Дисертації з теми "Transposal elements"
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Jesus, Erika Maria de. "Estudo de dois grupos de elementos de cana-de-açúcar homológos à superfamília hAT de transposons." Universidade de São Paulo, 2007. http://www.teses.usp.br/teses/disponiveis/41/41132/tde-29082007-120131/.
Повний текст джерелаTransposable elements (TEs) are mobile genetic sequences. Their mutagenic capacity makes them important sources of variation in the genomes. These elements have another important evolutionary role as donors of functional protein domains in the formation of new genes. 276 cDNA clones homologous to TEs were previously identified in the Brazilian Sugarcane Expressed Sequence Tag Project (SUCEST) databases. In this work, we have obtained the full sequences of 156 for these clones. These sequences were compared with Genbank database. We have identified 9 families of transposons and 11 families of retrotransposons. The most representative families found amongst the transposons were MuDr and hAT (wich encompass Ac and Tam3), with 43 and 32 cDNAs, respectively. Amongst the retrotransposons, the most representative family was Hopscotch, with 25 cDNAs. After this global analysis, we have focused our investigation in the hAT-like cDNAs. A comparative analysis of these cDNAs has revealed a profile of two distinct groups. Group I is composed of sequences with high conservation at nucleotide level, it is present in the genome of all grasses analysed (hybrids and parentals of sugarcane, maize and rice) with low copy number, it is expressed in leaves and roots of sugarcane, and more intensely in callus. In addition, group I sequences have clustered with domesticated transposases. The group II is composed of more heterogeneous sequences similar with the original elements that constitute the hAT superfamily: hobo (from Drosophilla melanogaster), Ac (from Zea mays) and Tam3 (from Antirrhinum majus). This group was shown to be restricted to the genome of Saccharum, with higher copy number than group one. Inverse-PCR assays has identified terminal inverted repeats (TIRs) to the cDNA TE221 from group II. Primers based on the sequences of the TIRs allowed us to recover three elements hAT-like from sugarcanes genomic DNA: one of 3,5kb and another of 4,2kb, and a MITE of 250 bp. These results corroborate the strategy applied in order to recover elements from the sugarcane´s genome. Sequences homologous to both sugarcane group I and group II were found also in maize and rice, as well as in arabidopsis databases. These data suggest that the divergence of the two groups occured before the separation between the classes Monocotiledonea and Eudicotiledonea. Based on our results, we suggest the existence of an ancestral transposon hAT-like, present in angiosperms before the separation between Monocotiledonea and Eudicotiledonea, of which the transposase was captured to compose a new gene with some cellular function. Since the domestication event, these transposases followed distinct evolutive pathways, one as a regular gene and another as a bona fide transposon. These two forms of hAT-like transposases could be found in the sugarcanes genome, represented by the elements from groups I and II, respectively.
Meister, Gerald Alan. "Dispersal of transposable elements." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape7/PQDD_0019/NQ46389.pdf.
Повний текст джерелаTeramoto, Shota. "Amplification of the MITE mPing with the embryogenesis-specific expression of the transposon Ping in rice." Kyoto University, 2014. http://hdl.handle.net/2433/189683.
Повний текст джерела0048
新制・課程博士
博士(農学)
甲第18526号
農博第2083号
新制||農||1026(附属図書館)
学位論文||H26||N4870(農学部図書室)
31412
京都大学大学院農学研究科農学専攻
(主査)教授 奥本 裕, 教授 米森 敬三, 教授 冨永 達
学位規則第4条第1項該当
Spengler, Ryan Michael. "Mechanisms Of MicroRNA evolution, regulation and function: computational insight, biological evaluation and practical application." Diss., University of Iowa, 2013. https://ir.uiowa.edu/etd/2636.
Повний текст джерелаBraga, Raíssa Mesquita. "Identificação e caracterização de elementos transponíveis da classe II em Colletotrichum graminicola." Universidade Federal de Viçosa, 2012. http://locus.ufv.br/handle/123456789/5350.
Повний текст джерелаCoordenação de Aperfeiçoamento de Pessoal de Nível Superior
Colletotrichum is one of the most important genera of plant-pathogenic fungi in the world. The pathogenic species of this genus have hemibiotrophic lifestyle and cause diseases in several economically significant crops. Besides the economic importance, Colletotrichum has great significance as a model system for studying the molecular and cellular bases of fungal pathogenicity. The species C. graminicola, causal agent of corn anthracnose (Zea mays), has rare sexual stage and was the first species of the genus to have its genome completely sequenced. The transposable elements are ubiquitous and constitute a source of new mutations, being an important source of genetic variability. These elements are divided into two classes according to the presence or absence of an RNA intermediate in transposition. Elements of class I transpose via RNA intermediate, while class II elements transpose directly as DNA. The transposable elements can be applied as mutagenic agents aimed at the identification and labeling of genes and in phylogenetic and population studies. Given the importance of transposable elements in the generation of genetic variability and its applications in research, the aim of this study was to identify and characterize the class II transposable elements in the genome of C. graminicola. For this purpose, we used a bioinformatic approach combined with experimental activities. We identified 132 complete sequences of transposable elements in the sequenced genome of C. graminicola, which represent a significant proportion of the genome (0.47%). The elements were classified into six families according to similarity, all elements have characteristics of Tc1-mariner superfamily. Although some of these elements possess putative transposases with conserved DDE domain, all are interrupted by multiple stop codons. None of the elements identified has all the necessary features to be considered an active element. In silico analysis revealed evidence that these sequences are mutated by RIP (repeat point induced mutation) mechanism. TCg1 element was amplified by PCR from a Brazilian isolate and has imperfect terminal inverted repeats and the putative transposase sequence has three conserved domains characteristic of transposases: DDE, CENPB and HTH. However, this sequence is interrupted by stop codons and lacks the initiation codon and termination codon, therefore, is probably inactive. The genomic DNA from 49 different isolates were analyzed by hybridization with a probe derived from the inner region of TCg1 and different profiles were identified. The strategy allowed the efficient identification of a variety of Tc1-Mariner transposable elements degenerated by mutations characteristics of RIP in C. graminicola. It is unlikely that any of the identified elements is autonomous, however, these elements must have an important role in the genetic variability of this fungus. The TCg1 element is present in the genomes of different isolates of C. graminicola and has the potential to be used as a molecular marker in population analyzes.
