Дисертації з теми "Mitogenomes"
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Shen, Hong. "Mitogenomic analysis of decapod phylogeny." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2012. http://dx.doi.org/10.18452/16505.
Повний текст джерелаFor a comprehensive study of decapod phylogeny at the mitochondrial genome level, I have sequenced the mitochondrial genome of 13 decapods. Together with available sequences of 31 decapods from GenBank, and the mitochondrial genome of Dromia personata provided by the Bonn University, the dataset now cover all major decapod taxa. Maximum likelihood (ML) and Bayesian inference (BI) of the nucleotide and amino acid datasets reveal similar topologies at the higher level relationships: (((((((Anomala, Brachyura), Thalassinida: Gebiidea) Thalassinida: Axiidea), Astacidea), Achelata), Stenopodidea), Caridea), Dendrobranchiata). Nevertheless, one problematic taxon, Polychelida, with ambiguous affinities is recognized. At the lower level, most taxa are monophyletic, whereas the Thalassinida is paraphyletic, which is consistent with some morphological and molecular results. An inversion spanning from S-E-F tRNA cluster to the I-Q-M tRNA cluster occurred in Procambarus fallax f. virginalis, Homarus gammarus, and one priapulid Priapulus caudatus. Compared with the gene arrangement of the horseshoe crab Limulus polyphemus, both astacids and the priapulid exhibit the same inversion, which is therefore supposed to be a convergent event of the clade Astacidea and Priapulida among Ecdysozoa. Other than this notable feature observed in astacids, the gene arrangements in all available decapods show some interesting characters. To explain these unique genomic features observed here, a new gene rearrangement model is proposed, which is called the “inversion triggered duplication” model.
Briscoe, Andrew G. "Advancing mitogenomics : a case study in the Araneae." Thesis, Bangor University, 2013. https://research.bangor.ac.uk/portal/en/theses/advancing-mitogenomics--a-case-study-in-the-araneae(f642bbb7-75fa-49ea-a59d-23274019e8fa).html.
Повний текст джерелаTabata, Ryouichi. "The origin, history and mitogenome evolution of fishes in Lake Biwa." 京都大学 (Kyoto University), 2016. http://hdl.handle.net/2433/215345.
Повний текст джерелаVan, de Paer Céline. "Diversité structurelle et évolution contrastée des génomes cytoplasmiques des plantes à fleurs : une approche phylogénomique chez les Oleaceae." Thesis, Toulouse 3, 2017. http://www.theses.fr/2017TOU30228/document.
Повний текст джерелаIn plants, the structural dynamics and concerted evolution of nuclear and cytoplasmic genomes are poorly understood. The objective of this thesis was to study the structural diversity and evolution of mitogenomes and plastomes in the family Oleaceae with a phylogenomic approach. First, we assembled mitogenomes from low-coverage sequencing data obtained from live and herbarium material. Considerable structural variation of mitogenomes was observed in the olive, and a chimeric gene potentially associated to a type of male sterility was detected. Finally, we studied the evolution of plastomes and mitochondrial genes in the Oleaceae. Accelerated evolution of plastomes was observed in two independent lineages. This change of evolutionary rate could be the consequence of an occasional transmission of plastids with pollen, modifying selective pressures on some genes
Garbutt, James. "The complete mitogenome of two Australian lampreys: mordacia mordax and mordacia praecox." Thesis, Garbutt, James (2015) The complete mitogenome of two Australian lampreys: mordacia mordax and mordacia praecox. Honours thesis, Murdoch University, 2015. https://researchrepository.murdoch.edu.au/id/eprint/30595/.
Повний текст джерелаRodovalho, Cynara de Melo [UNESP]. "Caracterização do transcriptoma e genoma mitocondrial da formiga cortadeira Atta laevigata (Formicidae : Attini)." Universidade Estadual Paulista (UNESP), 2011. http://hdl.handle.net/11449/100531.
