Dissertationen zum Thema „Lateral gene transfers“
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Vieira, Rute Gomes Velosa. „Bayesian phylogenetic modelling of lateral gene transfers“. Thesis, University of Newcastle upon Tyne, 2015. http://hdl.handle.net/10443/3018.
Der volle Inhalt der QuelleTofigh, Ali. „Using Trees to Capture Reticulate Evolution : Lateral Gene Transfers and Cancer Progression“. Doctoral thesis, KTH, Beräkningsbiologi, CB, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-10608.
Der volle Inhalt der QuelleQC 20100812
Belliardo, Carole. „Étude des transferts horizontaux de gènes chez les nématodes phytoparasites par l'exploitation de métagénomes du sol“. Electronic Thesis or Diss., Université Côte d'Azur, 2022. http://theses.univ-cotedazur.fr/2022COAZ6032.
Der volle Inhalt der QuellePlant-parasitic nematodes (PPN) are among the most important crop pests and threaten the world's food production. Besides the need to understand their biology to develop new control strategies, they are fascinating organisms in terms of genomic evolution. Plant parasitism has evolved several times independently in nematodes with some convergent evolutionary processes. For instance, all studied PPN have acquired bacterial and fungal genes by horizontal gene transfers (HGT). Some of the acquired genes are involved in essential parasitic functions like plant cell wall degradation or processing nutrients from the plant. However, several major questions concerning their origin, evolutionary fate and distribution in the genomes and timing of acquisition events remain unsolved. Most PPN live in soil; thus, we hypothesised that these genes originated from soil-dwelling microorganisms. However, the underrepresentation of soil microorganisms in generalist sequence libraries has previously limited HGT analyses.To circumvent this problem, we built a protein library including more than 6,800 soil metagenomes from the Joint Genome Institute's IMG/M server. The first challenge was to make this massive dataset more accurate and suitable for HGT analysis in PPN genomes. An important issue in metagenomic data is the underrepresentation of eukaryotes and their annotation with prokaryotic tools. To better represent the pool of genes present in the natural environments of PPN, we identified eukaryotic contigs and re-predicted proteins using Augustus, a eukaryotic dedicated gene predictor. Moreover, we reduced the protein sequence redundancy and refined the taxonomic assignment. After all these steps, we obtained an improved and non-redundant database that was more representative of the soil's natural biodiversity. This soil protein library, two times larger than the classic library, contains mainly organisms genetically divergent than lab-cultured.Then, we performed an HGT detection on proteins from 18 plant-parasitic nematode genomes of the Tylenchina clade, constituting a highly diverse group of PPN phenotypes, against our library enriched with soil protein. After manual curation, the proportion of genes acquired by horizontal transfers with phylogenetic confirmation is between 0.5 to 1.9% to protein-coding genes originating from HGT in PPN genomes. Those genes mainly originate from bacteria, but we also observed HGT from eukaryotic kingdoms such as fungi, protists and plants. The most represented taxa in donors are soil-dwelling species of clades Burkholderiaceae, Proteobacteria, Actinobacteria, Rhizobiales and Dikarya. The usage of metagenomic data clarified the history of previously described HGTs but also identified hundreds of new HGTs. Functional analyses of the newly identified HGTs indicate a wide diversity of potential functions whose biological implications can be more precisely described in in-vitro experiments. Integrating environmental data in our reference library has allowed us to extend the detection of HGTs and to complete the catalog of potential donor offspring
Lester, Leo. „On Lateral Gene Transfer“. Thesis, University of Reading, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.487489.
Der volle Inhalt der QuelleCheeseman, Kevin. „Aspects of Penicillium genomics : Molecular combing genome assembly, genetic exchange in food and potential for secondary metabolite production“. Thesis, Paris 11, 2013. http://www.theses.fr/2013PA112280/document.
Der volle Inhalt der QuellePenicillium are filamentous fungi belonging to the Ascomycota genus. Penicillium species have been used by Man for centuries in food making processes. More recently they have also been used in the biotechnology industry for the production of compounds of pharmaceutical interest. Some Penicillium species are food spoilage agents, pathogens of plants including fruits. Aspects of their genomics are largely unknown. In this study, we analysed the genomes of two newly sequenced species, Penicillium roqueforti and Penicillium camemberti. Here we report the development of a new methodology for improving and validating genome assembly using an original single DNA molecule technology, Molecular Combing. Using this methodology we were able to produce a high quality genome assembly of Penicillium roqueforti. This work also reports the multiple and recurrent horizontal transfer of a large genomic island of over half a megabase between several Penicillium species. This horizontal transfer indicates a higher frequency of lateral genetic exchange between cheesemaking fungi than previously expected. Finally, we present an early assessment of the genomic potential for secondary metabolite production in these important food associated penicilliums
Addario-Berry, Dana. „An analysis of models and algorithms for gene duplication and lateral gene transfer /“. Thesis, McGill University, 2004. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=80161.
Der volle Inhalt der QuelleThis thesis explores several aspects of both of these simplifed models of evolution. A brief exposition of the models is presented, along with previous results and various extensions to these models.