Colletotrichum é um dos gêneros mais importantes de fungos fitopatogênicos em todo o mundo. As espécies fitopatogênicas desse gênero apresentam ciclo de vida hemibiotrófico e causam doenças em diversas culturas economicamente importantes. Além da importância econômica, Colletotrichum possui grande relevância como um sistema modelo para o estudo das bases celulares e moleculares da patogenicidade fúngica. A espécie Colletotrichum graminicola, agente causal da antracnose do milho (Zea mays), possui ciclo sexual raro e foi a primeira espécie do gênero a ter o seu genoma completamente sequenciado. Os elementos transponíveis são ubíquos e constituem uma fonte de novas mutações, sendo, portanto, uma importante fonte de variabilidade genética. Esses elementos são divididos em duas classes de acordo com a presença ou ausência de um intermediário de RNA na transposição. Os elementos da classe I se transpõem via intermediário de RNA, enquanto os elementos da classe II se transpõem diretamente como DNA. Os elementos transponíveis podem ser utilizados como agentes mutagênicos visando à identificação e etiquetagem de genes e em estudos filogenéticos e populacionais. Tendo em vista a importância dos elementos transponíveis na geração de variabilidade genética e as suas aplicações na pesquisa, o objetivo deste trabalho foi identificar e caracterizar elementos transponíveis da classe II no genoma de C. graminicola. Para tanto, foi utilizada uma abordagem de bioinformática (análises in silico) aliada às atividades experimentais. Foram identificadas 133 sequências completas de elementos transponíveis no genoma sequenciado de C. graminicola, que representam uma proporção relevante do genoma (0,47%). Os elementos foram classificados em 6 famílias de acordo com a identidade e apresentam características da superfamília Tc1-Mariner. Apesar de algumas transposases putativas codificadas por esses elementos possuírem domínio DDE conservado, todas estão interrompidas por vários códons de parada. Nenhum elemento identificado possui todas as características necessárias para um elemento autônomo. A análise in silico revelou evidências de mutações geradas pelo mecanismo de RIP (Mutação de ponto induzida por repetição). O elemento TCg1, amplificado por PCR a partir de um isolado brasileiro de C. graminicola, possui extremidades repetidas invertidas imperfeitas e a sequência putativa da transposase apresenta os três domínios característicos conservados: DDE, HTH e CENPB. Entretanto, essa sequência está interrompida por códons de parada e não foram localizados os códons de iniciação e de terminação, sendo, portanto, provavelmente inativa. O DNA genômico de 49 diferentes isolados foi analisado por hibridização com uma sequência derivada da região interna de TCg1 e apresentaram diferentes perfis. A estratégia utilizada permitiu uma identificação eficiente de uma variedade de elementos transponíveis Tc1-Mariner degenerados por mutações características de RIP em C. graminicola. É improvável que algum dos elementos identificados seja autônomo, entretanto, esses elementos devem possuir um importante papel na variabilidade genética desse fungo. O elemento TCg1 está presente no genoma de diferentes isolados de C. graminicola e possui potencial para ser utilizado como marcador molecular em análises populacionais.
Linheiro, Raquel. "Computational analysis of transposable element target site preferences in Drosophila melanogaster." Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/computational-analysis-of-transposable-element-target-site-preferences-in-drosophila-melanogaster(33ac0a41-2fbd-4974-b6b6-db4e1e48a7b0).html.
Повний текст джерелаWang, Weimin. "Transposable elements for insect transformation, the Mariner element and the I-PpoI intron-encoded endonuclease." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape7/PQDD_0017/MQ55290.pdf.
Повний текст джерелаZampicinini, GianPaolo. "Insertional polymorphism of four transposable elements in European populations of chironomus riparius (Diptera Chironomidae) as detected by transposon insertion Display." Lyon 1, 2005. http://www.theses.fr/2005LYO10014.
Повний текст джерелаRius, Camps Nuria. "Analysis of Drosophila buzzatii transposable elements." Doctoral thesis, Universitat Autònoma de Barcelona, 2016. http://hdl.handle.net/10803/378034.
Повний текст джерелаTransposable genetic elements are genetic units able to insert themselves in other regions of the genomes they inhabit, and are present in almost all eukaryotes analyzed. The interest of transposable element analysis, it is not only because its consideration as intragenomic parasites. Transposable elements are an enormous source of variability for the genomes of their hosts, and are therefore key to understanding its evolution. In this work we addressed the analysis of Drosophila buzzatii transposable elements from two different approaches, the detailed study of one family of transposable elements and global analysis of all elements present in the genome. The study of chromosomal inversions in D. buzzatii led to the description of the non-autonomous transposable element, BuT5, which was later found to cause polymorphic chromosomal inversions in D. mojavensis and D. uniseta. In this work we have characterized the transposable element BuT5 and we have described its master element. BuT5 is found in 38 species of the group of species D. repleta. The autonomous element that mobilizes BuT5 is a P element, we described three partial copies in the sequenced genome of D. mojavensis and a complete copy in D. buzzatii. The full-length and putatively active copy has 3386 base pairs and encodes a transposase of 822 residues in seven exons. Moreover we have annotated, classified and compared the transposable elements present in the genomes of two strains of D. buzzatii, st-1 and j-19, recently sequenced with next-generation sequencing technology, and in the D. mojavensis, the phylogenetically closest species sequenced, in this case with Sanger technology. Transposable elements make up for 8.43%, the 4.15% and 15.35% of the assemblies of the genomes of D. buzzatii st-1, j-19 and D. mojavensis respectively. Additionally, we have detected a bias in the transposable elements content of genomes sequenced using next-generation sequencing technology, compared with the content in genomes sequenced with Sanger technology. We have developed a method based on the coverage that allowed us to correct this bias in the genome of D. buzzatii st-1 and have more realistic estimates of the content in transposable elements. Using this method we have determined that the transposable element content in D. buzzatii st-1 is between 10.85% and 11.16%. Additionally, the estimates allowed us to infer that the Helitrons order has undergone multiple cycles of activity and that the superfamily Gypsy and BelPao have recently been active in D. buzzatii.
Alvarez, Monica A. "Mosquito Transposable Elements and piwi Genes." Thesis, Virginia Tech, 2008. http://hdl.handle.net/10919/33162.
Повний текст джерелаThis research focuses on two related subjects, TEs and their regulation. The first subject is on a Long Terminal Repeat (LTR) retrotransposon in the African malaria mosquito, Anopheles gambiae, namely Belly. The second subject focuses on the characterization of piwi genes in the dengue and yellow fever mosquito, Aedes aegypti.
