Dissertationen zum Thema „Organellar genomes“
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Postel, Zoé. „Speciation and organellar genome evolution in lineages of Silene nutans (Caryophyllaceae)“. Electronic Thesis or Diss., Université de Lille (2022-....), 2022. http://www.theses.fr/2022ULILR080.
Speciation is the process by which the emergence of reproductive barriers isolate populations from one another and ultimately lead to the formation of new species. How these reproductive barriers emerge is a core question when thinking of speciation. Organellar genomes might be involved in the speciation process, through cytonuclear incompatibilities. Their mode of transmission might also influence the pace of reproductive isolation evolution. In my PhD, I worked on how organellar genomes influence the evolution of reproductive isolation between isolated lineages of S. nutans and which evo-demographic scenario shaped their evolution. Using plastid genomic and nuclear transcriptomic data we tried, in the first chapter, to identify candidates for plastid-nuclear incompatibilities involved in RI between lineages of S. nutans. We further dug into one plastid candidate complexe, the plastid ribosome. Because RI seems to be incomplete between lineages of S. nutans as some inter-lineage hybrids survived, we tested for paternal leakage of the plastid genome. We genotyped the surviving hybrids for plastid SNPs and analyzed whether they inherited the paternal or maternal plastid genomes. By allowing the transmission of the less incompatible plastid genome, paternal leakage rescued some of the inter-lineage hybrids. The mitochondrial genome could also be involved in the RI, through mito-nuclear incompatibilities. Because of their co-transmission, organellar genomes are supposed to be in tight linkage-disequilibrium, so exhibiting similar evolutionary patterns. Using genomic data for both organellar genomes for individuals of the four lineages we compared their evolutionary patterns. They were different with mitochondrial genes exhibiting many shared polymorphisms while plastid genomes many fixed substitutions between lineages. Recombination-like events were also identified in the mitochondrial genes. Lastly, we reconstructed the evo-demographic histories of the four lineages of S. nutans, using RNAseq data and ABC methods. Allopatric speciation was identified between the four lineages, with split times consistent with the glacial maxima
Silva, Saura Rodrigues da. „Genômica organelar e evolução de Genlisea e Utricularia (lentibulariaceae)“. Botucatu, 2018. http://hdl.handle.net/11449/153889.
Resumo: Utricularia e Genlisea são gêneros irmãos de plantas carnívoras da família Lentibulariaceae. Possuem aproximadamente 260 espécies representadas em diversas formas de vida. Para o Brasil foram catalogadas 82 espécies, das quais 27 são consideradas endêmicas. Além de dispor das armadilhas carnívoras mais complexas entre plantas, algumas de suas espécies apresentam os menores genomas e as maiores taxas de mutações entre as angiospermas relatadas até o momento. A respeito de seus genomas organelares, os estudos são pífios. Neste contexto, há a necessidade de se investigar como são os genomas organelares, suas estruturas, seus genes e como se deu a evolução das organelas nos gêneros. Portanto este estudo teve como objetivo, a partir de sequenciamento de nova geração e montagem de genomas, estudar e comparar os genomas organelares de Utricularia e Genlisea. Neste âmbito, foram montados e sequenciados os cloroplastos das espécies Utricularia foliosa, U. reniformis, G. aurea, G. filiformis, G. pygmaea, G. repens e G. tuberosa, e o genoma mitocondrial de U. reniformis. Os resultados obtidos revelaram que possivelmente há relação entre forma de vida e presença de genes ndhs nos gêneros, em razão de que para as espécies terrestres há deleção e “pseudogenização” de genes ndhs, já as espécies aquáticas detêm todo repertório de ndhs intacto. A partir das evidências encontradas, foi possível constatar transferência horizontal de genes, inclusive de genes ndhs, em mitocôndrias.