The expected number of gene duplications needed to explain disagreements between a random gene and species tree is investigated.
A method for incorporating edge weights into the species tree is proposed.
Khan, Mehmood Alam. „Computational Problems in Modeling Evolution and Inferring Gene Families“. Doctoral thesis, KTH, Beräkningsvetenskap och beräkningsteknik (CST), 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-193637.
Der volle Inhalt der QuelleQC 20161010
Wilber, Matthew. „Building a History of Horizontal Gene Transfer in E. Coli“. Scholarship @ Claremont, 2016. http://scholarship.claremont.edu/hmc_theses/75.
Der volle Inhalt der QuelleYan, Yongpan. „Computational analyses of microbial genomes operons, protein families and lateral gene transfer /“. College Park, Md. : University of Maryland, 2005. http://hdl.handle.net/1903/2596.
Der volle Inhalt der QuelleThesis research directed by: Cell Biology & Molecular Genetics. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
Andam, Cheryl Marie Palacay. „Role of lateral gene transfer in the evolution of legume nodule symbionts“. Diss., Online access via UMI:, 2007.
Den vollen Inhalt der Quelle findenPopa, Ovidiu-Nicolae [Verfasser]. „Directed phylogenomic networks of lateral gene transfer during prokaryotic evolution / Ovidiu-Nicolae Popa“. Kiel : Universitätsbibliothek Kiel, 2016. http://d-nb.info/1094661988/34.
Der volle Inhalt der QuelleSantos, Viviane Piccin dos [UNESP]. „Filogenia molecular de cianobactérias baseada em sequências do 16S-23S-ITS rDNA e PC-IGS: investigação de transferência lateral do PC“. Universidade Estadual Paulista (UNESP), 2011. http://hdl.handle.net/11449/87867.
Der volle Inhalt der QuelleFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
As cianobactérias apresentam uma ampla variabilidade fenotípica e ecológica. Porém, esta variabilidade, muitas vezes, não corresponde à sua diversidade genética. Assim, o uso de marcadores moleculares é fundamental para os estudos de filogenia neste grupo. Entretanto, a filogenia molecular enfrenta um desafio na seleção dos marcadores devido à ocorrência relativamente frequente da transferência de genes de forma lateral entre os procariotos. Em cianobactérias os marcadores dos espaçadores dos genes ribossomais (16S-23S-ITS rDNA) e do operon da ficocianina (PC-IGS) estão entre os mais utilizados nestes estudos. Contudo, alguns trabalhos sugerem que o PC-IGS possa ter sito transferido lateralmente em sua história evolutiva. A identificação de morfoespécies dos gêneros Microcystis e Geitlerinema é baseada em caracteres morfológicos que em geral não correspondem à sua variabilidade genética. Com o objetivo de investigar a transferência lateral do operon da ficocianina em Geitlerinema e Microcystis, foram obtidas e comparadas árvores filogenéticas de ambas espécies baseadas nos marcadores PC-IGS e 16S-23S-ITS rDNA. As topologias das árvores obtidas para ambos os marcadores foram muito semelhantes e indicaram que o PC-IGS é estável e indicado para os estudos de taxonomia e filogenia de linhagens de Geitlerinema e Microcystis. Assim, hipótese inicial de transferência lateral foi refutada. Algumas linhagens tiveram seu posicionamento divergente entre um marcador e outro, o que ressalta a importância do uso de mais de um marcador em estudos de filogenia. O marcador PC-IGS apresentou melhor desempenho que 16S-23S-ITS rDNA. As árvores filogenéticas de Geitlerinema baseadas em ambos os marcadores indicaram a ocorrência de espécies crípticas dentre as linhagens estudadas e corroboraram que G. amphibium e G. unigranulatum devem ser consideradas sinonímias...
Cyanobacteria show a wide phenotypic and ecological variability, but frequently this variability does not correspond to their genetic variation. Therefore, the use of molecular markes is critical for phylogenetic studies in this group. At the same time, the selection of molecular markers represents a challenge for the molecular phylogeny due to the horizontal gene transfer, witch is a relatively common process among the prokaryotes. In cyanobacteria, makers for the ribosomal genes spacer (16S-23S-ITS rDNA) and for the phycocyanin operon spacer (PC-IGS) are among of the most used for phylogeny. However, some studies suggest that the PC-IGS marker may have been horizontally transferred during its evolutionary history. The identification of the morphospecies from the genus Microcystis and Geitlerinema is based in their morphological characters, but they generally do not correspond to genetic variability. In order to investigate the possibility of horizontal transfer of the phycocyanin operon in Microcystis and Geitlerinema, phylogenetic trees based on the PC-IGS and 16S- 23S-ITS rDNA were generated and compared. The topologies obtained for both markers were very similar, indicating that the PC-IGS marker is stable and suitable for taxonomical and phylogenetic studies in Microcystis and Geitlerinema. Therefore, the initial hypothesis of horizontal transfer was rejected. Some strains were found to have divergent positions between the trees based on the two molecular markes, witch highlights the importance of using more than one marker in phylogenetic studies. The PC-IGS marker performed better than 16S-23SITS rDNA. The Geitlerinema phylogenetic trees based on both markers indicated the occurrence of cryptic species among the strains and corroborated that G. amphibium and G. unigranulatum should be treated as synonyms. The phylogenetic tree based on PC-IGS formed a monophyletic clade... (Complete abstract click electronic access below)
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.