For the first subject we characterized Belly by identifying the two identical LTRs and one intact open reading frame. We also defined the target site duplications and boundaries of the full-length Belly element. This novel retrotransposon has nine full-length copies in the An. gambiae sequenced genome and their nucleotide similarity suggests that there has been fairly recent retrotransposon. We have shown that Belly is transcribed and translated in An. gambiae. Single LTR circles were recovered from An. gambiae cells, which is consistent with active transposition of Belly.
The second subject focuses on the piwi genes of Ae. aegypti. We found nine potential piwi genes in Ae. aegypti and two in An. gambiae. Phylogenetic analysis suggests that these piwis formed two subgroups and gene duplication within each group occurred after the divergence between the two mosquito species. RT-PCR and transcriptome analysis showed Ago3 as well as all the seven tested piwi genes were expressed either in germline tissues or developing embryos. Differential expression patterns were observed. While most piwis were transcribed in the ovaries, testis, and embryos, two piwis appear to have a zygotic expression. Three piwi genes (piwi 3, piwi 4, and Ago3) were also
detected in adult somatic tissues of Ae. aegypti. The expansion of the number of piwi genes in Ae. aegypti compared to An. gambiae and D. melanogaster may be correlated with a larger genome size and greater amount of TEs. The finding of piwi expression in adult somatic tissues is intriguing. It is possible that these piwi genes were expressed in the adult stem cells. It is also possible that they may be involved with anti-viral defense. Both of these hypotheses require further testing.
Master of Science
Teixeira, Paula Rezende. "Identificação e caracterização de elementos de transposição no genoma de Rhynchosciara." Universidade de São Paulo, 2007. http://www.teses.usp.br/teses/disponiveis/46/46131/tde-12062008-100547/.
Повний текст джерелаTransposable elements are discrete sequences that are able to move from one locus to another within the genome, constituting a significant part of eukaryotic genome. They are grouped into two main types, Class I elements transpose via an RNA intermediate (retrotransposon), and Class II elements transpose via a DNA \"cut-and-paste\" mechanism (transposons). The analysis of sequences of a cDNA bank constructed from mRNA of the salivary glands of Rhynchosciara americana showed the presence of putative types of two classes elements. In the present thesis we describe four mariner elements, where the nucleotides consensus sequences were derived from multiple defective copies containing deletions, frame shifts and stop codons. Ramar1, a full-length element and Ramar2 is a defective mariner element that contains a deletion overlapping most of the internal region of the transposase ORF and the extremities of the element maintain intact. Ramar3 e Ramar4 are defective mariner element that were impossible to predict a complete ORF. Predicted transposase sequences demonstrated that Ramar1 and Ramar2 are phylogenetically very close to mariner-like elements of mauritiana subfamily. However, Ramar3 and Ramar4 belong to mellifera and irritans subfamilies, respectively. In situ hybridisations showed Ramar1 localized in several chromosome regions, mainly in pericentromeric heterochromatin and their boundaries, while Ramar2 appeared as a single band in chromosome A. More interesting data were the molecular characterization of the non-LTR retrotransposon element, called as RaTART, that probably is the responsible by telomeric reconstruction in R.americana, as well as the telomeric retrotransposable elements TART, Het-A and TAHRE of Drosophila. Southern blot analysis indicated that this transposable element is represented by repeat sequences in the genome of R. americana, and Northern blot analysis showed a expression in different developmental stages and the transcript of high molecular mass detected represents the full-length non-LTR retrotransposon. However, the chromosomal localization of the retroelement by in situ hybridisation showed a labelling predominant on chromosome ends, indicating possibly the first transposable element described in R.americana with a defined role in chromosome structure. The last retrotransposon, identified in this project, present in the genome of Rhynchosciara americana, called R2Ra, was isolated from screening of a lambda dash genomic library using as probe the recombinant pRa1.4 of rDNA. The analysis of sequence showed the presence of conserved regions, like transcriptase reverse domain and zinc finger motif in the amino terminal region. The insertion site is high conserved in R.americana and a phylogenetic analysis showed that this element belongs to the R2 clade. The chromosomal localization confirm that the R2Ra mobile element insert into the site specific in rDNA gene.
Harris, Nigel. "A transposable element of wheat." Thesis, University of Cambridge, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.330215.
Повний текст джерелаWang, Jichang [Verfasser]. "Transposable Elements and Human Pluripotency / Jichang Wang." Berlin : Freie Universität Berlin, 2015. http://d-nb.info/1075190843/34.
Повний текст джерелаJunior, Nilo Luiz Saccaro. "O sistema Mutator em cana-de-açúcar: uma análise comparativa com arroz." Universidade de São Paulo, 2007. http://www.teses.usp.br/teses/disponiveis/41/41132/tde-30012008-113943/.
Повний текст джерелаTransposable elements (TEs) constitute great part of eukaryote genetic material, in grasses, they comprise between 50-80% of the genome. Genome projects have significantly increased the amount of information about these elements, revealing their importance and allowing the development of new approaches for their study. The Mutator system (Mu) of maize is the most active and mutagenic plant transposon. Beyond the autonomous element, MuDR, the system comprises a very heterogeneous, in sequence and structure, set of elements, called MuLEs, that can contain even host gene fragments. The most abundant transposon related sequences expressed in sugarcane transcriptoma are the MuDR-like. They group into four clades (called Classes I, II, III and IV) that exist prior to the Mono and Eudicot split. The aim of this work is to gain knowledge about the Mutator system in sugarcane through the comparative analysis against rice (whose genome is completely sequenced). The results described the abundance and diversity of the Mu system in grasses, evidencing a clado-specific amplification with a burst of Class II along the evolution of this plant group. Structural analyses showed that, while Classes I and II comprise elements with transposon characteristics, Classes III and IV are domesticated transposases. One BAC clone from each sugarcane parental genotype (Saccharum officinarum and Saccharum spontaneum) have been completely sequenced, both containing Class III elements. These elements have been characterized and the sugarcane genomic sequences were compared with their orthologues in rice. The comparative analyses showed an accumulation of TEs in the intergenic regions.
Denby, Wilkes Cyril. "Ciblage & élimination des transposons et de leurs vestiges lors des réarrangements programmés du génome somatique de la paramécie." Thesis, Paris 11, 2014. http://www.theses.fr/2014PA112306/document.