Повний текст джерелаCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Formigas cortadeiras do gênero Atta, popularmente conhecidas como saúvas, são as mais derivadas dentro da tribo Attini. Apresentam grande importância ecológica, porém, pelo hábito de cortarem folhas para manutenção do fungo simbionte e pelo enorme tamanho das colônias, causam muitos prejuízos às lavouras, pastagens e plantações, sendo consideradas pragas agrícolas. Atta laevigata Smith, 1858 apresenta vasta distribuição pelo Brasil e é responsável pela herbivoria de inúmeras plantas dicotiledôneas, gramíneas e espécies nativas de diferentes biomas. O presente trabalho teve como objetivos a caracterização parcial do transcriptoma e do genoma mitocondrial de A. laevigata. Foram caracterizadas 2006 sequências únicas do transcriptoma, a partir de uma biblioteca de cDNA preparada com indivíduos inteiros da formiga. Entre essas sequências, 16 provavelmente representam genes com grande número de transcritos. Esses 16 genes estão relacionados a três funções celulares: (i) conservação de energia através de reações redox na mitocôndria; (ii) estrutural, pelo citoesqueleto e músculos; (iii) regulação da expressão gênica e metabolismo. Considerando o estilo de vida e processos biológicos chaves para essas formigas, 146 sequências foram identificadas com base na sua utilização para o controle de cortadeiras pragas. A partir de dados da biblioteca de cDNA e procedimentos envolvendo primer walking, o genoma mitocondrial de A. laevigata foi parcialmente caracterizado, apresentandose com 17920 pb, maior, portanto, do que outros já descritos em Hymenoptera, mesmo considerando-se a impossibilidade de determinação da sequência de uma pequena porção do mtDNA, envolvendo a região controle, uma parte do 12S e os tRNAs S1, V e M. Como já descrito para outros mitogenomas, o de A. laevigata apresentou alto conteúdo AT, os mesmos 13 genes codificadores...
Leafcutter ants from Atta genus, popularly known as “saúvas”, are the most derived of the tribe Attini. They have major ecological importance, but, because of their habit of cutting leaves for the maintenance of the symbiotic fungus and the huge colony size, they impose severe economic damages to plantations, pastures, and agriculture, being considered as agriculture pests. Atta laevigata shows wide distribution in Brazil and it is responsible for the herbivory of many dicots, grass, and native species from different biomes. The present work aimed to characterize the transcriptome and the mitochondrial genome of A. laevigata. 2,006 unique sequences of the transcriptome were characterized from a cDNA library constructed with whole individuals. Among those sequences, 16 are likely from genes with high number of transcripts. Those 16 genes are related with three cellular functions: (i) energy conservation through redox reactions in mitochondria; (ii) cytoskeleton and muscle structuring; (iii) regulation of gene expression and metabolism. Based on lifestyle and key biological processes of these ants, 146 sequences were identified with potential use for controlling pest leafcutters. Using data from cDNA library and primer walking proceedings, the mitochondrial genome of A. laevigata was partially characterized with 17,920 bp, being larger than the others already described for Hymenoptera. A small part of the mtDNA was not sequenced, including the control region, a portion of 12S and tRNAs S1, V, and M. As described before for other mitogenomes, A. laevigata mtDNA displayed high AT contain, the same 13 proteincoding genes and the two ribosomal subunits with length and location according to the hypothetic ancestral mitogenome. Rearrangements were found for the tRNAs, but the most remarkable difference were the high number and longer length of intergenic regions presented in the mtDNA... (Complete abstract click electronic access below)
McCullagh, Bonnie. "Sequence evolution among divergent mitochondrial haplotypes within species of Junonia butterflies." Journal of Asia-Pacific Entomology, 2015. http://hdl.handle.net/1993/31105.
Повний текст джерелаFebruary 2016
Finnegan, Kimberly A. "A Mitogenomics View of the Population Structure and Evolutionary History of the Basking Shark Cetorhinus maximum." NSUWorks, 2014. http://nsuworks.nova.edu/occ_stuetd/13.
