mistura CC, Soares-Bresolin AP, Llauro C, Panaud O, Picault N. (2015). Abiotic stress and genome dynamics: specific genes and transposable elements response to iron excess in rice. Rice. 8:13.


Drogue B, Sanguin H, Chamam A, Mozar M, Llauro C, Panaud O, Prigent-Combaret C, Picault N, Wisniewski-Dyé F. (2014). Plant root transcriptome profiling reveals a strain-dependent response during Azospirillum-rice cooperation. Front Plant Sci. 5:607.

Wang M, Yu Y, Haberer G, Marri PR, Fan C, Goicoechea JL, Zuccolo A, Song X, Kudrna D, Ammiraju JS, Cossu RM, Maldonado C, Chen J, Lee S, Sisneros N, de Baynast K, Golser W, Wissotski M, Kim W, Sanchez P, Ndjiondjop MN, Sanni K, Long M, Carney J, Panaud O, Wicker T, Machado CA, Chen M, Mayer KF, Rounsley S, Wing RA. (2014). The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nature Genetics. 46(9):982-8.

Panaud O, Jackson SA, Wendel JF (2014). Drivers and dynamics of diversity in plant genomes. New Phytologist. 202(1):15-8.

El Baidouri M, Carpentier MC, Cooke R, Gao D, Lasserre E, Llauro C, Mirouze M, Picault N, Jackson S, Panaud O (2014). Widespread and frequent horizontal transfers of transposable elements in plants. Genome Research. 24(5):831-8. Access the recommendation on F1000Prime


El Baidouri M, Chaparro C, Panaud O (2013). Use of Next Generation Sequencing (NGS) technologies for the genome-wide detection of transposition. Methods Mol Biol. 1057:265-74.

Collen J, Porcel B, Carré W, Ball SG, Chaparro C, Tonon T, Barbeyron T, Michel G, Noel B, Valentin K, Elias M, Artiguenave F, Arun A, Aury JM, Barbosa-Neto JF, Bothwell JH, Bouget FY, Brillet L, Cabello-Hurtado F, Capella-Gutiérrez S, Charrier B, Cladière L, Cock JM, Coelho SM, Colleoni C, Czjzek M, Da Silva C, Delage L, Denoeud MF, Deschamps P, Dittami SM, Gabaldón T, Gachon CMM, Groisillier A, Hervé C, Jabbari K, Katinka M, Kloareg B, Kowalczyk N, Labadie K, Leblanc C, Lopez PJ, McLachlan DH, Meslet-Cladiere L, Moustafa A, Nehr Z, Collén PN, Panaud O, Partensky F, Poulain J, Rensing SA, Rousvoal S, Samson G, Symeonidi A, Weissenbach J, Zambounis A, Wincker P, Boyen C (2013). Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida. PNAS 110(13):5247-52.

El Baidouri M and Panaud O (2013). Comparative Genomic Paleontology Across Plant Kingdom Reveals The Dynamics Of TE-driven Genome Evolution. Genome Biology and Evolution. 5(5):954-65.


Victoria Fde C, Bervald CM, da Maia LC, de Sousa RO, Panaud O, de Oliveira AC (2012). Phylogenetic relationships and selective pressure on gene families related to iron homeostasis in land plants. Genome. 55(12):883-900.

Ainouche A, Bétermier M, Chandler M, Cordaux R, Cristofari G, Deragon JM, Lesage P, Panaud O, Quesneville H, Vaury C, Vieira C, Vitte C (2012). International Congress on Transposable Elements (ICTE) 2012 in Saint Malo and the sea of TE stories. Mob DNA. 3(1):17.

