[show abstract][hide abstract] ABSTRACT: An international conference on Transposable Elements (TEs) was held 21--24 April 2012 in Saint Malo, France. Organized by the French Transposition Community (GDR Elements Genetiques Mobiles et Genomes, CNRS) and the French Society of Genetics, the conference's goal was to bring together researchers from around the world who study transposition in diverse organisms using multiple experimental approaches. The meeting drew more than 217 attendees and most contributed through poster presentations (117), invited talks and short talks selected from poster abstracts (48 in total). The talks were organized into four scientific sessions, focused on: impact of TEs on genomes, control of transposition, evolution of TEs and mechanisms of transposition. Here, we present highlights from the talks given during the platform sessions. The conference was sponsored by Alliance pour les sciences de la vie et de la sante (Aviesan), Centre national de la recherche scientifique (CNRS), Institut national de la sante et de la recherche medicale (INSERM), Institut de recherche pour le developpement (IRD), Institut national de la recherche agronomique (INRA), Universite de Perpignan, Universite de Rennes 1, Region Bretagne and Mobile DNA. Chair of the organization committee Jean-Marc Deragon Organizers Abdelkader Ainouche, Mireille Betermier, Mick Chandler, Richard Cordaux, Gael Cristofari, Jean-Marc Deragon, Pascale Lesage, Didier Mazel, Olivier Panaud, Hadi Quesneville, Chantal Vaury, Cristina Vieira and Clementine Vitte.
[show abstract][hide abstract] ABSTRACT: Molecular markers have been successfully used in rice breeding however available markers based on Oryza
sativa sequences are not efficient to monitor alien introgression from distant genomes of Oryza. We developed O. minuta (2n=48, BBCC)-specific clones comprising of 105 clones (266–715bp) from the initial library composed of 1,920 clones against
O. sativa by representational difference analysis (RDA), a subtractive cloning method and validated through Southern blot hybridization.
Chromosomal location of O. minuta-specific clones was identified by hybridization with the genomic DNA of eight monosomic alien additional lines (MAALs). The
37 clones were located either on chromosomes 6, 7, or 12. Different hybridization patterns between O. minuta-specific clones and wild species such as O. punctata, O. officinalis, O. rhizomatis, O. australiensis, and O. ridleyi were observed indicating conservation of the O. minuta fragments across Oryza spp. A highly repetitive clone, OmSC45 hybridized with O. minuta and O. australiensis (EE), and was found in 6,500 and 9,000 copies, respectively, suggesting an independent and exponential amplification of the
fragment in both species during the evolution of Oryza. Hybridization of 105 O. minuta specific clones with BB- and CC-genome wild Oryza species resulted in the identification of 4 BB-genome-specific and 14 CC-genome-specific clones. OmSC45 was identified as a fragment of RIRE1, an LTR-retrotransposon. Furthermore this clone was introgressed from O. minuta into the advanced breeding lines of O. sativa.
Oryza minuta-specific clones-Representational difference analysis-Highly repetitive sequence-Genomic conservation-MAALs-Introgression
[show abstract][hide abstract] ABSTRACT: LTR retrotransposons are one of the main causes for plant genome size and structure evolution, along with polyploidy. The characterization of their amplification and subsequent elimination of the genomes is therefore a major goal in plant evolutionary genomics. To address the extent and timing of these forces, we performed a detailed analysis of 41 LTR retrotransposon families in rice.
Using a new method to estimate the insertion date of both truncated and complete copies, we estimated these two forces more accurately than previous studies based on other methods. We show that LTR retrotransposons have undergone bursts of amplification within the past 5 My. These bursts vary both in date and copy number among families, revealing that each family has a particular amplification history. The number of solo LTR varies among families and seems to correlate with LTR size, suggesting that solo LTR formation is a family-dependent process. The deletion rate estimate leads to the prediction that the half-life of LTR retrotransposon sequences evolving neutrally is about 19 My in rice, suggesting that other processes than the formation of small deletions are prevalent in rice DNA removal.
Our work provides insights into the dynamics of LTR retrotransposons in the rice genome. We show that transposable element families have distinct amplification patterns, and that the turn-over of LTR retrotransposons sequences is rapid in the rice genome.
[show abstract][hide abstract] ABSTRACT: Transposable elements are the main components of complex genomes. Their impact on the genomes in terms of structural changes during evolution is thus one of the main focuses of today's structural genomics. Although non-autonomous transposable elements have been known for a long time, their contribution to genome evolution is poorly understood. Our present study describes two new non-autonomous LTR retrotransposons in the rice (Oryza sativa L) genome, Spip and Squiq, the LTR of which are closely related to those of the gypsy-like RIRE3 and RIRE8 LTR retrotransposon families, respectively, but the internal region of which is completely different and harbours none of the characteristic coding domains of LTR retrotransposons. Spip and Squiq thus belong to the class of LArge Retrotransposon Derivatives (LARDs).A phylogenetic study based on the sequence alignment of the LTRs of Spip/RIRE3, and of Squiq/RIRE8 show that both Spip and Squiq elements are of monophyletic origin. In addition, the estimation of the date of insertion of the copies suggests that Spip and Squiq families are of recent origin (that is, they amplified mainly within the last 2 My).Spip and Squiq are the fourth and fifth LARD families to be described in the rice genome, suggesting that this type of sequences is not rare. Moreover, these two families appear to be as numerous as their autonomous counterparts, suggesting that they have played an equivalent role in the recent history of rice.
