Many factors may explain why certain transposable elements (TEs) spread in some species and not others. On the one hand, they include processes that affect the rate of transposition, such as differences in the regulation of expression; on the other hand, they include characteristics of a genome that affect the consequences of transposition. In particular genome size may have an effect: a genome that is large due to non-essential repetitive DNA may be permissive for TE movement, as insertion events are less likely to be deleterious. Genome size may also help explain the pattern of TE distribution between species of mosquitoes, including the important vectors of arboviruses, Aedes aegypti and Culex pipiens sensu lato. These species have genomes 3- 5 times larger than a third genus, the Anopheles mosquitoes, which includes the malaria vectors. While all mosquitoes carry a diverse range of TEs, only culicines have the super abundant retroposon, Juan which can contribute up to 3% of the genome. The genome sequences of various insect species were compared and the mosquitoes show a significant trend of increase in genome size, which can be attributed to the increase in retroposon sequences. Two variants of Juan are reported, and new information is added regarding these elements. Previous publication of these elements contained errors in their sequences. A unique triple repeat of a cysteine rich region with a CCHC motif is present in the open reading frame. This sequence is a zinc-knuckle domain, important for the replication mechanism of these elements. In comparison, a third recently active but very low copy number retroposon, termed Pip1, is also described. The results show that Pip1 is related to the Juan elements and also possess the triple CCHC motif. The PCR results also supports previous findings of polymorphism in insertion sites of this element, suggesting that Pip1 was active after the establishment of the different strains. Pip1 copies can be grouped into three distinct groups based on nucleotide differences. Pip1 could also be using an alternative start codon to initiate transcription. Full length intact copies of the three TEs in this study were been cloned into a germline transformation vector based on piggyBac and used for germline transformation in Drosophila melanogaster. Drosophila melanogaster has no Juan or Pip1 elements and an even smaller genome than anophelines mosquitoes, so insertion events from unregulated TE movement should be more detectable. We found that the elements have been successfully introduced into the Drosophila lines. The lines were inbred to obtain a homozygous population. A range of transformed lines were monitored. No effects of hybrid dysgenesis was found. Flies with black spotted eyes were identified in a Pip1 line but this phenotype was not heritable. Whole genome sequencing was carried out on the flies using next generation sequencing (NGS) technology. Retroposon sequences was detected at a high frequency. Insertion junctions were not detected but this result does not eliminate the possibility that a junction is present but the sequencing was not sensitive enough. A possible explanation is the retroposon is present as extrachromosomal plasmid DNA.

Els elements transposables (TEs) són seqüències repetitives amb el tret definitori de canviar la seva posició al genoma. Ocupen fraccions importants dels genomes eucariotes, y, tot i que solen considerar-se paràsits genètics, també s'especula amb la possibilitat de que tinguessin alguna funció cel·lular que encara ens és desconeguda. Tot i així, sembla evident que tenen un paper important com facilitadors de l'evolució, ja que generen variabilitat al genoma de l'hoste. El TE Galileo està implicat en la generació de reordenacions cromosòmiques adaptatives naturals a l'espècie Drosophila buzzatii, en la que hauria generat variabilitat amb valor adaptatiu per a l'hoste. A més, tots els elements Galileo trobats en treballs anteriors eren defectius – composats bàsicament d'estructures similars a la dels elements Foldback – i no es van poder establir relacions d'homologia amb ninguna seqüència coneguda. Amb aquest rerefons, en aquesta tesi es va plantejar caracteritzar l'element genètic mòbil Galileo en diferents espècies de Drosophila i analitzar la seva dinàmica evolutiva. D'aquesta forma, en una primera fase es van buscar elements Galileo complets en diferents espècies del gènere Drosophila: D. buzzatii, D. mojavensis, D. virilis, D. willitoni, D. ananassae, D. pseudoobscura i D. persimilis, fent servir tant mètodes bioinformàtics com experimentals (depenent de si el genoma analitzat estava seqüenciat o no). Les còpies trobades presenten llargues Repeticions Invertides Terminals (TIR) de fins a 1,2 Kb, una elevada identitat amb seqüències de Galileo descrites anteriorment i, a més, contenen una zona codificant que ha permès classificar Galileo com a membre de la superfamília de l'element P. Posteriorment, mitjançant anàlisis filogenètiques, hem trobat l'existència de subfamílies de Galileo en tres espècies (D. buzzatii, D. mojavensis, D. virilis) i evidència d'activitat transposicional recent (D. willitoni, D. ananassae, D. pseudoobscura, D. persimilis i D. mojavensis). En una segona fase de la tesi, hem dut a terme experiments amb part de la proteïna que es codifica a Galileo i hem comprovat que interacciona amb les TIR de Galileo, confirmant que aquesta seqüència és la responsable de la reacció de transposició. Finalment, hem analitzat en detall la diversitat de Galileo al genoma de D. mojavensis i hem detectat una diversitat estructural molt important, on l'intercanvi de seqüències entre elements pareix força freqüent per l'evolució dels TEs. / Los elementos transponibles (TEs) son secuencias repetitivas cuya característica definitoria es la capacidad de cambiar de posición en el genoma. Ocupan fracciones muy importantes de los genomas de eucariotas, y aunque se suelen considerar parásitos genéticos, también se especula con la posibilidad de que pudieran tener alguna función celular que aún nos es desconocida. No obstante, parece evidente que tienen un papel importante como facilitadores de la evolución, al generar variabilidad en el genoma del huésped. El TE Galileo está implicado en la generación de reordenaciones cromosómicas adaptativas naturales en la especie Drosophila buzzatii, con lo que habría generado variabilidad adaptativa para el huésped. Además, todos los elementos Galileo encontrados en trabajos anteriores eran defectivos – compuestos básicamente de estructuras similares a las de los elementos Foldback – y no se pudieron establecer relaciones de homología con ninguna secuencia conocida. Con este trasfondo, en esta tesis se planteó caracterizar el elemento genético móvil Galileo en diferentes especies de Drosophila y analizar su dinámica evolutiva. De esta manera, en una primera fase se buscaron elementos Galileo completos en en diferentes especies del género Drosophila: D. buzzatii, D. mojavensis, D. virilis, D. willitoni, D. ananassae, D. pseudoobscura y D. persimilis, utilizando métodos tanto bioinformáticos como experimentales (dependiendo de si el genoma analizado estaba secuenciado o no). Las copias encontradas presentan largas Repeticiones Invertidas Terminals (TIR) de hasta 1,2 Kb, una elevada identidad con secuencias de Galileo descritas con anterioridad y, además, contienen una zona codificante que ha permitido clasificar Galileo como miembro de la superfamilia del elemento P. Posteriormente, mediante análisis filogenéticos, hemos encontrado la existencia de subfamilias de Galileo en tres especies (D. buzzatii, D. mojavensis, D. virilis) y evidencias de actividad transposicional reciente (D. willitoni, D. ananassae, D. pseudoobscura, D. persimilis y D. mojavensis). En una segunda fase de la tesis, hemos llevado a cabo experimentos con parte de la proteína que codifica Galileo y hemos comprobado que interacciona con las TIR de Galileo, confirmando que esta secuencia es la responsable de la reacción de transposición. Finalmente, hemos analizado en detalle la diversidad de Galileo en el genoma de D. mojavensis y hemos detectado una diversidad estructural muy importante, lo que sugiere que el intercambio de secuencias entre elementos podría ser bastante frecuente para la evolución de los TEs. / Transposable elements (TE) are repetitive sequences whose ability to change their location in the genome defines them. They made up a important proportion of the eukaryotic genomes, and although they are often considered as genetic parasites, it has been also argued that they might have some still unknown cellular function. Nevertheless, it is clear that they play a role as drivers of their host evolution, due to the fact that TEs generate genetic variability. The TE Galileo is involved in the generation of adaptive chromosomal rearrangements in natural populations of Drosophila buzzatii, indicating that