D'Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, Da Silva C, Jabbari K, Cardi C, Poulain J, Souquet M, Labadie K, Jourda C, Lengellé J, Rodier-Goud M, Alberti A, Bernard M, Correa M, Ayyampalayam S, Mckain MR, Leebens-Mack J, Burgess D, Freeling M, Mbéguié-A-Mbéguié D, Chabannes M, Wicker T, Panaud O, Barbosa J, Hribova E, Heslop-Harrison P, Habas R, Rivallan R, Francois P, Poiron C, Kilian A, Burthia D, Jenny C, Bakry F, Brown S, Guignon V, Kema G, Dita M, Waalwijk C, Joseph S, Dievart A, Jaillon O, Leclercq J, Argout X, Lyons E, Almeida A, Jeridi M, Dolezel J, Roux N, Risterucci AM, Weissenbach J, Ruiz M, Glaszmann JC, Quétier F, Yahiaoui N, Wincker P (2012). The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature. 488(7410):213-7.

Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN, Grimwood J, Jenkins J, Barry K, Lindquist E, Hellsten U, Deshpande S, Wang X, Wu X, Mitros T, Triplett J, Yang X, Ye CY, Mauro-Herrera M, Wang L, Li P, Sharma M, Sharma R, Ronald PC, Panaud O, Kellogg EA, Brutnell TP, Doust AN, Tuskan GA, Rokhsar D, Devos KM (2012). Reference genome sequence of the model plant Setaria. Nature Biotechnology. 30(6):555-61.


Calvayrac C, Martin-Laurent F, Faveaux A, Picault N, Panaud O, Coste C-M, Chaabane H, Cooper J-F (2011). Isolation and characterization of a bacterial strain degrading the herbicide sulcotrione from an agricultural soil. Pest Management Science. 68:340-347.

Sabot F, Picault N, Elbaidouri M, Llauro C, Chaparro C, Piegu B, Roulin A, Guiderdoni E, Delabastide M, McCombie R, Panaud O (2011).Transpositional landscape of rice genome revealed by Paired-End Mapping of high-throughput resequencing data. Plant Journal. 66:241-246.

Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN, Abrouk M, Murat F, Fouet O, Poulain J, Ruiz M, Roguet Y, Rodier-Goud M, Barbosa-Neto JF, Sabot F, Kudrna D, Ammiraju JS, Schuster SC, Carlson JE, Sallet E, Schiex T, Dievart A, Kramer M, Gelley L, Shi Z, Bérard A, Viot C, Boccara M, Risterucci AM, Guignon V, Sabau X, Axtell MJ, Ma Z, Zhang Y, Brown S, Bourge M, Golser W, Song X, Clement D, Rivallan R, Tahi M, Akaza JM, Pitollat B, Gramacho K, D'Hont A, Brunel D, Infante D, Kebe I, Costet P, Wing R, McCombie WR, Guiderdoni E, Quetier F, Panaud O, Wincker P, Bocs S, Lanaud C (2011). The genome of Theobroma cacao. Nature Genetics. 2011 Feb;43(2):101-8.


Shim J, Panaud O, Vitte C, Mendioro MS, Brar DS (2010). RDA derived Oryza minuta-specific clones to probe genomic conservation across Oryza and introgression into rice (O. sativa L.). Euphytica. 176:269-279.

Garavito A, Guyot R, Lozano J, Gavory F, Samain S, Panaud O, Tohme J, Ghesquière A, Lorieux M. (2010). A genetic model for the female sterility barrier between Asian and African cultivated rice species. Genetics. Aug;185(4):1425-40.

Roulin A, Chaparro C, Piegu B, Jackson S and O. Panaud (2010). Paleogenomic Analysis of the Short Arm of Chromosome 3 Reveals the History of the African and Asian Progenitors of Cultivated Rices. Genome Biology and Evolution. 2:132-139.


Petit J, Bourgeois E, Stenger W, Bes M, Droc G, Meynard D, Courtois B, Ghesquiere A, Sabot F, Panaud O and E. Guiderdoni (2009). Diversity of the Ty-1 copia retrotransposon Tos17 in rice (Oryza sativa L.) and the AA genome of the Oryza genus. Molecular Genetics and Genomics. 282(6):633-652.

Picault N, Chaparro C, Piegu B, Stenger W, Formey D, Llauro C, Descombin J, Sabot F, Lasserre E, Meynard D, Guiderdoni E, Panaud O (2009). Identification of an active LTR retrotransposon in rice. Plant journal, 58(5):754-765.