Der volle Inhalt der QuelleLateral 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.
Kamali-Moghaddam, Masood. „Co-operative recombination mechanisms promoting gene clustering and lateral transfer of antibacterial drug resistance“. Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2001. http://publications.uu.se/theses/91-554-4936-0/.
Der volle Inhalt der QuelleGalindo, González Luis Javier. „Deep eukaryotic phylogenomics : the holomycota branch Combined cultivation and single-cell approaches to the phylogenomics of nucleariid amoebae, close relatives of fungi Evolutionary Genomics of Metchnikovella incurvata (Metchnikovellidae): an early Branching Microsporidium A new fungal clade helps reconstructing the tree of Fungi and the evolution of the flagellum in Holomycota Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina–Blastocystis Stramenopile Lineage“. Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASS050.
Der volle Inhalt der QuelleDespite the astonishing diversity of plants, animals and macroscopic fungi, most eukaryotic diversity is actually microbial. The eukaryotic tree comprises several large monophyletic supergroups. One of these groups is the Opisthokonta, which encompasses two branches, Holozoa, including animals, and Holomycota, grouping Fungi and their unicellular relatives. While multicellular fungi are well known, knowledge on the diversity of unicellular Fungi and their phylogenetic relatives is still poor. This unicellular fraction includes several zoosporic lineages (e.g. Chytridiomycota and Blastocladiomycota) within Fungi, but also a variety of lineages related to the classical core Fungi: nucleariids, rozellids, aphelids and Microsporidia. However, the phylogenetic relationships of these lineages among them and with classical Fungi remain to be solidly established. Molecular phylogenetic trees of 18S rRNA genes retrieved from environmental studies have showed a wide diversity of unicellular holomycotans in almost all environments on Earth. However, the phylogenetic signal of this gene is limited and does not allow robustly resolving most deep phylogenetic relationships. During past years, high-throughput techniques have allowed sequencing hundreds of new genomes and transcriptomes. This has made possible to carry out multi-gene phylogenomic studies, which increase the available signal to resolve evolutionary relationships. Nevertheless, most sequenced genomes correspond to easy-to-culture fungal species, often with particular interest for humans (e.g. parasites, plant symbionts, yeast). Recently, single-cell omics has become a potential useful approach to study uncultured unicellular eukaryotes, making it possible to reconstruct robust phylogenetic analyses of a wide environmental diversity using genomic and transcriptomic data. During my PhD work, I have applied single-cell techniques to get phylogenetic information from divergent holomycotan lineages, clarify phylogenetic relationships among fungi and their close relatives and infer trait evolution. More specifically, I have used this approach to: 1) Generate genomic and transcriptomic data for nucleariids and better reconstruct inner relationships in the clade and the characters present in the nucleariid ancestor. Our results confirm that the cover-bearing unicellular genera Pompholyxophrys and Lithocolla are indeed nucleariids and branch together with Nuclearia, Parvularia and Fonticula. The reconstruction of a robust phylogeny for the group allowed us to infer the traits (e.g. no flagellum, glycocalyx, no cover) already present in their ancestor. 2) Sequence and comparatively analyze the genome of Metchnikovella incurvata, to confirm its relatively basal position within Microsporidia, and determine synapomorphies for the clade. Phylogenomic analysis of the metchnikovellid Metchnikovella incurvata confirmed that Metchnikovellidae branch at the base of Core-Microsporidia. We also confirmed their metabolic profile to be more similar to Core-microsporidia, being both similarly reduced in genes/functions. 3) Generate genomic data for Amoeboradix gromovi and Sanchytrium tribonematis, which form the newly described zoosporic fungal clade of sanchytrids, and resolve their phylogenetic position. The study of the two sanchytrid genomes clarified their placement within Fungi as a new clade sister to Blastocladiomycota. Comparative genomics showed that their metabolic composition was reduced in comparison with related lineages. This reduction was especially important in their flagellar toolkit when compared with other Holomycota, confirming 4 independent flagellum loss events in the clade
Santos, Viviane Piccin dos. „Filogenia molecular de cianobactérias baseada em sequências do 16S-23S-ITS rDNA e PC-IGS : investigação de transferência lateral do PC /“. Rio Claro : [s.n.], 2011. http://hdl.handle.net/11449/87867.