Повний текст джерелаShen, Hong [Verfasser], Gerhard [Akademischer Betreuer] Scholtz, Thomas [Akademischer Betreuer] Stach, and Lars [Akademischer Betreuer] Podsiadlowski. "Mitogenomic analysis of decapod phylogeny : (Crustacea, Malacostraca) / Hong Shen. Gutachter: Gerhard Scholtz ; Thomas Stach ; Lars Podsiadlowski." Berlin : Humboldt Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2012. http://d-nb.info/1022837559/34.
Повний текст джерелаROCHA, Patrícia Keytth Lins. "Qual região do DNA mitocondrial reflete a história evolutiva da ordem Lepidoptera?" Universidade Federal de Pernambuco, 2013. https://repositorio.ufpe.br/handle/123456789/13136.
Повний текст джерелаMade available in DSpace on 2015-04-14T15:05:53Z (GMT). No. of bitstreams: 2 Dissertação Patricia Rocha.pdf: 2020756 bytes, checksum: 96804531919a1d7e9cb5ab9787d73242 (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Previous issue date: 2013
FACEPE
A ordem Lepidoptera apresenta uma gama de espécimes de importância econômica, algumas são agentes polinizadores e outras são pragas. Vários estudos têm sido realizados com base na morfologia com base em dados moleculares para elucidar a evolução da ordem. O DNA mitocondrial é muito utilizado por proporcionar boa resolução filogenética. Com base em genes mitocondriais informativos, nós propusemos um conjunto de dados que pode ser utilizado em análise filogenética de Lepidoptera obtendo a mesma robustez que a análise com mtDNAs completos. Para isso, as sequências dos mitogenomas de Lepidoptera foram recuperadas no banco de dados do NCBI. Foi identificada a ordem gênica das sequências utilizando o programa MAUVE. As regiões de interesse em D. flavipennella foram sequenciadas para testar a eficiência dos marcadores moleculares em sequência nova. Foi realizada análise de entropia, teste de sinal filogenético e de saturação para verificar características de bons marcadores moleculares e foram realizadas análises filogenéticas nos programas PhyML e MrBayes. Foram realizados também testes com e sem a terceira posição dos códons para verificar a influência da terceira posição nas análises filogenéticas de Lepidoptera. As regiões estudadas foram concatenadas para aumentar os valores de confiança das árvores. Verificamos que com a concatenação dos genes COI, ATP6, COIII, ND3, ND5, CYTB, ND1 e 16S foi possível obter resultados com robustez semelhante a dos mitogenomas completos.
Dong, Jiajia. "Systematics and biogeography of the genus Cardiodactylus (Orthoptera : Eneopterinae : Lebinthini) in the Southeast Asia." Thesis, Paris, Muséum national d'histoire naturelle, 2017. http://www.theses.fr/2017MNHN0009.
Повний текст джерелаAmong the crickets of the subfamily Eneopterinae, Cardiodactylus Saussure, 1878 (Orthoptera: Eneopterinae: Lebinthini) is the most speciose and widely distributed genus. It consists of 82 species organized in two species groups (Noveaguineae and Efordi species groups). The species distributions encompass hundreds of islands and territories ranging from the coasts of Southeast Asia to the Samoan islands. Cardiodactylus species show contrastive distribution patterns, some being highly endemic while others are distributed in the whole Western Pacific region. This diversity coupled with the rich geological context of the Southeast Asian and Pacific regions, offers great opportunities to address biogeographical questions and investigate the dynamics of diversification in islands.Despite recent efforts to improve the taxonomical knowledge of Cardiodactylus, its diversity is so high that many new species still continue to be discovered. In a first stage, taxonomic studies based on morphological, molecular and acoustic data led to the description of five new species from Eastern New Guinea and to the redescription of two species. In a second stage, the molecular phylogeny of Cardiodactylus was reconstructed. The results support the monophyly of the genus, of the tested species, and of the Novaeguineae species group. The Efordi species group is clearly found paraphyletic, which tends to confirm the presence of a third species group, as suggested by the taxonomical study. According to the historical biogeographic analysis, the origin of Cardiodactylus was recovered in the Western Pacific during the Mid-Eocene (ca. 42 Ma). Through the transition zone of New Guinea, Cardiodactylus colonized Southeast Asia from East to West through three independent passageways: Java, Sulawesi and the Philippines. This work showed that the high diversity of Southeast Asian Cardiodactylus took place during the Miocene, as a result of accumulation of in situ diversification and immigration events. In a third stage, a protocol and sets of primers were designed to amplify mitogenomes in crickets. The method was exemplified by amplifying the mitogenome of the species Cardiodactylus muiri Otte, 2007 with a long-PCR approach combined with Next-Generation Sequencing. The purpose of this work is to obtain more informative molecular data with relatively low-cost but high taxonomic coverage for future phylogenetic reconstructions
Rodovalho, Cynara de Melo. "Caracterização do transcriptoma e genoma mitocondrial da formiga cortadeira Atta laevigata (Formicidae : Attini) /." Rio Claro : [s.n.], 2011. http://hdl.handle.net/11449/100531.