Worden AZ, Lee JH, Mock T, Rouze P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, Foulon E, Grimwood J, Gundlach H, Henrissat B, Napoli C, McDonald SM, Parker MS, Rombauts S, Salamov A, Von Dassow P, Badger JH, Coutinho PM, Demir E, Dubchak I, Gentemann C, Eikrem W, Gready JE, John U, Lanier W, Lindquist EA, Lucas S, Mayer KFX, Moreau H, Not F, Otillar R, Panaud O, Pangilinan J, Paulsen I, Piegu B, Poliakov A, Robbens S, Schmutz J, Toulza E, Wyss T, Zelensky A, Zhou K, Armbrust EV, Bhattacharya D, Goodenough UW, Van de Peer Y and IV Grigoriev IV (2009). Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas. Science. 324(5924):268-272

Roulin A, Piegu B, Fortune PM, Sabot F, D'Hont A, Manicacci D, Panaud O (2009). Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae. BMC Evolutionary Biology. 9(58).

O. Panaud (2008). The molecular bases of cereal domestication and the history of rice. CRAS. 332(2-3):267-272


Fortune PM, Roulin A, Panaud O (2008). Horizontal transfer of transposable elements in plants. Commun Integr Biol. 1(1):74-7.

Deragon JM, Casacuberta JM and Panaud O (2008). Plant transposable elements. Genome Dynamics. 4:69-82

Rice Annotation Project, Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, Kanno M, Kawahara Y, Kawashima H, Kubooka H, Matsuya A, Nakaoka H, Saichi N, Sanbonmatsu R, Sato Y, Shinso Y, Suzuki M, Takeda J, Tanino M, Todokoro F, Yamaguchi K, Yamamoto N, Yamasaki C, Imanishi T, Okido T, Tada M, Ikeo K, Tateno Y, Gojobori T, Lin YC, Wei FJ, Hsing YI, Zhao Q, Han B, Kramer MR, McCombie RW, Lonsdale D, O'Donovan CC, Whitfield EJ, Apweiler R, Koyanagi KO, Khurana JP, Raghuvanshi S, Singh NK, Tyagi AK, Haberer G, Fujisawa M, Hosokawa S, Ito Y, Ikawa H, Shibata M, Yamamoto M, Bruskiewich RM, Hoen DR, Bureau TE, Namiki N, Ohyanagi H, Sakai Y, Nobushima S, Sakata K, Barrero RA, Sato Y, Souvorov A, Smith-White B, Tatusova T, An S, An G, OOta S, Fuks G, Fuks G, Messing J, Christie KR, Lieberherr D, Kim H, Zuccolo A, Wing RA, Nobuta K, Green PJ, Lu C, Meyers BC, Chaparro C, Piegu B, Panaud O, Echeverria M (2008). The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acid Research (Database issue):D1028-33

A. Roulin, B. Piegu and O. Panaud (2008). Evidence of multiple horizontal transfers of the LTR-retrotransposon RIRE1 within the genus Oryza. Plant J. 53(6):950-959.


T.Wicker, F. Sabot, A. Hua-Van, J. Bennetzen, P. Capy, B. Chalhoub, A. Flavell, P. Leroy, M. Morgante, O. Panaud, E. Paux, P. SanMiguel and A. Schulman (2007). A unified classification system for eukaryotic transposable elements. Nature Reviews Genetics, 8(12):973-982.

J.S. Ammiraju, A. Zuccolo, Y. Yu, X. Song, B. Piegu, F. Chevalier, J.G. Walling, J. Ma, J. Talag, D.S. Brar, P.J. Sanmiguel, N. Jiang, S.A. Jackson, O. Panaud and R.A. Wing (2007). Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. Plant Journal. 52(2):342-51.

C. Vitte, O. Panaud, H. Quesneville (2007). LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss. BMC Genomics. 8:218.