it would be a driver of adaptation in its host. Moreover, all Galileo elements found in previous works were incomplete – mainly composed by Foldback-like structures – and homology relationships could not be established with any known sequence. With this background, this thesis was proposed to characterise the mobile genetic element Galileo in different Drosophila species and analyse its evolutionary dynamics. Thus, in a first phase we searched for complete copies of Galileo in different species of the Drosophila genus: D. buzzatii, D. mojavensis, D. virilis, D. willitoni, D. ananassae, D. pseudoobscura and D. persimilis, using both bioinformatic and experimental methods (depending on whether the analysed genome was available or not). The copies found present long TIR (up to 1.2 Kb), high sequence identity with previously found Galileo sequences and, moreover, they harbour coding sequences that have allowed the classification of Galileo as a member of the P-element superfamily. Subsequently, by means of phylogenetic analyses, we have found that there are Galileo subfamilies in three different species (D. buzzatii, D. mojavensis, D. virilis) and evidence of recent transpositional activity (in D. willitoni, D. ananassae, D. pseudoobscura, D. persimilis and D. mojavensis). In a second phase of the thesis, we have conducted experiments with part of the Galileo protein and detected specific binding to the Galileo TIR, confirming that this sequence is responsible for the transposition reaction. Finally, we have thoroughly studied the Galileo variability in the D. mojavensis genome and found a striking structural variation, suggesting that the exchange of sequences among different Galileo copies might be quite common and important for TEs evolution.

Thesis (Ph. D.)--Cornell University,1989. / Vita. Includes bibliographical references.

Repetitive sequences, including transposable elements, represent approximately half of the mammalian genome. Epigenetic mechanisms evolved to repress these potentially deleterious mobile elements. However, such elements can be variably silenced between individuals – so called ‘metastable epialleles’. The best known example is the Avy locus where an endogenous retrovirus (ERV) of the intracisternal A-particle (IAP) class was spontaneously inserted upstream of the agouti coat colour gene, resulting in variable IAP promoter DNA methylation, variable expressivity of coat phenotype, and environmentally modulated transgenerational epigenetic inheritance within genetically identical individuals. It is not known whether the behaviour exhibited by the ERV at Avy represents a common occurrence throughout the genome or is unusual. Taking a genetic approach in purified cell populations, I have conducted a systematic genome-wide screen of murine metastable epialleles. I have identified over 100 murine IAPs with properties of metastable epialleles. Like Avy, each exhibits a stable epigenetic state within an individual but epigenetic variability between individuals. Methylation levels are locus-specific within an individual, suggesting cis-acting control. The same screening strategy was applied for identification of metastable epialleles associated with other types of LTR-retroelements. However, many of identified candidates showed no inter-individual methylation variation upon experimental validation. These results suggest that IAPs are the dominant class of ERVs capable of acquiring epigenetic states that are variable between genetically identical individuals. I have conducted an analysis of IAP induced initiation and termination of transcription events using de novo assembled transcriptomes generated for B and T cells. 143 IAPs have been identified to overlap de novo assembled transcripts. 33 IAPs are metastable epialleles. Several of them show an inverse correlation between LTR promoter methylation and adjacent gene expression. In addition, I have shown that metastable epialleles have a characteristic pattern of histone modification and are flanked by the methylation sensitive binding factor CTCF, providing testable hypotheses concerning the establishment and/or maintenance of the variable methylation state. My findings indicate that metastability is, in general, specific to the IAP class of ERVs, that only around 1% of these elements have this unusual epigenetic property and that the ability to impact transcription, such as at agouti in Avy, is not a ubiquitous feature of these loci.