Abstract: Utricularia and Genlisea are sister genera in the carnivorous family Lentibulariaceae. There are aprproximately 260 species representing diverse life forms. For Brasil there are 82 species, 27 considered endemic. At the moment, besides having the most complex carnivorous traps between all plants, some of its species have miniature genomes and the highest mutational rates among angiosperms. There are few studies regarding its organellar genome. In this context, it is necessary to investigate how are these organellar genomes, its structure, genes, and how evolutionary forces govern these organelles in the different genera. Therefore, the aim of this study is to study and compare the organellar genomes of Utricularia and Genlisea, using next generation sequencing and genome assembly. In this context, chloroplasts of the species Utricularia foliosa, U. reniformis, Genlisea aurea, G. filiformis, G. pygmaea, G. repens and G. tuberosa, and the mitochondrial genome of U. reniformis were assembled and sequenced. The results show that possibly there is a connection between life form and the presence of ndhs genes in the genera, since for the terrestrial species there are ndhs genes that are deleted and pseudogenization, in contrary to the aquatic species which have all intact ndhs repertoir. Concerning the evidences, it was possible to verify horizontal transfer of ndhs and other genes as there are chloroplasts genes in the mitochondria.
Doutor
Dierckxsens, Nicolas. „Targeted organelle genome assembly and heteroplamsy detection“. Doctoral thesis, Universite Libre de Bruxelles, 2018. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/277507.
Doctorat en Sciences
info:eu-repo/semantics/nonPublished
Fisk, Dianna G. „CRP1 : founding member of a novel protein family that functions in organellar gene expression /“. view abstract of download file of text, 2000. http://wwwlib.umi.com/cr/uoregon/fullcit?p9987422.
Munoz, Víctor Hugo Anaya. „A theoretical model on the role of lateral gene transfer in the evolution of endosymbiotic genomes“. Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2012. http://dx.doi.org/10.18452/16446.
Lateral gene transfer has played a key role in the evolution of living beings. This process was first acknowledged in 1978 by Schwartz and Dayhoff but considered a relatively infrequent eccentricity and ignored. Later on, as DNA and protein sequences accumulated and more refined phylogenies were reconstructed, the contribution of lateral (or horizontal) gene transfer to the evolutionary history of living organisms gained relevance. Besides, gene transfer is known to occur not only between independent organisms but also, and more frequently between endosymbionts including eukaryotic organelles. I developed a theoretical model to study the lateral gene transfer process between cell organelles (but extendible to other endosymbionts) and the cell nucleus. The model explores the role of the lack of recombination in the organelles (Muller''s ratchet) as well as deviations from Muller''s ratchet in the form of non-symmetrical homologous recombination in relation with the gene transfer process. Also, nuclear incompatibilities resulting from the inclusion of a transferred gene, and cyto-nuclear incompatibilities between the mutant endosymbiotic genomes and the modified nuclear genome are investigated. The results obtained show that under certain circumstances the existence recombination or its non-existence produce the same results, and that deviations from symmetry in the recombination process might have important effects on the frequency of different alleles. It is also clear that there is a strong relation between nuclear and endosymbiotic genomes, and that the evolutionary fate of one largely depends on the forces affecting the other. When nuclear and cyto-nuclear incompatibilities are introduced in the model, the results show that lateral gene transfer-induced incompatibilities could potentially play a role in the speciation process similar to the one produced by mitochondria in the Nasonia species.
Meeusen, Shelly Lyn. „Analysis of the machinery regulating mitochondrial organelle and genome dynamics /“. For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2003. http://uclibs.org/PID/11984.
Ohniwa, Ryosuke L. „Comparative analyses of genome architectures among prokaryote, organelle and eukaryote by nano-scale imaging, molecular genetics and bioinformatics“. 京都大学 (Kyoto University), 2007. http://hdl.handle.net/2433/136993.
Richly, Erik. „Structural and functional genomics in semi-autonomous organelles composition and origin of proteomes of chloroplasts and mitochondria and related transcriptomics /“. [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=969512104.
Serafini, Annalisa. „A FRET-based genome wide high content screen identifies a novel role for the Parkinson's disease gene LRRK2 as modulator of endoplasmic reticulum-mitochondria tethering“. Doctoral thesis, Università degli studi di Padova, 2017. http://hdl.handle.net/11577/3422263.