Повний текст джерелаAbstract: Leafcutter ants from Atta genus, popularly known as "saúvas", are the most derived of the tribe Attini. They have major ecological importance, but, because of their habit of cutting leaves for the maintenance of the symbiotic fungus and the huge colony size, they impose severe economic damages to plantations, pastures, and agriculture, being considered as agriculture pests. Atta laevigata shows wide distribution in Brazil and it is responsible for the herbivory of many dicots, grass, and native species from different biomes. The present work aimed to characterize the transcriptome and the mitochondrial genome of A. laevigata. 2,006 unique sequences of the transcriptome were characterized from a cDNA library constructed with whole individuals. Among those sequences, 16 are likely from genes with high number of transcripts. Those 16 genes are related with three cellular functions: (i) energy conservation through redox reactions in mitochondria; (ii) cytoskeleton and muscle structuring; (iii) regulation of gene expression and metabolism. Based on lifestyle and key biological processes of these ants, 146 sequences were identified with potential use for controlling pest leafcutters. Using data from cDNA library and primer walking proceedings, the mitochondrial genome of A. laevigata was partially characterized with 17,920 bp, being larger than the others already described for Hymenoptera. A small part of the mtDNA was not sequenced, including the control region, a portion of 12S and tRNAs S1, V, and M. As described before for other mitogenomes, A. laevigata mtDNA displayed high AT contain, the same 13 proteincoding genes and the two ribosomal subunits with length and location according to the hypothetic ancestral mitogenome. Rearrangements were found for the tRNAs, but the most remarkable difference were the high number and longer length of intergenic regions presented in the mtDNA... (Complete abstract click electronic access below)
Orientador: Maurício Bacci Júnior
Coorientador: Henrique Ferreira
Banca: Flavio Henrique da Silva
Banca: Marco Antonio del Lama
Banca: Mariana Lúcio Lyra
Banca: Klaus Hartmann Hartfelder
Doutor
Botero-Castro, Fidel. "Systématique, phylogénie et évolution moléculaires des Phyllostomidae (Mammalia, Chiroptera) : une approche mitogénomique comparative." Thesis, Montpellier 2, 2014. http://www.theses.fr/2014MON20053/document.
