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Transposable
elements in plant genomes
Research Director : Olivier Panaud (PR UPVD) The research activities of the group concern the impact of Transposable Elements (TEs) on the structure, the evolution and the function of plant genomes. So far, we have been focusing on LTR-retrotransposons, a particular class of TE that increase their copy number while active. Our goal is to understand the process through which LTR-retrotransposons have shaped the rice genome. For example, we have recently shown that three LTR-retrotransposon families have undergone massive transposition bursts in one lineage of the genus Oryza (i.e. the species O. australiensis), leading to the doubling of its genome size compared to that of O. sativa (Piegu et al. 2006). Our research activities over the past four years have lead us to propose a new model for plant genome evolution (Vitte and Panaud, 2005). This model posits that the size of a plant genome at a given time is the balance between two counteracting forces : the retrotransposition, that builds up the genome buy adding new elements and a strong elimination force by either recombination (Vitte and Panaud, 2003) or deletion (Vitte et al., 2007). Our group is also involved in the annotation of the rice genome for LTR-retrotransposons within RAP3 (Rice Annotation Project 3). We are curating a database of the rice LTR-retrotransposons, available at www.retroryza.org (Chaparro et al., 2007). We also have been involved in the annotation of the TEs in two small eukaryotic genomes, that of Ostreococcus taurii (Derelle et al., 2006) and Micromonas pusilla. We are currently developing new research projects on the functional aspects of the TEs in rice genome. Our research activities are supported by CNRS, the french National Research Agency (ANR) and the Genoscope. Group
Publications 2008 Wicker T., Narechania A., Sabot F., Stein J., Vu G.T.H., Graner A., Ware D., Stein N. Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats BMC Genomics, 9: 518 - [PMID: WAITING] Wicker T., Sabot F., Hua-Van A., Bennetzen J., Capy P., Chalhoub B., Flavell A., Leroy P., Morgante M., Panaud O., Paux E., SanMiguel P., Schulman A. A unified classification system for eukaryotic transposable elements implemented in Repbase. Nature Reviews Genetics, 9(5):414 - [PMID: 18421313] 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. The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acid Research (Database issue):D1028-33 - [PMID: 18089549] Roulin A., Piegu B., Panaud O. Evidence of multiple horizontal transfers of the LTR-retrotransposon RIRE1 within the genus Oryza. Plant J. 53(6):950-9 - [PMID: 18088314] Chantret N., Salse J., Sabot F., Bellec A., Laubin B., Dubois I., Dossat C., Sourdille P., Joudrier P., Gautier M.F., Cattolico L., Beckert M., Aubourg S., Weissenbach J., Caboche M., Leroy P., Bernard M., Chalhoub B. Contrasted microcolinearity and gene evolution within a homoeologous region of wheat and barley species. J Mol Evol. 66(2):138-50 - [PMID: 18274696] Palmieri L., Picault N., Arrigoni R., Besin E., Palmieri F., Hodges M. Molecular identification of three Arabidopsis thaliana mitochondrial dicarboxylate carrier isoforms: organ distribution, bacterial expression, reconstitution into liposomes and functional characterization. Biochem J. 410(3):621-9 - [PMID: 18039180] Bies-Etheve N., Gaubier-Comella P., Debures A., Lasserre E., Jobet E., Raynal M., Cooke R., Delseny M. Inventory, evolution and expression profiling diversity of the LEA (late embryogenesis abundant) protein gene family in Arabidopsis thaliana. Plant Mol Biol. 67(1-2):107-24 - [PMID: 18265943] 2007 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 - [PMID: 17984973] 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 J.52(2):342-51 - [PMID: 17764506] C. Vitte, O. Panaud and H. Quesneville (2007). LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss. BMC Genomics. 