[show abstract][hide abstract] ABSTRACT: Long Terminal Repeat (LTR) retrotransposons are ubiquitous components of plant genomes. Because of their copy-and-paste mode of transposition, these elements tend to increase their copy number while they are active. In addition, it is now well established that the differences in genome size observed in the plant kingdom are accompanied by variations in LTR retrotransposon content, suggesting that LTR retrotransposons might be important players in the evolution of plant genome size, along with polyploidy. The recent availability of large genomic sequences for many crop species has made it possible to examine in detail how LTR retrotransposons actually drive genomic changes in plants. In the present paper, we provide a review of the recent publications that have contributed to the knowledge of plant LTR retrotransposons, as structural components of the genomes, as well as from an evolutionary genomic perspective. These studies have shown that plant genomes undergo genome size increases through bursts of retrotransposition, while there is a counteracting process that tends to eliminate the transposed copies from the genomes. This process involves recombination mechanisms that occur either between the LTRs of the elements, leading to the formation of solo-LTRs, or between direct repeats anywhere in the sequence of the element, leading to internal deletions. All these studies have led to the emergence of a new model for plant genome evolution that takes into account both genome size increases (through retrotransposition) and decreases (through solo-LTR and deletion formation). In the conclusion, we discuss this new model and present the future prospects in the study of plant genome evolution in relation to the activity of transposable elements.
Cytogenetic and Genome Research 02/2005; 110(1-4):91-107. · 1.84 Impact Factor
[show abstract][hide abstract] ABSTRACT: The origin of rice domestication has been the subject of debate for several decades. We have compared the transpositional history of 110 LTR retrotransposons in the genomes of two rice varieties, Nipponbare (Japonica type) and 93-11 (Indica type) whose complete sequences have recently been released. Using a genomic paleontology approach, we estimate that these two genomes diverged from one another at least 200,000 years ago, i.e., at a time which is clearly older than the date of domestication of the crop (10,000 years ago, during the late Neolithic). In addition, we complement and confirm this first in silico analysis with a survey of insertion polymorphisms in a wide range of traditional rice varieties of both Indica and Japonica types. These experimental data provide additional evidence for the proposal that Indica and Japonica rice arose from two independent domestication events in Asia.
Molecular and General Genetics 01/2005; 272(5):504-11. · 2.88 Impact Factor
[show abstract][hide abstract] ABSTRACT: We studied the dynamics of hopi, Retrosat1, and RIRE3, three gypsy-like long terminal repeat (LTR) retrotransposons, in Oryza sativa L. genome. For each family, we assessed the phenetic relationships of the copies and estimated the date of insertion of the complete copies through the evaluation of their LTR divergence. We show that within each family, distinct phenetic groups have inserted at significantly different times, within the past 5 Myr and that two major amplification events may have occurred during this period. We show that solo-LTR formation through homologous unequal recombination has occurred in rice within the past 5 Myr for the three elements. We thus propose an increase/decrease model for rice genome evolution, in which both amplification and recombination processes drive variations in genome size.
Molecular Biology and Evolution 05/2003; 20(4):528-40. · 10.35 Impact Factor
[show abstract][hide abstract] ABSTRACT: Representational Difference Analysis was applied to characterize genomic differentiations between rice ( Oryza sativa) and foxtail millet ( Setaria italica) and subsequently to identify rice transposable elements. Rice was used as the tester and millet as the driver. A total of eleven, non-redundant, positive clones were isolated from the library. Their analysis revealed that they all represent dispersed repetitive DNA sequences. In addition, homology searches using the BLAST procedure showed that they correspond to seven distinct rice transposable elements. Three had been previously identified as gypsy-like retroelements ( Retrosat1, RIRE3 and RIRE8). The remaining four are novel: we named them hipa (a CACTA-like transposon), houba (a copia-like retroelement), hopi and dagul (two gypsy-like retroelements). The RDA clones were used as probes in Southern hybridization experiments with genomic DNAs of several species from the family Poaceae. The results suggest that the genomic differentiations associated with the activity of these transposable elements are of relatively recent origin. In addition, comparison of the hybridization patterns obtained for several Oryza species suggests that several independent amplifications of these transposable elements might have occurred within the genus.
Molecular and General Genetics 10/2002; 268(1):113-21. · 2.88 Impact Factor