Повний текст джерелаNew sequencing technologies have revolutionized the acquisition of molecular data by increasing the amount of sequences at a considerably lower cost. These new technologies have also given access to samples previously neglected because they resulted in low-quantity and degraded DNA yields, as for example, old tissues, museum specimens and even fossil rests. An additional advantage comes from the possibility of multiplexing; this is, mixing several taxa in a single sample thanks to the use of tags or labels allowing late separating the sequences using bioinformatic tools. A molecular marker that has greatly benefited from these technologies is the mitochondrial genome. Indeed, we show that, thanks to the high per-cell ratio of mitochondrial to nuclear DNA, it's possible to obtain whole well-covered mitochondrial genomes without previous sample enrichment. This allows the accomplishment of projects of comparative mitogenomics for species-rich groups needing exhaustive taxon sampling and for which strong genetic divergences would difficult the use of classical sequencing.It is in this context that this thesis tackles the molecular systematics, phylogenetics and evolution of a Neotropical family of bats: the Phyllostomidae. This species-rich family, accounting for more than 160 species, is also the family of Mammals with the highest diversity of life history traits, for example, feeding on almost every possible source of food. This diversity results in convergent morphologies that make this kind of characters inadequate for reconstructing the evolutionary history of this group. Mitogenomics has proven useful in similar cases but no study of this kind has been conducted for this family. We got to sequence whole mitogenomes for representatives of all major lineages and covering the diversity of life history traits. We then show that using these mitogenomes allows solving intrafamilial relationships with a resolution similar to that resulting from a concatenation of mitochondrial and nuclear markers and with solid statistical support for most of the nodes of the phylogeny. This allowed clarifying several controversial relationships and confirming several clades proposed in previous studies. Next, we illustrate the evolution of mitogenomes and the influence of life history traits using the clade of vampire bats, the only hematophagous Mammals, whose mitogenome seem to have undergone an acceleration of evolutionary rate as a consequence of the combined action of neutral and selective forces in order to counter the constraints imposed by this feeding habit. Finally, the robust phylogenetic frame provided by the 100 mitogenomes that we sequenced, will be used for future studies about, for exemple, the diversification process of Phyllostomids
Al, Arab Marwa. "Sequences Signature and Genome Rearrangements in Mitogenomes." 2017. https://ul.qucosa.de/id/qucosa%3A20973.
Повний текст джерелаTeixeira, João Eduardo Afonso Teiga. "Mitogenomic Phylogeny of Freshwater mussels (Bivalvia: Unionida)." Master's thesis, 2021. http://hdl.handle.net/10348/10575.
Повний текст джерелаFreshwater mussels (Bivalvia: Unionida) play key ecological roles and provide important services to humans. However, they are among the most threatened faunal groups in the world. Most freshwater mussel species present two divergent mitochondrial DNA molecules (F-type or M-type) in males as a result of Doubly Uniparental Inheritance. The number of available freshwater mussel mitogenomes is low, particularly for M-type genomes. A further shortcoming is that published mitogenomes are restricted to only a few families within this order, with no mitogenomes being available for the others. In the present dissertation, 149 samples of freshwater mussels were newly sequenced by NextGeneration Sequencing (NGS) using MiSeq Illumina runs. Quality control of the obtained reads, assembly, and annotation was carried out using multiple bioinformatics tools. Comparative mitogenomic analyses were then performed using all obtained (F-type) mitogenomes with different evaluation metrics, e.g., mitogenome length, GC content, start and stop codon frequency, AT/GC skews, and Ka/Ks ratio on protein-coding genes. The results were compared with previous analyses on molluscan mitogenomes revealing interesting patterns that can be explored in future studies. A case study was carried out in a subset of the 149 mitogenomes, focusing on the subfamily Ambleminae, for which two out of five tribes lacked published complete mitogenomes. Phylogenetic analyses were carried out on these mitogenomes using standard methods, e.g., Maximum Likelihood and Bayesian Inference. The phylogeny on the newly analysed mitogenomes, i.e., Pleurobema oviforme, Amblema plicata, and Popenaias popeii, confirm the most recent tribal classification within Ambleminae. Results also suggest that all Ambelminae share the same gene arrangement (UF1).