While the study of transposable element evolution has been conducted in several model insect organisms such as Anopheles gambiae, Drosophila melanogaster, and Bombyx mori, little investigation has been conducted into the transposable element (TE) evolution within less commonly examined model and non-model taxa within Diptera. In this work we contributed two analyses to close this gap. First, TEs in the lepidopteran, Heliconius melpomene, were characterized, and it was determined that 25% of the genome is composed of TEs. Second, TEs in oestroid and muscid flies were characterized using survey sequencing rather than whole genomes. Comparative analyses were performed on Haematobia irritans, Sarcophaga crassipalpis, Phormia regina, and Cochliomyia hominivorax. TE proportions were 5.95%, 10.00%, 22.43%, and 30.67%, for C. hominivorax, P. regina, S. crassipalpis and H. irritans, respectively. These studies provide new insights into the diversity of TEs in Insecta and suggest that in general, TE diversity is high among insects.

Transposable elements (TEs), also known as jumping genes, are DNA sequences capable of mobilizing and replicating within the genome. In mammals, it is not uncommon for 50% of the genome to be derived from TEs, yet they remain an underutilized tool for tracking evolutionary change. With the increasing number of publicly funded genome projects and affordable access to next-generation sequencing platforms, it is important to demonstrate the role TEs may play in helping us understand evolutionary patterns. The research presented herein utilizes TEs to investigate such patterns at the genomic, specific, and generic levels in three distinct ways. First at the genomic level, an analysis of the historical TE activity within the thirteen-lined ground squirrel (Spermophilus tridecemlineatus) shows that non-LTR retrotransposon activity has been declining for the past ~26 million years and appears to have ceased ~5 million years ago. Since most mammals, and all other rodents studied to date, have active TEs the extinction event in S. tridecemlineatus makes it a valuable model for understanding the factors driving TE activity and extinction. Second, we examined TEs as factors impacting genomic and species diversity. We found that DNA transposon insertions in Eptesicus fuscus, appear to have been exapted as miRNAs. When placed within a phylogenetic context a burst of transposon-driven, miRNA origination and the vespertilionid species radiation occurred simultaneously ~30 million years ago. This observation implies that lineage specific TEs could generate lineage specific regulatory pathways, and consequently lineage specific phenotypic differences. Finally, we utilized TEs to investigate their phylogenetic potential at the level of genus. In particular a method was developed that identified, over 670 thousand Ves SINE insertions in seven species of Myotis for use in future phylogenetic studies. Our method was able to accurately identify insertions in taxa for which no reference genome was available and was confirmed using traditional PCR and Sanger sequencing methods. By identifying polymorphic Ves insertions, it may be possible to resolve the phylogeny of one of the largest species radiations in mammals.

Les éléments transposable (Ets) ont un rôle important dans l’évolution, puisque ce sont des séquences d’ADN qui ont la capacité de se déplacer dans le génome hôte. Nous cherchons à comprendre l’activité dans les croisements entre la Drosophile mojavensis et D. arizonae. La thèse est divisée en quatre chapitres, le première présente une analyse détaillée d'un rétrotransposon non-LTR appelé I , connu pour causer dysgénésie hybride D. melanogaster. Les analyses phylogénétiques réalisés, ont montré que les séquences I chez D. mojavensis et nourri par ceux d'autres espèces de Drosophila appartiennent, à des familles différentes d’ET. Les analyses d'expression par RTQ-PCR, a montré que cet élément est une activité de transcription dans les ovaires et les testicules des deux espèces et leurs hybrides, et ont une grande expression dans les testicules mais pas dans les ovaires des hybrides, qui pourraient être associés avec le mâle hybride phénotype de stérilité. Dans le deuxième chapitre sont présentées les analyses de TE exprimés dans les ovaires des deux souches parentales et leurs hybrides par l'ARN-Seq. Les résultats montrent des espèces spécifiques expression de TE chez les parents et les hybrides et d'une manière sans précédent, ET sont généralement réglementés en ce qui concerne les hybrides avec leurs parents, bien que certains d'entre eux sont surexprimés. Dans le troisième chapitre sont présentés les résultats de l'expression de