C. Vitte, H. Quesneville and O. Panaud (2007). Spip and Squiq, two novel rice non-autonomous LTR-retroelements families related to RIRE3 and RIRE8. Plant Science. 172:8-19.

C. Chaparro, R. Guyot, A. Zuccolo, B. Piégu and O. Panaud (2007). RetrOryza, a database of rice LTR-retrotransposons. Nucleic Acids Research, 35(Database issue):D66-70.


B. Piegu, R. Guyot, N. Picault, A. Roulin, A. Saniyal, H-R. Kim, K. Collura, D.S. Brar, S. Jackson, R.A. Wing and O. Panaud (2006). Doubling genome size without polyploidization : direct evidence of retrotransposition-driven genomic bursts in Oryza genus. Genome Research. 16:1262-1269.

E. Derelle, C. Ferraz, S. Rombauts, P. Rouzé, A.Z. Worden, F. Partensky, S. Robbens, S. Degroeve, S. Echeynié, R. Cooke, Y. Saeys, J. Wuyts, K. Jabbari, C. Bowler, O. Panaud, B. Piégu, S. Ball, J-P. Ral, F-Y. Bouget, G. Piganeau, B. De Baets, A. Picard, M M. Delseny, J. Demaille, Y. Van de Peer and H.Moreau (2006). Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. PNAS 103:11647-11652.

N. Grati-Kamoun, F.L. Mahmoud, A. Rebai, A. Gargouri, O. Panaud and A. Sarr (2006). Genetic diversity of Tunisian olive tree (Olea europaea L.) cultivars assessed by AFLP markers. Genetic Resources and Crop Evolution. (2): 265-275


C. Vitte and O. Panaud (2005). LTR retrotransposons and plant genome size: emergence of the increase/decrease model. Cytogenetics and Genome Research. 110:91-107.

S. Margali, O. Panaud, F. Lamy, S. Ghariani, A. Sarr, M. Marrakchi and N. Trifi-Farah (2005). Exploration of intra- and inter-population genetic diversity in Hedysarum coronarium L. by AFLP markers. Genetic Resources and Crop Evolution. 52 (3): 277-284

-> 2004

C. Vitte, F. Lamy, T. Ishii, D.S. Brar and O. Panaud (2004). Genomic paleontology provides evidence for two distinct origins of asian rice (Oryza sativa, L.). Mol Gen Genomics. 272 :504-511.

C. Vitte and O. Panaud (2003). Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L. Mol. Biol. Evol. 20(4) : 528-540

C. Vitte, J. D. Talag, O. Panaud, M. A. Bernardo and D. S. Brar (2003). Development of O. minuta specific clones using representational difference analysis (RDA). Rice Genet. Newsl. 20:121-124.

O. Panaud, C. Vitte, J. Hivert, S. Muzlak, J. Talag, D.S. Brar and A. Sarr (2002). Characterization of transposable elements in the genome of rice (Oryza sativa L.) using Representational Difference Analysis (RDA). Mol Gen Genomics. 268: 113-121

O. Panaud, A. Chaib and A. Sarr (2002). Dynamic conservation of apricot (Prunus armeniaca) in saharian oases : use of AFLP markers to assess genetic diversity in traditional orchards . Euphytica. 128(3) :301-305.

M.Q. Yu, J. Chen, G.B. Deng, M. Cerbah, X.R. Ma, O. Panaud and S. Yakovlev (2001). Identification for H. Villosa chromatin in wheat lines using genomic in situ hybridization, C-banding and gliadin electrophoresis techniques. Euphytica. 121:157-162

M. Elias, D. McKey, O. Panaud, M.C. Anstett and T. Robert (2001). Traditional management of cassava morphological and genetic diversity by the Makushi Amerindians (Guyana, South America): Perspectives for on-farm conservation of crop genetic resources. Euphytica. 120 (1) : 143-157.

M. Elias, L. Penet, P. Vindry, D. McKey, O. Panaud and T. Robert (2001). Unmanaged sexual reproduction and the dynamics of genetic diversity of a vegetatively propagated crop plant, cassava (Manihot esculenta Crantz), in a traditional farming system. Molecular Ecology. 10:1895-1907.