Os bivalves de água doce (Bivalvia: Unionida) desempenham papéis ecológicos essenciais e fornecem serviços importantes para os seres humanos. No entanto, eles são um dos grupos faunísticos mais ameaçados do mundo. A maioria dos bivalves de água doce apresentam duas moléculas de DNA mitocondrial divergentes nos machos (Fêmea ou tipo F e Macho ou Tipo M) como resultado de Herança Duplamente Uniparental. O número de mitogenomas de bivalves de água doce é baixo, particularmente para genomas tipo M. Uma outra limitação é que os mitogenomas publicados são restritos a apenas algumas famílias dentro desta ordem, sem mitogenomas disponíveis para as outras. Na presente dissertação, 149 amostras de bivalves de água doce foram sequenciadas por Sequenciação de Nova Geração (NGS) usando Illumina MiSeq. O controle de qualidade das reads, assembly e anotação foram realizadas usando várias ferramentas bioinformáticas. As análises mitogenômicas comparativas foram realizadas usando todos os mitogenomas do tipo F com diferentes métricas de avaliação, como comprimento do mitogenoma, conteúdo de GC, frequência de codões de iniciação e terminação, AT/GC skews e rácio Ka/Ks em genes codificadores de proteínas. Os resultados foram comparados com análises anteriores em mitogenomas de moluscos, revelando padrões interessantes que podem ser explorados em estudos futuros. Um estudo foi realizado num subconjunto dos 149 mitogenomas, com foco na subfamília Ambleminae, na qual duas entre cinco tribos não tinham mitogenomas completos publicados. Análises filogenéticas foram realizadas nestes mitogenomas usando métodos como Máxima Verossimilhança e Inferência Bayesiana. A filogenia nos mitogenomas analisados Pleurobema oviforme, Amblema plicata, e Popenaias popeii, confirmam a classificação tribal mais recente em Ambleminae. Os resultados revelam também que todos os mitogenomas partilham a mesma ordem dos genes (UF1).
Lin, Jia-Sian, and 林佳賢. "Evolution and phylogeny of Microhyla fissipes and its relavent taxa infering from mitogenome." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/geg8ju.
Повний текст джерела國立中央大學
生命科學系
106
Microhyla fissipes was first recognized in Tainan, Taiwan (type locality), however it is not highly accepted. Herein, author used the sample from Yi-Lan, Taiwan as a representative of Taiwan samples and obtained the complete mitochondrial genome sequence (accession number: MF673131) in order to study the phylogeny of Microhyla fissipes and its relevants, especially in the comparison with the China sample (NC_009422). Although the genome of our sample (16,729 base pairs) contains genes and gene order almost identical to other amphibians’, some variations have been accumulated between Taiwan and China samples. Interestingly, we noticed that ND5 and ND6 genes evolved very differently from other genes. Also there were strongly codon usage bias with high thymine frequency at the second codon and very low guanine frequency at the third codon.
Chao, Shu-Chen, and 趙淑貞. "Mitogenome comparison and phylogeography of the Pygoplites diacanthus(Pomacanthidae) geminate species in Indo-Pacific Ocean." Thesis, 2015. http://ndltd.ncl.edu.tw/handle/89453090955497138238.
Повний текст джерела國立臺灣海洋大學
環境生物與漁業科學學系
103
There are 8 genus and around 90 species of Pomacanthidae in the world. The Royal angelfish or regal angelfish, Pygoplites diacanthus, is a species of marine angelfish of the family Pomacanthidae, and the monotypic genus Pygoplites. It was found in tropical Indo-Pacific oceans, ranged from East Africa, Red Sea, east to French Polynesia Tuamotu Archipelago, north to Japan and south to Australia. This species is popular in aquarium trade because of its colorful body patterns. The Royal angelfish in Indian and Pacific Oceans have has different color morph, The Indian Royal angelfish has an orange face; while Pacific one has a grey face. Whether the Royal angelfish in different Ocean represent different populations or different species is still unclear. The establishment of mitogenome and the analysis of DNA barcode may help to resolve the questions of population genetics, molecular phylogenetics, and evolution for Royal angelfishes. Firstly, we used Next Generation Sequencing (NGS) for the short reads sequencing to decode the mitogenome of Royal angelfish from Pacific (Indonesia) and Indian Ocean (Maldives). The mitogenome of Pacific Royal angelfish was totally 16,784 bp, including 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNAs and one control region; while the mitogenome of Indian Ocean Royal angelfish was 16,767 bp.The nucleotides composition is similar between two geminate species, including 28.5% A, 28.9%C, 16.3%G and 26.3%T. The mitogenome difference between these two morph types is about 1.55%. The most different region was 10% for control region, then 1.73% for ND6. The analyses of life barcode COI suggested that Royal angelfishes can be divided was into two groups. The estimated divergence time based on the molecular clock concept was about 0.5 My, it could because of the low sea level during Pleistocene ice ages, the emerge of the Indo-Australian Archipelago may form vicariance which direct to the divergence of Royal angelfish in different Oceans and led to the formation of many geminated species in Indo-Pacific.