La comunicazione tra organelli cellulari è una caratteristica fondamentale delle cellule eucariotiche ed esercita un ruolo fondamentale in molti processi cellulari. Uno dei processi di comunicazione tra organelli cellulari tra i più caratterizzati è quello dovuto ai siti di contatto tra le membrane di mitocondri e reticolo endoplasmatico (ER). Anche noti come "Mitochondria-associated ER membranes" (MAMs) o "Mitochondria-ER contact sites" (MERCs), la loro esistenza è stata scoperta 50 anni fa tramite studi di microscopia elettronica, ma il loro significato funzionale è iniziato ad emergere solo alla fine degli anni 90 quando è stato dimosdtrato il ruolo dei MERCs nello scambio di calcio dall'ER. Nonostante l'importanza di questi siti di contatto tra organelli sia in fisiologia sia in patologia, solo poche proteine coinvolte nel mantenimento strutturale della distanza tra i due organelli sono state finora identificate nei mammiferi. Mitofusina2 (MFN2) è stato il primo "tether" strutturale ad essere identificato. E' stato rilevato che MFN2 è localizzata sia nella membrana mitocondriale esterna (OMM) sia sulla superficie citosolica dell'ER ed ' in grado di formare intrazioni omo- ed eterotipiche con MFN1, mantenendo quindi la distanza tra i due organelli. Poiché una residua giustapposizione tra i due organelli è stata osservata in cellule MFN2-/-, ulteriori proteine che esercitano questo ruolo devono esistere. Per identificarle, abbiamo stabilito un protocollo ed eseguito due repliche di uno screening genomico su larga scala in fibroblasti embrionali di topo (MEF). Per eseguire questo screening, abbiamo sfruttato un biosensore basato sulla FRET, dove la proteina fluorescente CFP fusa con il dominio funzionale FRB e la proteina fluorescente YFP fusa con il dominio funzionale FKBP vengono fatte localizzare rispettivamente all'ER (grazie alla sequenza di segnale Sac1) ed ai mitocondri (grazie alla sequenza di segnale Akap1) (Csordas G. et al., 2010). Abbiamo modificato questo costrutto inserendo tra i cDNA delle due proteine il peptide autocatalitico Tav2A per ottenere un singolo mRNA e quindi l'espressione equimolare delle due proteine. I domini funzionali FKBP e FRB sono in grado di eterodimerizzare con l'aggiunta di Rapamicina, permettendo così la misurazione non solo dei livelli di giustapposizione basale tra i due organelli, ma anche del massimo livello di contatti che possono avvenire in una cellula. Abbiamo chiamato questo nuovo costrutto FRET ER-mitochondria probe (FEMP). Le caratteristiche uniche del FEMP ci consentono didiscriminare tra le proteine il cui ruolo è quello di mantenere i due organelli vicini, chiamate "tethers", e proteine che invece tengono i due organelli più distanti, definiti "spacers". Le immagini ottenute dallo screening sono state analizzate e sono stati calcolati due indici, chiamati "basal MERC index" e "maximum MERC index", che rappresentano rispettivamente il livello di contatti osservabili in qualsiasi momento in una cellula e il massimo livello di contatti possibile. A seguito di un'analisi delle immagini automatizzata e di un'analisi statistica effettutata su ~10,000 geni, dopo un processo di selezione abbiamo identificato 205 geni come "tethers" (geni che una volta eliminati aumentano la distanza tra i due organelli) tra mitocondri e ER e 59 geni come "spacers" (geni che una volta eliminati diminuiscono la distanza tra i due organelli) che influenzano sia il basal sia il maximum MERC index in entrambe le repliche. Inoltre, sono stati identificati 625 tethers e 696 spacers che influenzano solo il basal MERC index; e 519 tethers e 67 spacers che modificano solo il maximum MERC index. Analisi delle classi di proteine presenti in questi tre gruppi tramite Panther ha rivelato sia classi di proteine il cui ruolo in questo processo era noto, sia nuove classi di proteine il cui ruolo nella comunicazione tra ER e mitocondri deve ancora essere esplorato. Analisi della localizzazione cellulare per identificare proteine localizzate sia nell'ER sia nei mitocondri delle liste di geni esposte in precedenza, ha rivelato l'esistenza di 13 proteine tra i tethers e gli spacers comuni, 30 proteine che influenzano solo il basal MERC index e 16 proteine che influenzano solo il maximum MERC index localizzate in entrambi gli organelli. Una delle proteine presente nell'ultimo gruppo è "Leucine Rich Repeat Kinase 2" (LRRK2) che abbiamo ulteriormente caratterizzato come tether tra ER e mitocondri. Esperimenti di frazionamento cellulare dimostrano che LRRK2 è localizzata principalmente nelle MAMs. Come previsto per un tether, il livello di prossimità tra ER e mitocondri, misurato tramite FEMP, sono diminuiti in MEF LRRK2-/-. La prossimità tra i due organelli è pienamente recuperata dalla reintroduzione in MEF LRRK2-/- della proteina WT, ma non dei mutanti associati alle forme di Parkinson familiare. In conclusione, abbiamo sviluppato un nuovo metodo per determinare la prossimità tra ER e mitocondri e abbiamo utilizzato questa tecnologia per eseguire due repliche di uni screening gnomico su larga scala identificando nuovi componenti strutturali dei contatti tra mitocondri e ER.