V. Zoldos, S. Siljak-Yakovlev, D. Papes, A. Sarr and O. Panaud (2001). Representational difference analysis reveals DNA differences between Q. robur and Q. suber ; an implication in the study of genome evolution in Quercus genus. Mol. Gen. Genomics. 265 :234-241.

M. Ellias, O. Panaud and T. Robert (2000). Assessment of genetic variability in traditional cassava (Manihot esculenta Crantz) farming systems using AFLP markers. Heredity. 85(3):219-30.

M. Le Thierry d'Ennequin, O. Panaud, B. Toupance and A. Sarr (2000). Assessment of genetic relationships between Setaria italica and its wild relative S. viridis using AFLP markers. Theor. Appl. Genet. 100(7) :1061-1066

V. Zoldos, D. Papes, M. Cerbah, O. Panaud, V. Besendorfer and S. Siljak-Yakovlev (1999). Molecular cytogenetic studies of ribosomal genes and heterochromatin reveal conserved genome organization among eleven Quercus species. Theor. Appl. Genet. 99(6) :969-977

M.W. Blair, O. Panaud and S.R. McCouch (1999). Inter-simple sequence repeat (ISSR) amplification for analysis of microsatellite motif frequency and fingerprinting in rice (Oryza sativa L.). Theor. Appl. Genet. 98:780-792

M. Le Thierry d'Ennequin, O. Panaud, S. Brown, S. Siljak-Yakovlev and A. Sarr (1998). First evaluation of DNA content in Setaria gene pool using flow cytometry. J of Heredity, 89(6):556-558

V. Zoldos, D. Papes, S. Brown, O. Panaud and S. Siljak-Yakovlev (1998). Genome size and base composition of seven oak species and several populations of Q. petreae L. and Q. robur L. estimated by flow cytometry. Genome, 41: 162-168.

M. Le Thierry d'Ennequin, O. Panaud, T. Robert, and A. Ricroch (1997). Assessment of genetic relationships among sexual and asexual forms of Allium cepa using morphological traits and RAPD markers. Heredity 78:403-409.

S.R. McCouch, X. Chen, O. Panaud, S. Temnykh, Y. Xu, Y.G. Cho, N. Huang, T. Ishii, and M. Blair (1997). Microsatellite mapping and applications of SSLPs in rice genetics and breeding. Plant Molecular Biology 35:89-99.

O. Panaud, X.L. Chen and S. McCouch (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Molecular General Genetics 252:597-607.

Y.G. Cho, O. Panaud and S. McCouch (1996) Cloning and mapping of variety-specific rice genomic DNA sequences: Amplified fragment length polymorphisms (AFLP) from silver-stained polyacrylamide gels. Genome 39(2):373-378.

O. Panaud, X.L. Chen and S. McCouch (1996) Frequency of microsatellite sequences in rice (Oryza sativa L.). Genome, 38: 1170-1176

E. Martel, V. Poncet, O. Panaud and A. Sarr (1995) Genomic relationships between Pennisetum species with 2n=2x=14 chromosomes using genomic in situ hybridization. Chromosome Research 3, suppl 1:55-56

A. Ghesquière, O. Panaud, P. Marmey, M.C. Gavalda, O. Leblanc et D. Grimanelli (1994). Suivi des introgressions dans les croisements interspécifiques chez le riz : utilisation des marqueurs moléculaires. Genet Sel Evol 26, suppl 1: 67-80.

O. Panaud, G. Magpantay and S. McCouch (1993) A protocole for non-radioactive DNA labelling and detection in the RFLP analysis of rice and tomato using single-copy probes. Plant molecular Biology reporter 11(1) : 54-59.

T. Ishii, O. Panaud, D.S. Brar and G.S. Khush (1990) Use of non-radioactive, digoxigenin-labeled DNA probes for RFLP analysis in rice. Plant molecular Biology reporter 8(3) : 167-171.