Der volle Inhalt der QuelleBanca: Luiz Henrique Zanini Branco
Banca: Mariana Cabral de Oliveira
Resumo: As cianobactérias apresentam uma ampla variabilidade fenotípica e ecológica. Porém, esta variabilidade, muitas vezes, não corresponde à sua diversidade genética. Assim, o uso de marcadores moleculares é fundamental para os estudos de filogenia neste grupo. Entretanto, a filogenia molecular enfrenta um desafio na seleção dos marcadores devido à ocorrência relativamente frequente da transferência de genes de forma lateral entre os procariotos. Em cianobactérias os marcadores dos espaçadores dos genes ribossomais (16S-23S-ITS rDNA) e do operon da ficocianina (PC-IGS) estão entre os mais utilizados nestes estudos. Contudo, alguns trabalhos sugerem que o PC-IGS possa ter sito transferido lateralmente em sua história evolutiva. A identificação de morfoespécies dos gêneros Microcystis e Geitlerinema é baseada em caracteres morfológicos que em geral não correspondem à sua variabilidade genética. Com o objetivo de investigar a transferência lateral do operon da ficocianina em Geitlerinema e Microcystis, foram obtidas e comparadas árvores filogenéticas de ambas espécies baseadas nos marcadores PC-IGS e 16S-23S-ITS rDNA. As topologias das árvores obtidas para ambos os marcadores foram muito semelhantes e indicaram que o PC-IGS é estável e indicado para os estudos de taxonomia e filogenia de linhagens de Geitlerinema e Microcystis. Assim, hipótese inicial de transferência lateral foi refutada. Algumas linhagens tiveram seu posicionamento divergente entre um marcador e outro, o que ressalta a importância do uso de mais de um marcador em estudos de filogenia. O marcador PC-IGS apresentou melhor desempenho que 16S-23S-ITS rDNA. As árvores filogenéticas de Geitlerinema baseadas em ambos os marcadores indicaram a ocorrência de espécies crípticas dentre as linhagens estudadas e corroboraram que G. amphibium e G. unigranulatum devem ser consideradas sinonímias... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: Cyanobacteria show a wide phenotypic and ecological variability, but frequently this variability does not correspond to their genetic variation. Therefore, the use of molecular markes is critical for phylogenetic studies in this group. At the same time, the selection of molecular markers represents a challenge for the molecular phylogeny due to the horizontal gene transfer, witch is a relatively common process among the prokaryotes. In cyanobacteria, makers for the ribosomal genes spacer (16S-23S-ITS rDNA) and for the phycocyanin operon spacer (PC-IGS) are among of the most used for phylogeny. However, some studies suggest that the PC-IGS marker may have been horizontally transferred during its evolutionary history. The identification of the morphospecies from the genus Microcystis and Geitlerinema is based in their morphological characters, but they generally do not correspond to genetic variability. In order to investigate the possibility of horizontal transfer of the phycocyanin operon in Microcystis and Geitlerinema, phylogenetic trees based on the PC-IGS and 16S- 23S-ITS rDNA were generated and compared. The topologies obtained for both markers were very similar, indicating that the PC-IGS marker is stable and suitable for taxonomical and phylogenetic studies in Microcystis and Geitlerinema. Therefore, the initial hypothesis of horizontal transfer was rejected. Some strains were found to have divergent positions between the trees based on the two molecular markes, witch highlights the importance of using more than one marker in phylogenetic studies. The PC-IGS marker performed better than 16S-23SITS rDNA. The Geitlerinema phylogenetic trees based on both markers indicated the occurrence of cryptic species among the strains and corroborated that G. amphibium and G. unigranulatum should be treated as synonyms. The phylogenetic tree based on PC-IGS formed a monophyletic clade... (Complete abstract click electronic access below)
Mestre
Oliveira, Amanda Carolina Paulino de [UNESP]. „Caracterização de transglicosilases líticas de mureína em xanthomonas citri subsp. citri 306 e estudo funcional das lts mltb2.1 e mltb2.2 associadas ao elemento Tnxax1“. Universidade Estadual Paulista (UNESP), 2018. http://hdl.handle.net/11449/154759.
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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Xanthomonas citri subsp. citri 306 (XccA) é o agente causal do cancro cítrico (CC), doença endêmica que afeta a citricultura. Durante a interação patógeno-hospedeiro o sistema de secreção tipo três (SST3) codificado pela XccA age na translocação de efetores e no estabelecimento da doença. A montagem do aparato de SST3 depende da síntese, remodelagem e degradação da parede celular bacteriana, sendo este processo realizado pela ação enzimática de transglicosilases líticas de mureína (LTs). XccA codifica diversas LTs, porém, pouco é conhecido sobre a diversidade de famílias e relação com a virulência. Dentre as LTs com provável relação com a virulência, duas ORFs parálogas presentes no cromossomo e plasmídeo pXAC64, respectivamente; são genes passageiros do TnXax1, um transposon da família Tn3, relacionado a evolução e emergência da patogenicidade nas Xanthomonadales. Portanto, este estudo objetivou elucidar o provável papel e diversidade das LTs presentes no genoma de XccA, caracterizando funcionalmente as LTs presentes em TnXax1 pela técnica de mutação sítio dirigida. Foram identificadas no genoma de XccA 13 LTs, sendo 12 pertencentes às famílias: 1A, 1B, 1C, 1D, 1F, 1G, 3A, 3B (2 cópias), 5A e 6A, e uma não classificada. A LT não classificada, é exclusiva do gênero Xanthomonas e relacionada à família 3B, porém contém um domínio adicional relacionado ao metabolismo de carboidratos. As LTs classificadas em famílias apresentam provável função relacionada com a remodelagem da parede celular para inserção de sistemas de secreção tipo 3, 4 e 6, inserção de flagelo, divisão celular, reciclagem da parede celular e degradação e controle da produção do peptidoglicano. As LTs do TnXax1 pertencem a família 3B, não são essenciais para XccA e desenvolvimento do CC, porém estão relacionadas ao aumento da virulência, diminuição da formação de biofilme, agregação e aumento na produção de goma xantana, corroborando o papel do TnXax1 como agente propagador da patogenicidade e virulência em Xanthomonadales. Em resumo, os resultados lançam novos conhecimentos frente ao papel das LTs com o metabolismo do peptidoglicano e relação com os mecanismos de transferência lateral, virulência e patogenicidade de XccA.