Tourmente, Sylvette. „Evolution des mitochondries pendant l'ovogenese de drosophile : morphologie, distribution, replication et expression du genome“. Clermont-Ferrand 2, 1987. http://www.theses.fr/1987CLF21073.
Chemudupati, Mahesh. „Investigating the effects of nuclear envelope proteins on nuclear structure and organization in Aspergillus nidulans“. The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu148009978216118.
Ferreira, Ana Rita Moreira. „Variation detection in organelle genomes of Quercus species“. Master's thesis, 2021. http://hdl.handle.net/10348/10416.
The use of next-generation sequencing (NGS) technologies has been revolutionizing the study of genetics. The big amount of generated data by these technologies allows the characterization of species genomes and genomic variation between species and within the same one. The present dissertation focused on the study of single nucleotide polymorphisms (SNPs) in organelle genomes of two well-known species of Quercus: Quercus suber and Quercus ilex rotundifolia, commonly named cork oak and holm oak respectively. Chloroplasts and mitochondria are organelles present in plant cells and play a crucial role in photosynthesis and energy metabolism, respectively, among other important physiological functions. Each of these organelles has its own genome, distinct from the nuclear genome. Within the Quercus genus, the chloroplast genome sequences have been determined for over 20 species, including cork oak which was assembled by the Genosuber consortium, and only the cork oak mitochondrial genome has been determined to date. Moreover, the amount of information on genomic variation is very scarce in chloroplast genomes, or non-existent in mitochondrial genomes. Therefore, there is a clear need to increase our knowledge in this field, given the importance of these species in the ecosystem and their socio-economic impact especially in the south region of the Iberic Peninsula. The pipeline of this study involves the use of high-throughput sequencing data of 47 individuals (39 cork oaks and 8 holm oaks) using NGS techniques and tools to perform quality control, preprocessing, read mapping, variant calling and annotation. Additionally, to achieve the best performance on preprocessing and variant calling the used tools were tested using different parameters on a smaller group of individuals. As it was expected given the higher conservation of chloroplast genomes, the presented results show a higher variation on mitochondrial genomes, especially when comparing cork oak with holm oak trees. These variations suggest a different capacity in both species and some studies have been reporting that holm oak is more resistant than cork oak and these variations may be the reason for that. With this in mind, it is possible to say that holm oak trees have greater ability to withstand climate change and therefore be a good model for selection of important molecular markers.