Golombek, Anja. "Inferring the phylogeny of problematic metazoan taxa using mitogenomic and phylogenomic data." Doctoral thesis, 2019. https://repositorium.ub.uni-osnabrueck.de/handle/urn:nbn:de:gbv:700-201905231583.
Повний текст джерелаChuang, Yao-Yang. "Mitogenomics and molecular evolution of the group I intron in the cytochrome oxidase I gene of Siderastrea (Cnidaria;Scleractinia;Siderastreidae)." 2006. http://www.cetd.com.tw/ec/thesisdetail.aspx?etdun=U0001-2507200610263700.
Повний текст джерелаChuang, Yao-Yang, and 莊曜陽. "Mitogenomics and molecular evolution of the group I intron in the cytochrome oxidase I gene of Siderastrea (Cnidaria;Scleractinia;Siderastreidae)." Thesis, 2006. http://ndltd.ncl.edu.tw/handle/27301651163856695895.
Повний текст джерела國立臺灣大學
海洋研究所
94
Animal mitochondrial genome was well studied in past decades with a closed circular structure containing 13 protein coding regions, 2 rRNAs and 22 tRNAs. Nevertheless, mitochondrial genomes of the Anthozoa are different from the typical animal mt genome in several characteristics including, losing most of the tRNAs, possessing group I introns, incompact gene arrangement, and slow evolution. Even within the major lineages of the Anthozoa, the gene containing group I intron and gene arrangement could be very different. Thus, more information should be obtained in order to address the molecular evolution of mitochondrial genome in the Anthozoa. In this study, I determined 3 mt genomes of Siderastrea corals and compared to the published mt genomes of the scleractinian corals. Mt genome gene arrangement of Siderastrea is nearly identical to the published scleractinian mt genomes except the existence of cox1 intron. Mt genomes are longer (19387-19619 bp) than those of other scleractinian corals (16138-18338 bp). Comparing the phylogenetic relationship of these corals, the loosen mt genome of Siderastrea is probably an ancestral character of the mitochondrial evolution in the Scleractinia. Cox1 group I introns were detected in Siderastrea species with a LAGLI-DGEG homing endonuclease to perform intron translocation function. Cox1 group I introns were also found in Actiniaria (Metridium senile) with the same insertion site and higher similarity than that of fungi’s cox1 intron, suggesting that the insertion event was ancient probably prior to the split of the common ancestor of Scleractinia and Actiniaria. The group I intron was probably lost several times during the course of evolution in most of the scleractinian lineages. The finding of coxI group I introns in the three Siderastrea species from the Caribbean, Indian Ocean, and Pacific Ocean suggested that this intron existed before the divergence of the common ancestor of Siderastrea. The genetic divergence was accumulated in both intron as well as the other mitochondrial regions after these species become relict and endemic in these Oceans. The result also demonstrated that the deep divergence within genus might not be caused by obscuring of conventional taxonomy. Siderastrea represents an old and reliable taxonomic group and may provide a new perspective view for evolution of the Scleractinia.
Campbell, Véronique. "Chimères, données manquantes et congruence : validation de différentes méthodes par simulations et application à la phylogénie des mammifères." Thèse, 2009. http://hdl.handle.net/1866/6604.