8:218 - [PMID: 17617907] 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. Piegu and O. Panaud (2007). RetrOryza, a database of rice LTR-retrotransposons. Nucleic Acids Research, 35(Database issue):D66-70 - [PMID: 17071960] J. Tanskanen, F. Sabot, C. Vicient and A.H. Schulman (2007). Life without GAG: The BARE-2 retrotransposon as a parasite’s parasite. Gene. 390(1-2):166-174 - [PMID: 17107763] F. Sabot and A.H. Schulman (2007). Template switching can create complex LTR retrotransposon insertions in Triticeae genomes. BMC Genomics. 8:247 - [PMID: 17650302] F. Sabot, R. Kalendar, M. Jääskeläinen, W. Chang, J. Tanskanen and A.H. Schulman (2007). Retrotransposons: metaparasites and agents of genome evolution. Israel Journal of Ecology and Evolution. 52:319-330. 2006 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 - [PMID: 16963705] 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 - [PMID: 16868079] 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. 53 (2): 265-275. F. Sabot, P. Sourdille, N. Chantret and M. Bernard (2006). Morgane, a new LTR retrotransposon group, and its subfamilies in wheats. Genetica. 128(1-3):439-47 - [PMID: 17028971] F. Sabot and A.H. Schulman (2006). Parasitism and the retrotransposon life cycle in plants: a hitchhiker's guide to the genome. Heredity. 97(6):381-8. Review - [PMID: 16985508] L. Gayet, N. Picault, A.C. Cazalé, A. Beyly, P. Lucas, H. Jacquet, H.P. Suso, A. Vavasseur, G. Peltier and C. Forestier (2006). Transport of antimony salts by Arabidopsis thaliana protoplasts over-expressing the human multidrug resistance-associated protein 1 (MRP1/ABCC1). FEBS Lett. 580(30):6891-7 - [PMID: 17150215] N. Picault, A.C. Cazalé, A. Beyly, S. Cuiné, P. Carrier, D.T. Luu, C. Forestier and G. Peltier (2006). Chloroplast targeting of phytochelatin synthase in Arabidopsis: effects on heavy metal tolerance and accumulation. Biochimie. 88(11):1743-50 - [PMID: 16766112] 2005 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 - [PMID: 16093661] 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. F. Sabot, P. Sourdille and M. Bernard (2005). Advent of a new retrotransposon structure: the long form of the Veju elements. Genetica. 125(2-3):325-32. [PMID: 16247703] F. Sabot, R. Guyot, T. Wicker, N. Chantret, B. Laubin, B. Chalhoub, P. Leroy, P. Sourdille and M. Bernard (2005). Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations. Mol Genet Genomics. 274(2):119-30 - [PMID: 1603462] N. Chantret, J. Salse, F. Sabot, S. Rahman, A. Bellec, B. Laubin, I. Dubois, C. Dossat, P. Sourdille, P. Joudrier, M.F. Gautier, L. Cattolico, M. Beckert, S. Aubourg, J. Weissenbach, M. Caboche, M. Bernard, P. Leroy and B. Chalhoub (2005). Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops). Plant Cell. 17(4):1033-45 - [PMID: 15749759] R. Guyot, X. Cheng, Y. Su, Z. Cheng, E. Schlagenhauf E, B. Kellerand H.Q. Ling (2005). Complex organization and evolution of the tomato pericentromeric region at the FER gene locus. Plant Physiol. 138(3):1205-15 - [PMID: 16009996] 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 - [PMID: 15503144] N. Chantret, A. Cenci, F. Sabot, O. Anderson and J. Dubcovsky (2004). Sequencing of the Triticum monococcum hardness locus reveals good microcolinearity with rice. Mol Genet Genomics. 271(4):377-86 - [PMID: 15014981] N. Picault, M. Hodges, L. Palmieri and F. Palmieri (2004). The growing family of mitochondrial carriers in Arabidopsis. Trends Plant Sci. 9(3):138-46. Review - [PMID: 15003237] C. Lopez, V. Jorge, B. Piégu, C. Mba, D. Cortes, S. Restrepo, M. Soto, M. Laudié, C. Berger, R. Cooke, M. Delseny, J. Tohme and V. Verdier (2004). A unigene catalogue of 5700 expressed genes in cassava. Plant Mol Biol. 56(4):541-54 - [PMID: 15630618] R. Guyot and B. Keller (2004). Ancestral genome duplication in rice. Genome. 47(3):610-4 - [PMID: 15190378] U. Ryser, M. Schorderet, R. Guyot and B. Keller (2004). A new structural element containing glycine-rich proteins and rhamnogalacturonan I in the protoxylem of seed plants. J Cell Sci. 117(Pt 7):1179-90 - [PMID: 14996940] R. Guyot, N. Yahiaoui, C. Feuillet and B. Keller (2004). In silico comparative analysis reveals a mosaic conservation of genes within a novel colinear region in wheat chromosome 1AS and rice chromosome 5S. Funct Integr Genomics. 4(1):47-58 - [PMID: 14767678] |