Повний текст джерелаTransposable 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
Piriyapongsa, Jittima. "Origin and evolution of eukaryotic gene sequences derived from transposable elements." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/24766.
Повний текст джерелаCommittee Chair: Jordan, I. King; Committee Member: Borodovsky, Mark; Committee Member: Bunimovich, Leonid; Committee Member: Choi, Jung; Committee Member: McDonald, John.
Saint, leandre Bastien. "La régulation des éléments transposables par la voie des piARN : Les différences entre lignées germinales mâles et femelles et leurs conséquences sur la dynamique de transposition." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLS084/document.
Повний текст джерелаTransposable Elements (TEs) are genomic parasites characterized by their ability to replicate faster than any other genetic element in the genomes. The piRNA mediated silencing is of central importance to limit TE expansion in the germline of animal species. The present dissertation explores the relationship between TEs and piRNAs alongside their evolutionary dynamics.The first question raised here was to understand how the genome responds to a new TE invasion. For that purpose, we injected a mariner Class II transposon into D. melanogaster genome that does not naturally contain the element. We found that, after its self-replication into the genome, the element have reached a copy number equilibrium since a de novo piRNA mediated regulation have been acquired.Second, we studied the mariner rewiring activity during the colonization of geographical temperate regions. From a large sampling of D. simulans natural populations, we found the mean activity of mariner to be strikingly higher in non-African populations compared to the African ones. These findings support the idea that selection acting on piRNA effector proteins has been of central importance to explain TE lineages diversification during colonization process.The third chapter provides evidences to propose that, the strong TE activity in testes, is a general phenomenon in Drosophila. We also observed that TE landscape divergence between the two sister species, have affected the genomic response mediated by the piRNAs. As a response of their recent bursts of transposition, TEs overexpressed in testes are preferentially silenced by piRNAs in D. melanogaster ovaries. By contrast, we assumed the D. simulans piRNA response to be the relic of a past regulation that still persists mostly against inactive TEs.The piRNA silencing in the germline, is assumed to be the “vanguard of genome” defense and integrity due to its active role against TEs. However, while natural selection purifies the genome from its deleterious parasites, it seems that the host regulation contributes to genome homeostasis by limiting their expansion, and somehow, favors their longterm maintenance. Thus, another interpretation would have been that piRNA silencing is the “vanguard of genome” diversification due to its active role in facilitating TE accumulation
Hawkins, Jennifer S. "Transposable elements and genome size dynamics in Gossypium." [Ames, Iowa : Iowa State University], 2007.
Знайти повний текст джерелаWarren, Ann. "Transposable genetic elements in the mosquito Aedes aegypti." Thesis, University of Liverpool, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.237672.
Повний текст джерелаSmith, Jill. "Mariner-analysis of a Drosophila transposable element." Thesis, University of Edinburgh, 1999. http://hdl.handle.net/1842/11923.
Повний текст джерелаHuda, Ahsan. "Epigenetic regulation of the human genome by transposable elements." Diss., Georgia Institute of Technology, 2010. http://hdl.handle.net/1853/34665.
Повний текст джерелаMcGraw, James. "Persistence of bacterial transposable elements in a fluctuating environment." Thesis, University of Nottingham, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.490829.
Повний текст джерелаStyles, Pamela. "The evolution of transposable elements in humans and Drosophila." Thesis, University of Nottingham, 2010. http://eprints.nottingham.ac.uk/11241/.
Повний текст джерелаHudson, A. D. "Changes in stability of transposable elements in Antirrhinum majus." Thesis, University of East Anglia, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.380962.
Повний текст джерелаGbadegesin, Adedapo. "Characterisation of transposable elements of cassava (Manihot esculenta Crantz)." Thesis, University of Bath, 2005. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.415767.
Повний текст джерелаVives, i. Cobo Cristina. "Impact of transposable elements in the evolution of plant genomes." Doctoral thesis, Universitat Autònoma de Barcelona, 2017. http://hdl.handle.net/10803/456558.
Повний текст джерелаEls transposons són elements genètics que tenen la capacitat de modificar la seva posició dins el genoma. Com a conseqüència, tenen un impacte en l’evolució del genomes inactivant o alterant els gens de l’hoste i proporcionant noves funcions gèniques. Els transposons ocupen una fracció important de tots els genomes seqüenciats. L’objectiu del treball presentat en aquesta tesis consisteix en estudiar els diversos impactes de transposons tant en els gens com en l’evolució dels genomes de diferents espècies de plantes. En aquesta tesis, s’ha analitzat la fracció de transposons en meló i cogombre, dues espècies molt properes. Els resultats suggereixen que els transposons han proliferat més en meló, causant un augment de la mida del genoma. Els transposons no es troben distribuïts habitualment de forma homogènia i tendeixen a acumular-se en les regions pericentromèriques heterocromàtiques, com el cas dels genomes de meló i cogombre. Curiosament, els resultats presentats mostren que els transposons han expandit les regions pericentromèriques en meló, demostrant que els transposons poden modificar l’estructura dels genomes. El número de genomes de referència de plantes disponibles i el número de varietats reseqüenciades ha crescut exponencialment permetent estudiar la correlació entre les variacions genètiques i fenotípiques. El propòsit del treball resumit en la segona part d’aquesta tesis consisteix en analitzar l’impacte dels transposons en genomes d’espècies cultivables detectant els polimorfismes deguts a la presència o absència de transposó en un locus concret, comparant una varietat reseqüenciada respecte al seu genoma de referència. L’anàlisi d’insercions polimòrfiques de transposons s’ha realitzat en tres espècies diferents: meló, palmera datilera i Physcomitrella patens. Els resultats obtinguts poden ajudar a identificar famílies de transposons actives recentment i proporcionar informació nova sobre polimorfismes genètics que poden estar lligats a caràcters seleccionats durant l’evolució recent d’aquestes tres espècies. Per tal d’estudiar l’impacte de la transposició en la regulació gènica, el treball presentat en la tercera part d’aquesta tesis se centra en la capacitat dels transposons en amplificar i redistribuir llocs d’unió a factors de transcripció. Els resultats mostren que algunes famílies de MITEs s’han amplificat i han redistribuït els llocs d’unió del factor de transcripció E2F durant l’evolució d’algunes espècies del gènere Brassica. L’objectiu d’aquest treball és avaluar l’impacte dels llocs d’unió a E2F localitzats dins de transposons reprogramant la regulació de gens de la xarxa transcripcional de E2F. Els resultats obtinguts han determinat que els llocs d’unió a E2F localitzats dins de transposons tenen la capacitat d’unir-se als factors de transcripció de E2F in vivo, independentment de les marques epigenètiques de la regió. A més a més, els transposons s’han convertit en eines genètiques útils per generar col·leccions de mutants en animals i plantes degut a la seva capacitat d’integrar còpies en el genoma. En plantes, alguns retrotransposons s’integren preferentment a prop de gens sent particularment interessants per la mutagènesis. Entre tots ells, el retrotransposó de tabac Tnt1 s’ha utilitzat per generar mutants en diferents espècies de plantes. L’última part d’aquesta tesis consisteix en analitzar la capacitat del retrotransposó de tabac Tnt1 en transposar en la molsa Physcomitrella patens. S’ha demostrat que Tnt1 transposa eficientment en P. patens i s’integra preferentment a prop de gens. Aquest estudi presenta vectors derivats de Tnt1 dissenyats per transposar amb alta eficiència i ser utilitzats per generar col·leccions de mutants amb insercions estables en aquest briòfit.