quatre rétrotransposons (Helena, I, Copia et Osvaldo) quantifiés par RTQ -PCR; et enfin, dans le dernier chapitre, nous avons présenté des estimations de la taille du génome (C-valeur) dans les deux espèces parentales et hybrides réciproques. Dans l'ensemble, cette thèse révèle un scénario d'expression de TE spécifiques D. mojavensis et D. arizonae, et de sa réglementation dans les hybrides de rares exceptions près, qui peut nous aider à comprendre la complexité de la dynamique et de l'action de ces éléments mobiles dans la spéciation procédé de différentes espèces / The transposable elements (TEs) have an important role in evolution, since they are DNA sequences that have the ability to move into the host genome. We seek to understand the activity of the TEs in crosses between Drosophila mojavensis and D. arizonae. The thesis is divided into four chapters. The first presents a detailed analysis of an non- LTR retrotransposon called I, known to cause hybrid dysgenesis in D. melanogaster. Putatively active sequences similar to the I element were identified and characterized in the genome of D. mojavensis. The performed phylogenetic analyzes showed that the I sequences in D. mojavensis and those harbored by other Drosophila species belong to different I families. Expression analyses by RTq-PCR showed that this element is transcriptionally active in ovaries and testes of both species and their hybrids, and have high expression in the testes, but not in the hybrids ovaries, which could be associated with the male hybrid sterility phenotype. In the second chapter are presented analyses of expressed TEs in the ovaries of two parental strains and their hybrids by RNA-Seq. The results show species-specific expression of TEs in the parents and hybrids; and, in an unprecedented manner, that TEs are generally regulated in hybrids regarding with their parents, although some of them are overexpressed. In the third chapter are presented results of expression of four retrotransposons (Helena , I, Copia and Osvaldo) quantified by RTq-PCR; and finally, in the last chapter, we presented estimates of the genome size ( C - value), in both parental species and reciprocal hybrids. Overall, this thesis reveal a scenario of expression of specific TEs in D. mojavensis and D. arizonae, and its regulation in hybrids with rare exceptions, which can help us to understand the complexity of the dynamics and action of these mobile elements in the speciation process of different species

Les éléments transposables (ET) et leur reliques sont des composants majeurs des génomes eucaryotes. Ils sont potentiellement hautement mutagéniques car leur prolifération peut engendrer des réarrangements chromosomiques, des interruptions de gènes ou affecter l’expression génique par interférence transcriptionnelle. Néanmoins, peu d’ET sont généralement mobiles dans les génomes grâce à l’action de mécanismes qui restreignent leur activité comme la méthylation de l’ADN chez les mammifères et les plantes. De fait, chez Arabidopsis thaliana, une perte sévère de méthylation de l’ADN causée par une mutation dans le gène codant la protéine remodeleuse de chromatine DDM1 (DECREASE IN DNA METHYLATION 1) engendre l’accumulation massive de transcrits correspondants à des séquences d’ET. En revanche, peu d’ET semblent être mobilisés suite à cette réactivation transcriptionnelle. Nous proposons ici de déterminer (1) l’étendue de la mobilisation des ET suite à la perte de méthylation de l’ADN, (2) la distribution des nouvelles insertions d’ET le long du génome d’Arabidopsis et (3) les conséquences des nouvelles insertions d’ET sur l’expression des gènes situés à proximité. Dans ce but, nous avons séquencé le génome d’une cinquantaine d’epiRIL (epigenetic Recombinant Inbred Lines) dérivées d’un croisement entre une plante sauvage et un mutant ddm1. Suite au croisement retour de la F1 avec une plante sauvage et sélection des individus F2 homozygotes pour l’allèle sauvage DDM1, les epiRIL ont été propagées au travers de 6 autofécondations successives. Les epiRIL permettent donc l’étude détaillée des évènements de transpositions juste après qu’ils aient eu lieu. Pour identifier les évènements de transpositions dans ces lignées nous avons mis au point TE-tracker, un programme basé sur les données issues du séquençage Illumina de banques maite-pair. Par cette approche, nous avons montré que les ET mobiles dans ddm1 et les epiRIL appartiennent à seulement une quinzaine environ des >300 familles identifiées dans le génome d’Arabidopsis. Qui plus est, on observe des variations importantes de fréquences et dynamiques de transpositions entre les différentes familles d’ET ce qui suggère l’existence de mécanismes