Xanthomonas citri subsp. citri 306 (XccA) is a causal agent of type A citrus canker (CC), one of the most devastating citriculture diseases. Type 3 Secretion Systems (T3SS) play a fundamental role in XccA pathogenicity. T3SS components are embedded in the bacterial inner and outer membrane and act as a channel for injection of effector proteins directly into the plant host cell cytosol. T3SS assembly and installation relies on bacterial cell wall synthesis, remodeling and degradation. Murein lytic transglycosylases (LT) are important in this process and are responsible for peptidoglycan cleavage and its remodeling. Information about the XccA LT arsenal is scarce: little is known about family diversity, their exact role and their connection to virulence in this bacterium. Among the LTs with probable relation to virulence, two paralogue ORFs (one in chromosome, one in pXAC64 plasmid) are passenger genes of the Tn3 family transposon TnXax1, known to play a significant role for evolution and emergence of pathogenicity in Xanthomonadales. This study addresses LT diversity in the XccA genome and examines the role of plasmid and chromosomal TnXax1 LT passenger genes using site-directed deletion mutagenesis and functional characterization. We identified 13 XccA LTs: 12 belong to families 1A, 1B, 1C, 1D (2 copies), 1F, 1G, 3A, 3B (2 copies), 5A, 6A and one which is non-categorized. This noncategorized gene, is exclusive to the Xanthomonas genus and related to the 3B family but contains an additional domain linked to carbohydrate metabolism, whilst the other catalyzes peptidoglycan biosynthesis, and is widely distributed in gammaproteobacteria. The categorized LTs are probably involved in cell wall remodeling to allow insertion of type 3, 4 and 6 secretion systems, flagellum assembly, division and recycling of cell wall and degradation and control of peptidoglycan production. The TnXax1 passenger LTs (3B family) are not essential to XccA and CC development but are implicated in virulence, biofilm production and aggregation decrease and xanthan gum production increase, corroborating the role of TnXax1 transposon as a virulence and pathogenicity propagating agent in XccA. These findings also suggest that LTs acquisition by horizontal gene transfer mediated by TnXax1 improved bacterial fitness, bringing adaptive advantages to the plant-pathogen interaction process.
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Driscoll, Timothy. „Host-Microbe Relations: A Phylogenomics-Driven Bioinformatic Approach to the Characterization of Microbial DNA from Heterogeneous Sequence Data“. Diss., Virginia Tech, 2013. http://hdl.handle.net/10919/50921.
Der volle Inhalt der QuellePh. D.
Albaaj, Mohammed. „Diversity of β-Lactamase Genes in Gram-Negative Soil Bacteria from Northwest Ohio“. Bowling Green State University / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1566553116919146.
Der volle Inhalt der QuelleXie, Gang. „Evolution of aromatic metabolism a genomic perspective on the complexity contributed by genome expansion, reductive evolution, and lateral gene transfer /“. [Gainesville, Fla.] : University of Florida, 2002. http://purl.fcla.edu/fcla/etd/UFE1001196.
Der volle Inhalt der QuelleArellano, Davin Adrian. „Utilisation des transferts horizontaux de gènes pour dater des phylogénies“. Thesis, Lyon, 2017. http://www.theses.fr/2017LYSE1299.