A utilização de tecnologias de next-generation sequencing (NGS) tem vindo a revolucionar os estudos genéticos. A grande quantidade de dados gerados por estas tecnologias permite a caracterização dos genomas das espécies e a variação genómica entre espécies e dentro da mesma. A presente dissertação focou-se no estudo de polimorfismos de nucleótidos únicos (SNPs) em genomas de organelos de duas espécies bem conhecidas de Quercus: Quercus suber e Quercus ilex rotundifolia, vulgarmente designadas por sobreiro e azinheira, respetivamente. Os cloroplastos e mitocôndrias são organelos presentes nas células vegetais e desempenham um papel crucial na fotossíntese e no metabolismo energético, respetivamente, entre outras importantes funções fisiológicas. Cada um destes organelos tem o seu próprio genoma, distinto do genoma nuclear e pouco se sabe sobre eles em espécies de Quercus. No entanto, as sequências do genoma do cloroplasto foram determinadas em mais de 20 espécies, incluindo o sobreiro cujo assembly foi feito pelo consórcio Genosuber. Por outro lado, apenas o genoma mitocondrial do sobreiro foi determinado até à data. Além disso, a quantidade de informação sobre a variação genómica é muito escassa nos genomas dos cloroplastos, ou inexistente nos genomas mitocondriais. Portanto, existe uma clara necessidade de aumentar os nossos conhecimentos neste campo, dada a importância destas espécies no ecossistema e o seu impacto socioeconómico, especialmente na região sul da Península Ibérica. A estrutura deste estudo envolve a utilização de dados de sequenciação de alto rendimento de 47 indivíduos (39 sobreiros e 8 azinheiras) utilizando técnicas e ferramentas de NGS para realizar o controlo de qualidade, pré-processamento, mapeamento, determinação de variantes e anotação. Para além disso, para alcançar o melhor desempenho no pré-processamento e na determinação de variantes, as ferramentas utilizadas foram testadas utilizando diferentes parâmetros num grupo mais pequeno de indivíduos. Como era de esperar dada a maior conservação dos genomas dos cloroplastos, os resultados apresentados mostram uma maior variação nos genomas mitocondriais, especialmente quando se compara o sobreiro com a azinheira. Estas variações sugerem uma capacidade diferente em ambas as espécies e alguns estudos têm relatado que a azinheira é mais resistente do que o sobreiro e estas variações podem ser a razão para isso. Com isto em mente, é possível dizer que as azinheiras têm maior capacidade de resistir às alterações climáticas e, portanto, ser um bom modelo para a seleção de marcadores moleculares importantes.
Smith, David Roy. „THE EVOLUTION OF ORGANELLE GENOME ARCHITECTURE“. 2010. http://hdl.handle.net/10222/13028.
Richly, Erik [Verfasser]. „Structural and functional genomics in semi-autonomous organelles : composition and origin of proteomes of chloroplasts and mitochondria and related transcriptomics / vorgelegt von Erik Richly“. 2003. http://d-nb.info/969512104/34.
Parent, Jean-Sébastien. „Identification et caractérisation de facteurs impliqués dans la réplication et la stabilité des génomes des organelles de plantes“. Thèse, 2010. http://hdl.handle.net/1866/4975.
Compared to the nuclear genome, very little is known about the genomes of the two plant cytoplasmic organelles, the plastid and the mitochondria. Indeed, very few factors involved in either the replication or the repair of these genomes have been identified. Here we show the implication of the Whirly protein family in the maintenance of organellar DNA. Indeed, mutations in Whirly genes lead to DNA rearrangements in both Arabidopsis thaliana and Zea mays plastids. These rearrangements are the product of microhomology-mediated break-induced replication that rarely occurs in wild-type plants but increases in absence of Whirly proteins. In a mutant plant devoid of plastidial Whirly proteins, these new DNA molecules can be amplified up to fifty times the normal DNA level and cause a variegated phenotype. In the course of the study of the Whirly mutant plants, we developed a strategy, based on the use of the antibiotic ciprofloxacin, to induce DNA double-strand breaks specifically in plant organelles. The Arabidopsis mutant plants without Whirly proteins in the plastids are more sensitive to the antibiotic ciprofloxacin than wild-type plants. Accordingly, there is a much larger increase in the number of rearranged DNA molecules in the plastids of the mutant plants than in the control plants. Surprisingly, while the mutant plants devoid of Whirly proteins in the mitochondria do not show increased sensitivity to the drug, they do accumulate more rearrangements in their mitochondrial DNA compared to wild-type plants. These results suggest that the Whirly proteins are involved in the repair of DNA double-strand breaks in the plant organelle genomes. Our study of the plant organelle genome stability has lead us to a family of proteins homologous to the DNA polymerase I in bacteria. This family has been proposed to be responsible for most of the DNA-synthesis activity in the plant organelles. We bring genetic proof to support this hypothesis using mutants of the two PolI genes of Arabidopsis. The combined mutation of both genes is lethal and the single mutations cause a decrease in the relative DNA levels in the organelles, thus confirming the involvement of both genes in DNA replication. Interestingly, mutants of the PolIB but not PolIA gene shows increase sensitivity to ciprofloxacin suggesting a function in DNA repair. In line with these results, a cross between a PolIB mutant and the mutant of plastid Whirly genes resulted in plants with severe growth defects and numerous rearrangements in the plastid DNA. In conclusion, we have identified two factors involved in the metabolism of organelle DNA and proposed a simple model of how these genomes are maintained in the plant cell.