additionnels contrôlant la transposition. Les analyses moléculaires réalisées sur un sous-ensemble des ET mobilisés appartenant à différentes familles ont notamment montré que ces différences sont dues en grande partie aux différentes modalités d’établissement du contrôle épigénétique sur les ET nouvellement insérés. D’autre part, nos analyses indiquent que la distribution des nouvelles insertions d’ET diffère grandement de celle des copies résidentes. Ce résultat suggère donc que la suraccumulation des séquences d’ET dans les régions péricentromériques du génome d’Arabidopsis n’est pas due à un ciblage spécifique des insertions dans ces régions, mais est plutôt la conséquence de leur élimination des bras chromosomiques. Enfin, nous avons cherché à déterminer dans quelle mesure la méthylation de l’ADN associée aux séquences répétées a un impact sur l’expression des gènes situés à proximité en étudiant des mutants affectés dans les différentes voies de la méthylation de l’ADN. Par des analyses phénotypiques et moléculaires nous avons montré que, même si la plupart des gènes d’Arabidopsis n’est pas affectée par l’état de méthylation des séquences répétées situées à proximité, deux voies de la méthylation de l’ADN agissent ensemble pour maintenir l’expression normale d’un petit nombre de gènes ayant des effets pléiotropes situés proximité de séquences répétées. La méthylation de l’ADN agit donc comme un double système de contrôle pour assurer l’expression normale d’un petit nombre de gènes clefs localisés a proximité de séquences répétées. / Transposable elements (TEs) and their relics are major components of eukaryotic genomes. TEs are potentially highly mutagenic as their proliferation can cause chromosomal rearrangements, disrupt genes or affect gene expression through transcriptional interference. However, few TEs are usually mobile within genomes at any one time thanks to potent mechanisms that restrain their activity, such as DNA methylation in mammals and plants. Thus, in the flowering plant Arabidopsis, severe loss of DNA methylation caused by mutations in the chromatin remodeler gene DDM1 triggers massive accumulation of transcripts corresponding to TEs. Yet, comparatively few TEs appear to be mobilized as a result. Here, we set out to determine (1) the extent to which DNA methylation prevents TE mobilization, (2) where do TEs insert following their reactivation and (3) what are the consequences of new TE insertions on the expression of neighboring genes. To this ends, we have sequenced the genome of over 50 epigenetic Recombinant Inbred Lines (epiRILs) that were derived from a cross between a wild type and an isogenic ddm1 mutant line. After backcrossing of the F1 and selection of the progeny homozygous for wild-type DDM1, the epiRILs were propagated through six rounds of selfing. The epiRILs therefore permit a detailed assessment of transposition events soon after they have occurred. In order to identify TE mobilization in the epiRILs we developed TE-tracker, a pipeline based on Illumina sequencing of mate pairs libraries. Using this approach, we could show that although both retroelements and DNA transposons are mobilized in ddm1 and the epiRILs, mobile TEs belong to only a dozen or so of the >300 TE families identified in the Arabidopsis genome. Furthermore the rate and dynamics of transposition vary dramatically between TE families, suggesting the existence of additional mechanisms controlling transposition. Molecular analysis performed on a subset of those mobile TEs belonging to distinct families show that these differences are greatly due to different modality of establishment of epigenetic control over newly inserted TEs. In addition, our analysis indicates that the distribution of new TE insertions differs dramatically from the one of resident copies. These findings provide compelling evidence that over accumulation of TE sequences in the pericentromeric regions of the Arabidopsis genome is not due to specific targeting of TEs, but rather to their elimination from chromosome arms. Finally, we assessed the extent to which repeat-associated DNA methylation impacts the expression of neighboring genes by studying mutants affected in different methylation pathways. Phenotypic and molecular analyses reveal that, even though most Arabidopsis genes are not detectably sensitive to the methylation status of neighboring repeats, two DNA methylation pathways act together to maintain the normal expression of only a very small number of genes near repeats and that these genes tend to have pleiotropic effects. Then, DNA methylation acts as a double-lock system to ensure the normal expression of a small number of key genes located near repeats.