Der volle Inhalt der QuelleHaving a dated genealogy of living organisms is one of the major goals of evolutionary biology. This enterprise faces two major challenges. The first one is the scarcity and incompleteness of the fossil record, virtually nonexistent for microbes and essential to provide a time scale of life history. The second one is the intrinsic difficulty of obtaining phylogenies in organisms whose genome has been extensively shaped by Lateral Gene Transfer (LGT). The acquisition of new genes from distant organisms creates important differences among genes trees and complicates the reconstruction of the species history. In this thesis work I show how we can use those differences to our advantage to infer ancient events of LGT and how they provide a temporal scale of evolution. Transfers can supply an important amount of information on divergence times in organisms whose fossils are very scarce, acting as a new dating source independent of the geological record and taking us a step closer to building a whole dated phylogeny of Life. In the first part, I perform genomic-scale analyses to show how phylogenetic reconciliations can be used to detect donor and recipient lineages of LGT events. Moreover, they also provide a detailed view of how gene families evolve along species trees. Using ALE, a probabilistic reconciliation software that accounts for the uncertainty in gene trees, we are able to map events of duplication, loss and transfer in phylogenies of cyanobacteria and fungi. We also show how methods that ignore the information contained in gene trees underestimate the real frequency of LGT. In the second part, I present in detail how LGT carries a temporal signal and how this signal can be used to infer dated trees. I explain a new method called MaxTiC, that finds the best dated tree by maximizing the number of transfers that are time-compatible with a phylogeny. By simulations we show how robust the method is to errors in the species tree and how many gene families are required to obtain reliable dated trees. Finally, to confirm our results I present different metrics to compare the divergence times inferred by transfers with those inferred by molecular clocks. We perform a phylogenomic analysis to detect thousands of LGT events in cyanobacteria, Deltaproteobacteria, Archaea and fungi and obtain their dated phylogenies. We find a broad agreement between both dating methods, a result robust to the use of different priors on divergence times and different models of relaxed molecular clock. We also show that some of the dates inferred by using LGT are not recovered by molecular clocks. These results altogether suggest that the use of LGT in future dating studies may have a big impact on the inferred dates of major evolutionary events and can lead to an important change of our view of the History of Life
Jerlström-Hultqvist, Jon. „Hidden Diversity Revealed : Genomic, Transcriptomic and Functional Studies of Diplomonads“. Doctoral thesis, Uppsala universitet, Mikrobiologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-182831.
Der volle Inhalt der QuelleAvsaroglu, M. Dilek. „Isolation, Molecular Characterization Of Food-borne Drug Resistant Salmonella Spp. And Detection Of Class 1 Integrons“. Phd thesis, METU, 2007. http://etd.lib.metu.edu.tr/upload/12608844/index.pdf.
Der volle Inhalt der Quellerkiye and 49 Salmonella strains obtained from National Salmonella Reference Laboratories of Germany were analysed. For the characterization of strains, analyses such as serotyping, phage typing, antibiotyping and molecular biological characterization were done. The strains exhibited 17 different serotypes with S. Enteritidis serotype and PT21 phage type being the most prevalent in Turkish isolates. The highest antimicrobial resistance was observed against NAL for Turkish strains, whereas it was against SUL for strains from German origin. Molecular typing of all strains exhibited different plasmid profiles and PFGE patterns. There were 1-4 plasmids/profile for Turkish strains and 1-7 plasmids/profile for German strains. The PFGE patterns revealed 42 different subgroups, having two major clusters with 44,3% arbitrary homology. Among 72 resistant strains, the most prevalent resistance genotypes were observed as blatem-1 (%56, AMP resistance)
floR (%100, CHL and FFC resistance)
aphA1 (%100, KAN and NEO resistance)
tet(A) (%53, TET resistance)
aadA1 (%82, SPE and STR resistance)
sulI (%78, SUL resistance). The class I integron variable region analyses exhibited 700 bp (1 strain), 1000 bp (37 strain), 1200 bp (16 strain) and 1600 bp (3 strain) integrons.
Fonseca, Luciane Schons da. „Caracterization of the SOS response in Leptospira interrogans sorovar Copenhageni“. Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/46/46131/tde-25032015-110306/.
Der volle Inhalt der QuelleLeptospira é um gênero basal em um grupo já considerado um dos mais ancestrais, as espiroquetas. As espécies patogênicas são responsáveis pela leptospirose, uma doença presente em todo o mundo e de principal importância em países tropicais em desenvolvimento. L. interrogans sorovar Copenhageni é o agente da maior parte dos casos no Brasil. Nesse trabalho, utilizamos diversas abordagens experimentais para caracterizar o sistema SOS nesse sorovar, identificar seu impacto na resposta geral a danos no DNA, assim como avaliar as funções de reparo de DNA disponíveis em leptospiras patogênicas e saprofíticas. Identificamos um repressor LexA adicional, adquirido por transferência horizontal e exclusivo do sorovar Copenhageni. Observamos também que irradiação por UV-C causou significativa morte celular e bloqueio da divisão celular dos sobreviventes. Ambos os repressores são ativos e identificamos as sequências que utilizam para se ligar aos promotores dos genes regulados. Entretanto, o SOS box de LexA1 foi redefinido após uma busca de novo por motivos enriquecidos nas sequências recuperadas por ChIP-seq. Esse regulador ligou-se ao menos a 25 locais do genoma. A maioria desses alvos teve aumento de expressão após UV-C. Danos no DNA também causaram um importante rearranjo metabólico: houve aumento de expressão em transposons e profagos, além de indutores de mutagênese e vias de reparo; por outro lado, mobilidade, crescimento celular e quase todos os fatores de virulência foram reprimidos. Dois profagos induzidos durante essa resposta, possivelmente proporcionam algumas proteínas de funções importantes. Nós também avaliamos a presença de genes envolvidos no reparo de DNA em três espécies de leptospira: L. biflexa, L. interrogans e L. borgpetersenii. L. interrogans é a espécie com maior diversidade e redundância de genes de reparo. Além disso, transferência horizontal parece ser um importante fornecedor de funções de reparo nesse gênero. Leptospiras também apresentam genes característicos tanto de bactérias Gram-positivas quanto Gram-negativas. Genes representando diferentes vias de reparo foram induzidos durante infecção em modelo animal, sugerindo que essas vias estão ativas no curso da doença. Todos esses dados, em conjunto, sugerem que elementos genéticos móveis são de extrema importância na evolução do gênero e das vias de reparo. Assim, durante a resposta a danos no DNA, diversos mecanismos dependentes e independentes de SOS são empregados para frear o crescimento celular e virulência em favor da indução controlada de mecanismos para aumentar variabilidade genética.