Transposable elements are genetic elements that have the capacity to modify their position within the genome. As a consequence, they impact the evolution of genomes by inactivating or altering host genes and by providing new gene functions. Transposons account for an important fraction of all sequenced genomes. The goal of the work presented in this dissertation is to investigate the diverse impacts of transposons on gene and genome evolution in different plant species. The transposon content has been analyzed in melon and cucumber, two closely related species. The results suggest that transposons have proliferated to a greater extend in melon, causing an increase of its genome size. Transposable elements are usually not homogenously distributed and tend to accumulate in heterochromatic pericentromeric regions. This is also the case of melon and cucumber genomes. Interestingly, the results presented show that transposons have expanded the pericentromeric regions in melon, showing that transposons can modify the structure of genomes. The number of plant reference genomes made available and the number of varieties resequenced is growing exponentially, and this is allowing to study the correlation between genetic and phenotypic variations. The purpose of the work summarized in the second part of this dissertation is to analyze the impact of transposons in crop genomes by detecting polymorphisms due to the presence or absence of transposon at a given locus, comparing one resequenced variety respect to the reference genome. The analysis of transposon-related polymorphism insertions has been performed in three different species: melon, date palm and Physcomitrella patens. The results obtained can help to identify the transposon families recently active and to provide new information on genetic polymorphisms that can be linked to traits selected during the recent evolution of these three species. In order to study the impact of transposition on gene regulation, the work reported in the third part of this dissertation focuses on the capacity of transposons to amplify and redistribute transcription factor binding sites. The results show that some MITE families have amplified and redistributed the binding sites of E2F transcription factor during Brassica evolution. The goal of this study was to assess the impact of E2F binding sites located within a transposon in reprogramming gene regulation on the E2F transcriptional network. The results obtained have determined that E2F binding sites located within transposons have the capacity to bind E2F transcription factor in vivo, regardless the epigenetic mark context. Moreover, transposons have become a useful genetic tool to generate mutant collections in animals and plants due to the capacity to insert copies into the genome. In plants, some retrotransposons have been shown to integrate preferentially near genes making them particularly interesting for mutagenesis. Among them, the tobacco retrotransposon Tnt1 has been used to generate mutants in different plant species. The last part of this dissertation consists in analyzing the capacity of the tobacco retrotransposon Tnt1 to transpose in the moss Physcomitrella patens. It shows that Tnt1 efficiently transposes in P. patens and inserts preferentially in genic regions. This work presents Tnt1-derived vectors designed for high efficiency transposition that could be used to generate stable insertion mutant collections in this bryophyte species.
Yang, Guojun. "Miniature inverted repeat transposable elements in rice - origin and function." Texas A&M University, 2004. http://hdl.handle.net/1969.1/318.
Повний текст джерелаHolmquist, Isabel Rosa. "A population genetics study of transposable elements as genetic drivers." Thesis, Imperial College London, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.516357.
Повний текст джерелаTurner, A. Keith. "Analysis of class II bacterial transposable elements TN2501 and TN3926." Thesis, University of Bristol, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.330037.
Повний текст джерелаFultz, Dalen R. "The Silencing of Endogenous and Exogenous Transposable Elements in Arabidopsis." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1492468003210374.
Повний текст джерелаMarshall, John Macky. "The dynamics of transposable elements in genetically modified mosquito vectors." Diss., Restricted to subscribing institutions, 2008. http://proquest.umi.com/pqdweb?did=1666911641&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.
Повний текст джерелаBogaerts, Márquez María 1991. "Identification of environmental variables in Drosophila melanogaster natural populations." Doctoral thesis, TDX (Tesis Doctorals en Xarxa), 2022. http://hdl.handle.net/10803/673159.
Повний текст джерелаUnderstanding how species adapt to the environment is still an open question in Evolutionary Biology. While the focus has been on the genetic basis, the analysis of the environmental factors which drive these adaptive processes lags behind. Our main goal is to identify the main environmental variables that contribute to adaptation. We used natural D. melanogaster populations from Europe and North America, and analyzed both SNPs and transposable elements (TEs). To accurately detect and estimate TE population frequencies, we updated the T-lex algorithm and released a new version: T-lex3. We performed a Genome-Environment Analysis (GEA) to associate TEs and SNP allele frequencies with several environmental variables, and we identified temperature, rainfall and wind as the relevant variables involved in environmental adaptation. In addition, we found 10 TEs associated with an environmental variable. Finally, we developed a bioinformatic pipeline that integrates >200 D. melanogaster world-wide genomes, which will facilitate environmental analysis in space and time.
Mouz, Sébastien. "Régulation de l'expression des gènes bph du transposon Tn4371 chez Ralstonia eutropha CH34." Grenoble 1, 1998. http://www.theses.fr/1998GRE10185.
Повний текст джерелаEkaterinaki, Nelly. "Expression and function of TN7 transposition proteins." Thesis, University of Glasgow, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.303343.
Повний текст джерелаCharles, Mathieu. "Evolution des génomes du blé (genres aegilops et Triticum) au sein des Poaceae : dynamique rapide de l'espace occupé par les éléments transposables et conservation relative des gènes." Thesis, Evry-Val d'Essonne, 2010. http://www.theses.fr/2009EVRY0023/document.