Maréchal, Alexandre. „Un rôle pour les protéines de la famille Whirly dans le maintien de la stabilité du génome des organelles chez Arabidopsis thaliana“. Thèse, 2009. http://hdl.handle.net/1866/3343.
Maintenance of genome stability is essential for the accurate propagation of genetic information and for cell growth and survival. Organisms have therefore developed efficient strategies to prevent DNA lesions and rearrangements. Much of the information concerning these strategies has been obtained through the study of bacterial and nuclear genomes. Comparatively little is known about how organelle genomes maintain a stable structure. This study implicates the single-stranded nucleic acid-binding proteins of the Whirly family in the maintenance of plant organelle genome stability. Here we report that the plastid-localized single-stranded DNA binding proteins of the Whirly family are required for plastid genome stability in Arabidopsis thaliana and Zea mays. Absence of plastidial Whirlies favors the accumulation of rearranged molecules that arise through a non-homologous recombination mechanism mediated by regions of microhomology. This mechanism is similar to the microhomology-mediated break-induced replication (MMBIR) described in bacteria, yeast and humans. Additionally we show that plant organelles can repair double-strand breaks using a MMBIR-like pathway. Plants lacking Whirly proteins accumulate elevated levels of microhomology-mediated DNA rearrangements upon double-strand break induction, indicating that Whirlies also contribute to the accurate repair of plant organelle genomes. Using biological and structural data, we propose a working model in which Whirlies modulate the access of repair proteins and complementary DNA to single-stranded regions, thereby regulating the choice of repair pathways and maintaining plant organelle genome stability. The various aspects of this model will be tested in future experiments which should allow a better understanding of the mechanisms underlying genome stability in plant organelles.
Cappadocia, Laurent. „Étude structurale du mode de liaison des protéines Whirly de plantes à l’ADN monocaténaire“. Thèse, 2010. http://hdl.handle.net/1866/4957.
Plants must protect the integrity of three genomes located respectively in the nucleus, the chloroplasts and the mitochondria. Although DNA repair mechanisms in the nucleus are the subject of multiple studies, little attention has been paid to DNA repair mechanisms in chloroplasts and mitochondria. This is unfortunate since mutations in the chloroplast or the mitochondrial genome can lead to altered plant growth and development. Our laboratory has identified a new family of proteins, the Whirlies, whose members are located in plant mitochondria and chloroplasts. These proteins form tetramers that bind single-stranded DNA and play various roles associated with DNA metabolism. In Arabidopsis, two Whirly proteins maintain chloroplast genome stability. Whether or not these proteins are involved in DNA repair has so far not been investigated. Our studies in Arabidopsis demonstrate that DNA double-strand breaks are repaired in both mitochondria and chloroplasts through a microhomology-mediated repair pathway and indicate that Whirly proteins affect this pathway. In particular, the role of Whirly proteins would be to promote accurate repair of organelle DNA by preventing the repair of DNA double-strand breaks by the microhomology-dependant pathway. To understand how Whirly proteins mediate this function, we solved the crystal structure of Whirly-DNA complexes. These structures show that Whirly proteins bind single-stranded DNA with low sequence specificity. The DNA is maintained in an extended conformation between the β-sheets of adjacent protomers, thus preventing spurious annealing with a complementary strand. In turn, this prevents formation of DNA rearrangements and favors accurate DNA repair. We also show that upon binding long ssDNA sequences, Whirly proteins assemble into higher order structures, or hexamers of tetramers, thus forming spherical particles of twelve nanometers in diameter. We also demonstrate that a lysine residue conserved among plant Whirly proteins is important for the stability of these higher order structures as well as for cooperative binding to DNA and for DNA repair. Overall, our study elucidates some of the mechanisms of DNA repair in plant organelles as well as the roles of Whirly proteins in this process.