Anaya, Munoz Víctor Hugo Verfasser], Peter [Akademischer Betreuer] [Hammerstein, Hans-Jörg [Akademischer Betreuer] Rheinberger und Daniel Piñero [Akademischer Betreuer] Dalmau. „A theoretical model on the role of lateral gene transfer in the evolution of endosymbiotic genomes / Víctor Hugo Anaya Munoz. Gutachter: Peter Hammerstein ; Hans-Jörg Rheinberger ; Daniel Piñero Dalmau“. Berlin : Humboldt Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2012. http://d-nb.info/1019165677/34.
Der volle Inhalt der QuellePetersen, Jörn. „Duplikationen und lateraler Transfer von Genen als Motor der Evolution : molekulare Studien am GAPDH-Gensystem von Grünalgen, Landpflanzen und Chlorarachniophyta /“. [S.l. : s.n.], 1999. http://www.gbv.de/dms/bs/toc/307555755.pdf.
Der volle Inhalt der QuelleReboul, Guillaume. „Metabarcoding and metagenomic approaches to decipher microbial communities in suboxic environments Microbial eukaryotes in the suboxic chemosyn- thetic ecosystem of Movile Cave, Romania Hyper- diverse archaea near life limits at the polyextreme geothermal Dallol area Performance of the melting seawater-ice elution method on the metabarcoding characterization of benthic protist communities Core microbial communities of lacustrine microbialites sampled along an alkalinity gradient Environmental drivers of plankton protist communities along latitudinal and vertical gradients in the oldest and deepest freshwater lake Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina-Blastocystis Stramenopile Lineage Marine signature taxa and microbial community stability along latitudinal and vertical gradients in sediments of the deepest freshwater lake“. Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASL041.
Der volle Inhalt der QuelleMicrobial ecology is the science of micro-organisms and their biotic and abiotic interactions in a given ecosystem. As technology has advanced, molecular techniques have been widely used to overcome the limitations of classical approaches such as culturing and microscopy. Indeed, the development of Next Generation Sequencing (NGS) technologies in the past twenty years has largely helped to unravel the phylogenetic diversity and functional potential of microbial communities across ecosystems.Nonetheless, most of the environments studied through these techniques concentrated on relatively easily accessible, tractable and host-related ecosystems such as plankton (especially in marine ecosystems), soils and gut microbiomes. This has contributed to the rapid accumulation of a wealth of environmental diversity and metagenomic data along with advances in bioinformatics leading to the development of myriads of tools. Oxygen-depleted environments and especially their microbial eukaryote components are less studied and may lead to future phylogenetic and metabolic discoveries.In order to address this, we conducted analyses on two poorly studied suboxic ecosystems: Movile Cave (Romania) and lake Baikal sediments (Siberia, Russia). In this task, we aimed at unveiling the taxonomic and functional diversity of microorganims in these environments.To do so, I first evaluated the available bioinformatics tools and implemented a bioinformatics pipeline for 16S/18S rRNA gene-based metabarcoding analysis, making reasoned methodological choices. Then, as a case study, I carried out metabarcoding analyses of the water and floating microbial mats found in Movile Cave in order to investigate its protist diversity. Our study showed that Movile Cave, a sealed off chemosynthetic ecosystem, harbored a substantial protist diversity with species spanning most of the major eukaryotic super groups. The majority if these protists were related to species of freshwater and marine origins. Most of them were putatively anaerobic, in line with the cave environment, and suggesting that in addition to their predatory role, they might participate in prokaryote-protist symbioses.In a second study, I applied my metabarcoding pipeline to explore unique and relatively unexplored environment of Lake Baikal sediments. I first applied a metabarcoding approach using 16S and 18S rRNA genes to describe prokaryotic as well as protist diversity. Overall, the communities within these ecosystems were very diverse and enriched in ammonia-oxidizing Thaumarchaeota. We also identified several typical marine taxa which are likely planktonic but accumulate in sediments. Finally, our sampling plan allowed us to test whether differences across depth, basin or latitude affected microbial community structure. Our results showed that the composition of sediment microbial communities remained relatively stable across the samples regardless of depth or latitude.In a third study, we applied metagenomics to study the metabolic potential of communities associated to Baikal sediments and to reconstruct metagenome-assembled genomes (MAGs) of dominant organisms. This revealed the considerable ecological importance of Thaumarchaeota lineages in lake Baikal sediments, which were found to be the major autotrophic phyla and also very implicated in the nitrogen cycle. Chloroflexi and Proteobacteria-related species also appeared ecologically important.This PhD thesis reveals the taxonomic diversity of poorly studied suboxic ecosystems and therefore contributes to our knowledge of microbial diversity on Earth. Additionally, the analyses of surface sediment samples in lake Baikal adds new light on freshwater-marine transitions. The metagenomic analyses reported here allowed us to postulate a model of nutrient cycle carried out by microorganismsin these sediments. Overall, this work sheds light on the microbial ecology of oxygen-depleted environments, and most notably lake Baikal surface sediments
Johansson, Carolina. „Mechanisms and DNA Specificity in Site-specific Recombination of Integron Cassettes“. Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl [distributör], 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7429.