Повний текст джерелаMy PhD aims to characterize dynamic evolution and organization of wheat genomes from différent species (Triticum and Aegilops genera) in relation to transposable element (TE) proliferation in their genomes (>80%), polyploidizations and synteny with other Poaceae species. By constituting and comparing representative genomic sequences and analyzing haplotype variability of the wheat genomes, I have characterized dynamics and differential proliferation of TEs, as resulting from the combinations of their insertions and deletions. Mean replacement rate of the TE space, which measures sequence differences due to insertion and removal of TEs between two haplotypes, was estimated to 86% per one million year (My). This is more important than the well-documented haplotype variability found in maize. It was observed that TE insertions and DNA elimination by illegitimate recombination (implicating several ‘tens’ of kb) as well as homologous recombination between divergent haplotypes represent the main molecular basis for rapid change of the TE space. At a longer evolutionary scale (60 My), I have compared gene conservation at the Ha locus region between different Poaceae species. The comparative genome analysis and evolutionary comparison with genes encoding grain reserve proteins of grasses suggest that an ancestral Ha-like gene emerged, as a new member of the Prolamin gene family, in a common ancestor of the Pooideae (wheat and Brachypodium from the Triticeae and Brachypodieae tribes) and Ehrhartoideae (rice), between 60 and 50 My, after their divergence from Panicoideae (Sorghum)
Lopez-Maestre, Hélène. "Analyses et méthodes pour les données transcriptomiques issues d’espèces non modèles : variation de l’expression des éléments transposables (et des gènes) et variants nucléotidiques." Thesis, Lyon, 2017. http://www.theses.fr/2017LYSE1025/document.
Повний текст джерелаNext-generation high throughput sequencing technologies provide efficient, rapid, and low cost access to sequencing. Its application to transcriptomes, called RNA-seq, enables the study of both the sequence and the expression of the transcripts. Many bio-informatics methods are still developed for RNA-seq data processing, trying to get the maximum out of it. Assembly methods allow us to study non-model species (no reference genome available) as well as model species. The work presented here is mostly related to RNA-seq data on non-model species.In the first study, to understand the initiation of hybrid incompatibility, we performed a genome-wide transcriptomic analysis on ovaries from parental lines and on hybrids from reciprocal crosses of \emph{D. mojavensis} and \emph{D. arizonae}. We didn't see a global deregerulation of genes or transposable element. Instead, we show that reciprocal hybrids presented specific gene categories and few transposable element families misexpressed relative to the parental lines. The analytical workflow developed for this project will be used to analyze transcriptomic data from the testis, but also to study the reciprocal crosses from other lines of D. mojavensis with D. arizonae leading to variable levels of sterility in hybrids. A second project tacked here is the identification and quantification of SNPs from RNA-seq data without a reference genome with KisSplice. Kissplice was developed to identified several type of variants (splicing events, indels) directly from the de Bruijn graph, build from the sequenced reads. We also developed other KisSplice-tools, for downstream analyses of the SNPs, including the prediction of their impact on the protein sequence
Horváth, Vivien 1990. "Unravelling the role of transposable elements in the eukaryotic stress response." Doctoral thesis, Universitat Pompeu Fabra, 2020. http://hdl.handle.net/10803/669757.
Повний текст джерелаEl estrés ambiental es un aspecto importante de la vida y un factor limitante en la supervivencia y distribución de las especies. Entender la respuesta a estrés a nivel de organismo y los mecanismos desarrollados para enfrentarlo son indispensable para mitigar sus efectos negativos. Muchos estudios se han centrado en el rol de los polimorfismos de nucleótido único, mientras que otros potentes mutágenos, como son los elementos transponibles (TEs), han sido ignorados. En la primera parte de esta tesis, hemos estudiado la contribución de los TEs en la respuesta eucariótica a estrés utilizando un enfoque específico al mecanismo molecular. Al estudiar seis tipos de respuesta a estrés diferentes en humanos y en Drosophila melanogaster hemos demostrado que los TEs pueden regular la expresión de genes de respuesta a estrés gracias a la adición de sitios de unión de factores de transcripción. En la segunda parte, hemos escogido un enfoque específico de estrés y hemos descrito las bases transcriptómicas y fisiológicas de la tolerancia a la desecación en D. melanogaster. Además, hemos observado que los los TEs podrían estar involucrados en la respuesta a estrés por desecación, aunque no parecen ser la principal mutación causante de la respuesta a este estrés. En conjunto, se muestra que los TEs tienen un rol importante en la respuesta eucariótica a estrés, sin embargo, su contribución parecería ser específica del estrés.
Hoen, Douglas. "Coevolution of transposable elements and plant genomes by DNA sequence exchanges." Thesis, McGill University, 2012. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=107660.
Повний текст джерелаLes éléments transposables (ET) sont des séquences d'ADN capables de se déplacer et de s'autoreproduire dans un génome, un mécanisme appelé transposition. Ces éléments représentent l'une des composantes les plus importantes des génomes nucléaires eucaryotes. Cette capacité à s'autoreproduire, grâce aux protéines codées par les ET autonomes, a permis aux ET de persister et de peupler les génomes sans nécessairement apporter un avantage adaptatif immédiat à l'organisme hôte. À cet égard, les ET sont parfois considérés comme des éléments égoïstes ou parasites, ou de l'ADN « poubelle ». Néanmoins, les ET ont joué un rôle important au cours de l'évolution en générant diverses adaptations essentielles aux eucaryotes. Ainsi, les ET peuvent coévoluer avec les gènes du génome hôte par l'échange direct de séquence d'ADN. Les ET peuvent se dupliquer et mobiliser des gènes hôtes ; à l'inverse, des séquences d'ADN dérivées de ET peuvent avoir le même niveau de conservation que des gènes hôtes. Dans le cadre de ma thèse, j'ai utilisé des analyses bio-informatiques à l'échelle du génome afin d'identifier des échanges directs de brins de séquence d'ADN à partir de génomes de plantes vers les ET, et vice-versa, et de caractériser leurs fonctions et leurs effets évolutifs. Ma thèse débutera par une recension des diverses publications scientifiques dans le domaine. Je dresserai ensuite un portrait des éléments mobiles Mutator-like (MULE) dans le génome du riz qui ont entraîné la duplication et la mobilisation de milliers de fragments de gènes codants normaux, un procédé appelé transduplication. Contrairement à ce qui avait été rapporté dans des publications antérieures, ces séquences transdupliquées ne semblent pas produire des protéines fonctionnelles malgré le fait qu'elles puissent avoir des fonctions régulatrices. En second lieu, j'examinerai une famille de gènes, appelée Kaonashi (KI), qui proviendrait d'un événement de transduplication présent dans les MULE de l'Arabidopsis thaliana, mais également conservé dans les ET. La présence de la famille KI nous montre que le procédé de transduplication permet à l'occasion des duplications fonctionnelles de gènes. Cependant, du moins dans le cas de la KI, le procédé n'entraîne pas la création d'un nouveau gène normal, mais bien d'un nouvel élément transposable. En troisième lieu, j'examinerai les gènes hôtes présents dans le génome de la plante A. thaliana qui proviendrait de ET, un procédé appelé domestication moléculaire. En plus des trois cas de familles d'éléments transposables domestiquées (ETD) déjà connues dans l'espèce A. thaliana, j'ai identifié 23 nouvelles familles potentielles. L'ensemble de ces résultats tend à démontrer que, malgré le fait qu'ils persistent dans les génomes grâce à leur capacité d'autoreproduction, les ET ne sont pas des parasites moléculaires, mais bien des éléments clés faisant partie intégrale des génomes eucaryotes.