Les éléments transposables (ET) ont un impact majeur sur le fonctionnement etla dynamique des génomes, à l’échelle de l’individu et de l’espèce. Le cilié Parameciumest un modèle original pour l’étude des ET. Chaque individu unicellulaire a un génomegerminal qui subit, lors des processus sexuels, des réarrangements massifs, comprenantl’élimination des ET et de leurs vestiges à copie unique, pour former un génome somatiqueoptimisé pour l’expression des gènes. La programmation épigénétique de cesréarrangements implique des petits ARN dans un processus complexe de soustractiongénomique.Au cours de ma thèse, j’ai effectué des analyses bioinformatiques et biostatistiques dedonnées hétérogènes à l’échelle du génome pour : (i) Identifier et analyser des propriétésintrinsèques, de dizaines de milliers de vestiges d’ET à copie unique, appelés "InternalEliminated Sequences" (IES). (ii) Comprendre le rôle de déterminants génétiques et dedifférents facteurs épigénétiques dans le ciblage et l’élimination des IES.L’ensemble de ces analyses met en lumière la co-Évolution des ET et des mécan-Ismes de défense de l’hôte. / Transposable elements (TE) have major impact on the function and dynamicsof genomes, both at the level of the individual and of the species. The ciliate Parameciumprovides an original model for studies of TE. Each individual unicell has a germlinegenome that undergoes massive rearrangements at each sexual generation including thephysical elimination of TE and their single copy remnants, yielding a somatic genomestreamlined for gene expression. The epigenetic programming of the rearrangementsinvolves small RNAs in a complex process of genomic subtraction.During my thesis, I carried out bioinformatic and biostatistical analyses of heteroge-Neous, genome-Scale datasets in order to : (i) Identifiy and study the intrinsic propertiesof tens of thousands of TE remnants know as "Internal Eliminated Sequences" (IES).(ii) Explore the roles of genetic determinants and epigenetic factors in the targeting andelimination of the IESs.Taken together, the studies illustrate the co-Evolution of TE and host defense mecha-Nisms.

Miniature Inverted-repeat Transposable Elements (MITEs) are a type of transposable element (TE) that lacks coding capacity. It has been established that in rice that certain Stowaway MITEs are mobilized by transposases from the Tc1/Mariner superfamily of TEs. To retrieve all Tc1/Mariner TEs from the genome, bioinformatic approaches were performed. A total of 295 Tc1/Mariner TEs that encoded a full or partial transposase were recorded which 100 were newly described. Sequence alignment, and identification of the catalytic motif placed these transposases into eight groups. A functional link was established by comparing the terminal sequences of the Stowaway-like MITEs to the termini of the terminal sequences of Tc1/Mariner TEs. A yeast excision assay was used to experimentally test these functional links. Majority of the Stowaway-like MITE and transposase combinations tested did not indicate a functional link. However, a possible functional link was observed between the AATp3-13 transposase and AAStow-5 Stowaway-like MITEs.