Der volle Inhalt der Quellede, Koning Audrey Patricia. „Lateral gene transfer from bacteria to protists“. Thesis, 2002. http://hdl.handle.net/2429/12456.
Der volle Inhalt der QuelleEveleigh, Robert. „Being Aquifex aeolicus: Untangling a hyperthermophile's Checkered Past“. Thesis, 2011. http://hdl.handle.net/10222/14412.
Der volle Inhalt der QuelleMukhopadhyay, Aindrila. „Initiating lateral gene transfer : analysis of the VirA/VirG two component system in vivo /“. 2002. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:3070198.
Der volle Inhalt der QuelleMeehan, Conor J., und R. G. Beiko. „A phylogenomic view of ecological specialization in the Lachnospiraceae, a family of digestive tract-associated bacteria“. 2014. http://hdl.handle.net/10454/17256.
Der volle Inhalt der QuelleSeveral bacterial families are known to be highly abundant within the human microbiome, but their ecological roles and evolutionary histories have yet to be investigated in depth. One such family, Lachnospiraceae (phylum Firmicutes, class Clostridia) is abundant in the digestive tracts of many mammals and relatively rare elsewhere. Members of this family have been linked to obesity and protection from colon cancer in humans, mainly due to the association of many species within the group with the production of butyric acid, a substance that is important for both microbial and host epithelial cell growth. We examined the genomes of 30 Lachnospiraceae isolates to better understand the origin of butyric acid capabilities and other ecological adaptations within this group. Butyric acid production-related genes were detected in fewer than half of the examined genomes with the distribution of this function likely arising in part from lateral gene transfer (LGT). An investigation of environment-specific functional signatures indicated that human gut-associated Lachnospiraceae possess genes for endospore formation, whereas other members of this family lack key sporulation-associated genes, an observation supported by analysis of metagenomes from the human gut, oral cavity, and bovine rumen. Our analysis demonstrates that adaptation to an ecological niche and acquisition of defining functional roles within a microbiome can arise through a combination of both habitat-specific gene loss and LGT.
Canadian Institute for Health Research (grant number CMF-108026), Genome Atlantic and the Canada Research Chairs program to R.G.B.
Hall, Charles Robert. „The Contribution of Horizontal Gene Transfer to the Evolution of Fungi“. Diss., 2007. http://dukespace.lib.duke.edu/dspace/bitstream/10161/202/1/D_Hall_Charles_Robert_a_052007.pdf.
Der volle Inhalt der QuelleWhidden, Chris. „Efficient Computation and Application of Maximum Agreement Forests“. 2013. http://hdl.handle.net/10222/35349.
Der volle Inhalt der QuelleRohrbacher, Fanny. „Structure fonctionnelle du plasmidome rhizosphérique dans un contexte de contamination aux hydrocarbures“. Thèse, 2017. http://hdl.handle.net/1866/19565.
Der volle Inhalt der QuellePhytoremediation, a bioremediation technique that uses plants, is considered to be an effective and affordable “green technology” to clean up hydrocarbon contaminated soils. Plants essentially act indirectly through the stimulation of rhizosphere microorganisms. Root exudation is thought to be one of the predominant drivers of microbial communities in the rhizosphere and is therefore a potential key factor behind enhanced hydrocarbon biodegradation. Many of the genes responsible for bacterial adaptation in contaminated soil and the plant rhizosphere are thought to be carried by conjugative plasmids and transferred among bacteria. A better understanding of these phenomena could thus inform the development of techniques to manipulate the rhizospheric microbiome in ways that improve hydrocarbon bioremediation. This research aims to study the plasmidome (the overall plasmid content) in the rhizosphere of willow growing in hydrocarbon contaminated and non-contaminated soils, as compared with unplanted soil. Metagenomic analyses based on Illumina sequencing were used to highlight functions carried by plasmids. Our results indicate a strong effect of hydrocarbon contamination on plasmid composition. Furthermore, plasmids harbored genes involved in several metabolic pathways, such as hydrocarbon biodegradation, energy production, signal transduction, chemotaxis, metabolisms of carbohydrates, amino acids and secondary metabolites. To date, this is the first comparative soil metagenomics documenting the plasmidome diversity in a phytoremediation system. The results provide new knowledge on the role of lateral gene transfer in the bacterial adaptation in rhizosphere and in hydrocarbon contaminated soil.
Petersen, Jörn [Verfasser]. „Duplikationen und lateraler Transfer von Genen als Motor der Evolution: Molekulare Studien am GAPDH-Gensystem von Grünalgen, Landpflanzen und Chlorarachniophyta / von Jörn Petersen“. 1999. http://d-nb.info/958119082/34.
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