Karzand, Masoud. "Impact of transposable elements and repeats on mappability across human genome." Thesis, McGill University, 2014. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=123270.
Повний текст джерелаDans cette thèse, nous étudions la "visibilité" du génome humain par des méthodes séquençage modernes et nous regardons quelles sont les raisons qui pourraient causer l'absence de visibilité dans une région donnée. Nous montrons que les éléments transposables et les duplications de génome sont les principaux obstables à la visibilité de régions génomiques. Dans cette analyse, nous avons utilisé des reads simulés, de types individuels ou pairés, de 6 longueurs différentes et nous avons utilisé BWA pour assigner ces reads au génome humain. Nous avons supposé que la position dans le génome est visible s'il y a au moins un read unique assigné à cette position. Nous avons examiné les régions non visibles et la fraction d'éléments transposables ou des duplications de génome correspondant à ces régions. Nous avons également examiné la distribution d'âge des éléments transposables et des duplications de génome qui sont dans les régions non visibles. Nos résultats montrent que les régions qui sont des éléments plus jeunes et plus transposable sont plus difficiles à séquencer. Afin de comparer nos données simulées avec les données réelles de séquençage, nous avons utilisé des données de reséquençage provenant d'un séquençage Illumina pour comparer la couverture observée du génome avec nos résultats provenant de données simulées. Nous montrons que 4,1% du génome qui est visible dans nos simulations a une faible couverture dans les données de séquençage réelles. Nous avons également étudié les raisons pouvant expliquer une faible couverture dans les régions visibles. Les résultats de nos simulations montrent l'impact des éléments transposables et les autres répétitions sur la visibilité dans le génome humain et nous montrent que l'utilisation de long reads pairés améliorent la visibilité du génome humain.
McCurrach, Karen J. "Investigation of transposon-like elements in the genome of Physarum polycephalum." Thesis, University of Aberdeen, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.352927.
Повний текст джерелаGrace, Cooper A. "Evolutionary genomics of transposable elements in the Saccharomyces sensu lato complex." Thesis, University of Huddersfield, 2018. http://eprints.hud.ac.uk/id/eprint/34743/.
Повний текст джерелаLai, Chaoqiang. "Quantitative genetic variation induced by P transposable elements in Drosophila melanogaster." Thesis, University of Edinburgh, 1990. http://hdl.handle.net/1842/15184.
Повний текст джерелаPanta, Manisha. "Prediction of Hierarchical Classification of Transposable Elements Using Machine Learning Techniques." ScholarWorks@UNO, 2019. https://scholarworks.uno.edu/td/2677.
Повний текст джерелаBlauth, Monica Laner. "Expressão de elementos transponíveis em Drosophila willistoni." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2005. http://hdl.handle.net/10183/15806.
Повний текст джерелаStudies accomplished in the Laboratory of Drosophila of UFRGS have been characterizing strains of Drosophila willistoni in respect to the presence of Transposable Elements (TEs) and to the occurrence of the Hybrid Dysgenesis phenomenon in this species. As a consequence of these studies, the present work aimed to broaden the knowledge about the role of these elements in the genesis of variability in this species, by approaching the transcriptional expression of P, hobo, gypsy and 412 TEs, already described in the D. willistoni genome. In our work, we verified the presence of P, gypsy, and 412 transcripts in adults, suggesting post-transcriptional regulation, like already described for P element in D. melanogaster, considering that the strains studied were not characterized by hypermutability. Due to the previous description of the Hybrid Dysgenesis Syndrome in the offspring resulting of crosses between 17A2 and Wip D. willistoni strains, their P element expression pattern during the embryonic development was established. The embryonic P element expression pattern in D. melanogaster was also established, for comparative purpose, since the occurrence of a horizontal transfer event of this element from D. willistoni to D. melanogaster is accepted. The similarity among these expression patterns in both species suggests that P element is regulated by its own promoter and that it’s not dependent of the insertion sites neighboring genes promoters. The presence of putative P element transcripts of transposase and of the transposase repressor was established in the analyzed embryos. Besides the transposase repressor transcript, that is result of an alternative splicing of the transposase transcript, it was obtained indication of the presence of antisense transcripts of P element in the embryos, suggesting the regulation by RNA interference (RNAi) in this stage of development of Drosophila. Transcriptional differences of the P element between D. willistoni and D. melanogaster, are related to the number of deleted transcripts of P that are expressed in larger number in D. melanogaster than in D. willistoni, corroborating the idea of the recent invasion of the genome of the first species by this element. The expression of TEs described in this work suggests a complex regulation of these elements, evidencing the importance of the continuity of this study.
Deprá, Maríndia. "Elementos hAT de Drosophila : análise de expressão e distribuição." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2009. http://hdl.handle.net/10183/29227.
Повний текст джерелаTransposable elements (TEs) are ubiquitous and abundant in several analyzed genomes. In this work two TE families (hosimary and hobo), belonging to the hAT superfamily, were studied. Here is described a new family, called hosimary, that was arised of analyzes of two sequences initially described by our research group (hosim e hosec). By performing PCR analysis in 50 drosophilidae species, sequences homologous to hosim and hosec were detected in Drosophila species of the melanogaster subgroup and in Zaprionus indianus. The number of copies observed among these species showed to be variable and most sequences presented coding potential. High similarity between these sequences, which belong to two distinct genera, as well as some inconsistencies among the phylogeny of the host species and the TEs were observed. This can be an indicative of horizontal transfer of these elements. Additionally, the sequences presented more than 90% of mutual similarity and no significant similarity with other already described element. This led us to suggest this new transposon family, that we called hosimary. The other family analyzed in this work includes the hobo and hoboVA (or hoboVAHS) elements. These elements may be involved in a hypermutability phenomenon observed by our research group. Sense and antisense transcripts were detected by transcriptional expression analysis, which suggests an RNA interference mechanism (iRNA) controlling the activity of these elements. in situ hybridization of whole mount embryo analysis showed similarity of the hobo and hoboVAHS expression pattern with patterns observed in developmental genes. This led us to suggest the existence of cis-regulatory sequences into the elements that can be interacting with the host genes. The presence of these cis-regulatory sequences in TEs can be related to evolutionary issues since they can be responsible for genetic variability.
Ludwig, Adriana. "Diversidade e evolução de elementos de transposição em Drosophila." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2010. http://hdl.handle.net/10183/142648.
Повний текст джерелаTransposable elements (TEs) are segments of DNA that have the ability to move and replicate within the genome. They are present in nearly all organisms, composing a significant fraction of their genomes. Two classes of TEs are widely recognized, the retrotransposons (class I) that transpose through a RNA intermediate and transposons (class II) that use DNA as a direct intermediate of transposition. The diversity, complexity and ubiquity of transposable elements, the extensive phenotypic and molecular variation produced in their hosts as a consequence of its transposition, as well as genetic horizontal transmission between species, indicate that TEs play an important role in evolution of genomes, substantiating the importance their study in different organisms. This study aimed to explore the evolutionary history of different transposable elements in Drosophila to contribute to the understanding of the co-evolution of these sequences with the host genome. Our main focus was to investigate the evolution of Drosophila endogenous retroviruses and we found several examples of horizontal transfer between species. Some of these retroviruses may still be active and are potentially infectious agents, which help to explain the high number of horizontal transfer events. We also investigate the distribution and evolution of a non-autonomous family of DNA transposons, which can be considered as MITEs (Miniature Inverted-repeat Transposable Elements). Our analyses confirm that several processes have contributed to the evolution and distribution of transposable elements in the genomes, such as vertical transmission, stochastic loss, ancestral polymorphism with independent assortment of copies during speciation, introgression and horizontal transfer.
Marzo, Llorca Mar. "The transposon Galileo in the Drosophila genus." Doctoral thesis, Universitat Autònoma de Barcelona, 2011. http://hdl.handle.net/10803/83991.
Повний текст джерелаLos 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.
Romero, Soriano Valèria. "Transposable element misregulation in Drosophila buzzatii–Drosophila koepferae interspecific hybrids." Doctoral thesis, Universitat Autònoma de Barcelona, 2016. http://hdl.handle.net/10803/393906.
Повний текст джерелаTransposable elements (TEs) are mobile genetic units present in almost all the eukaryotic sequenced genomes. Their mobilizing capacity, together with their repetitive nature, makes them powerful endogenous mutators able to create novel genetic variants, which will be then subject to selection. However, their mutagenic potential can also endanger their host’s fitness, which has led to the development of several regulatory strategies against TE mobilization in eukaryotic organisms. These are especially important in the germline, where mutations can be transmitted to the offspring. In Drosophila ovaries, TEs are mainly regulated by a small RNA-mediated silencing mechanism, the piRNA (Piwi-interacting RNA) pathway, which affects transcriptional and post-transcriptional TE silencing. This strong regulation can be relaxed under several stress conditions, including interspecific hybridization, a genomic stressor that promotes TE mobilization. Several cases of transposition events have been described in hybrids of different species, including both animals and plants. In the case that concerns us, D. buzzatii–D. koepferae hybrids, a previous survey in our group detected mobilization of at least 28 TEs. However, the molecular mechanisms underlying this TE release remain elusive, although recent studies on hybrid TE expression seem to point to a transcriptional deregulation. Furthermore, little is known about the effects this phenomenon can have in the genome of the hybrid progeny. In this work, we first assess the impact that hybridization-induced TE proliferation has on the genome size of D.buzzatii–D. koepferae hybrids, throughout four generations of hybridization (an interspecific cross followed by three backcrosses). We demonstrate the existence of a sex-specific genome expansion, that affects only females at the first backcross. These results provide the first evidence of genome size increase in interspecific hybrids of animal species. We hypothesize that a TE deregulation at a transcriptional level occurs in F1 females, leading to new TE insertions that result in a genome size increase in the following generation. In order to test this hypothesis, we address two TE expression studies in the same hybrids, using two different approaches. First, we perform an in-depth analysis of the expression of one of the mobilized transposons, Helena, in both sexes and different tissues. We show that Helena expression in somatic tissues is not altered after hybridization, whereas in gonads sex-biased effects are observed. Indeed, Helena is repressed in F1 testes, in concordance with the unaltered genome size in males. In ovaries, an early Helena overexpression seems to occur in young flies, being then controlled in older ones. We subsequently performed a global analysis using a transcriptomic approach, in order to evaluate if the results for Helena could be extended to other TEs. To disentangle the molecular mechanisms involved in TE deregulatiom, we analysed the piRNA populations of parental species and hybrids. We show that F1 testes indeed tend to present a TE expression lower than D. buzzatii, which is coupled with a global increase of piRNA amounts. In ovaries, TE overexpression is the more common effect, and seems to be mainly due to differences in piRNA production strategies between parental species. Actually, the piRNA pathway proteins are divergent between parental species and could be at the origin of the hybrid instability. Moreover, differences in piRNA amounts between D. buzzatii and D. koepferae cytoplasms could also account for some cases of deregulation, as occurs in hybrid dysgenesis syndrome. Finally, other explanations are needed to account for the whole pattern of deregulation, such as the failure of histone modification’s deposition or of other TE silencing pathways.
Louwerse, Jeanine Danielle. "Transformation of barley with the maize transposable element En/Spm." Thesis, Heriot-Watt University, 2002. http://hdl.handle.net/10399/490.
Повний текст джерелаHarden, Nicholas. "Characterisation of the transposable element FB-NOF in Drosophila melanogaster." Thesis, University of Cambridge, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.316754.
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