Повний текст джерелаCapt, Charlotte. "Démystifier le lien entre la double transmission uniparentale des mitochondries et la détermination du sexe chez les bivalves." Thèse, 2019. http://hdl.handle.net/1866/23494.
Повний текст джерелаSexual systems and sex determining mechanisms described among animals are extraordinarily diverses. This amazing diversity is present in bivalves where both environment and genetic factors occur, leading to, among others, gonochoric and simultaneous or sequential hermaphroditic species. The most impressive discovery is a sex-determining system that would involve mitochondria. Specifically, a unique mitochondrial DNA inheritance system, known as Doubly Uniparental Inheritance (DUI), would be related to the maintenance of gonochorism in some bivalve species. DUI involves two mitochondrial DNA lineages, one that is maternally transmitted (F mtDNA) to females and males, and the other that is transmitted paternally (M mtDNA) to males only. The F and M mtDNAs, in DUI species, are characterized by unique traits, such as a modification of the cox2 gene, or the presence of new genes associated with each of the mitochondrial genomes (sex-specific genes) that have a function other than energy production, unlike other typical mitochondrial genes. Since the link between DUI and sex determination is still unclear, three approaches have been proposed to help demystify it, with each of the approaches constituting a chapter of this thesis. The first two chapters focused on freshwater mussel species of the order Unionida, where a correlation between gonochorism and DUI and hermaphroditism and SMI (Strictly Maternally Inheritance) was described. The first approach was to produce a comparative transcriptomic analysis between the male and female gonads of two gonochoric DUI species; Venustaconcha ellipsiformis and Utterbackia peninsularis (Unionidae family), to better understand the mechanisms underlying sex determination and DUI in these bivalves. This study revealed 12,000 orthologous genes, with 2 583 genes differentially expressed in both species, including Sry, Dmrt1, and Foxl2 known to be key sex-determining genes in vertebrates and other bivalve species. Our results were also compared with other DUI species, including the marine clam Ruditapes philippinarum, to identify shared elements between distant species that may be responsible for DUI regulation. Overall, these results support the hypothesis that a modified ubiquitination mechanism may be responsible for the retention of paternal mtDNA in male bivalves. The analyzes also revealed that DNA methylation could be involved in DUI regulation. 7 A second comparative transcriptomic analysis was performed to discern the mechanisms underlying sex determination and DUI between the gonochoric DUI species, U. peninsularis, and the closely related SMI hermaphroditic species, U. imbecillis. This study supported the hypothesis of an involvement of ubiquitination and methylation mechanisms in DUI regulation, as well as confirmed a role of conserved genes related to sex determination in hermaphroditic bivalves. Our results also revealed novel candidate genes with potential roles in DUI, including nucleases and factors involved in autophagy / mitophagy mechanisms. Finally, to identify mitochondrial genetic elements that could be part of the mechanisms underlying DUI and sex determination in bivalves, we sequenced the complete F and M mtDNAs of two new DUI species, from two families of the order Venerida; Scrobicularia plana (Semelidae family) and Limecola balthica (Tellinidae family). The complete description of mtDNAs in DUI species has been carried out for several species of freshwater mussels (Unionoida order), but very few species have been described for the orders Mytilida and Venerida. Such studies are essential for tracing mitochondrial genetic signatures shared by different DUI species. Our results revealed the largest differences in size (>10kb) and nucleotide divergence (up to 50% divergence) between M and F mtDNAs, among all DUI species. These differences in size are mainly due to a huge insertion (> 3.5kb) in the cox2 gene of the M mtDNA from both species, a trait previously described in freshwater mussels. The cox2 gene in S. plana males represents the longest cox2 sequence across the animal kingdom. Another important feature of F and M mtDNAs is the presence of new sex-specific genes, as reported in all other DUI species so far. The combined results of this thesis support the sharing of several key genetic elements among DUI species. In addition, a parallel with the Cytoplasmic Male Sterility (CMS) system in plants, the only other organisms with a sex determination system that involves mitochondria, is proposed to explain the role of mtDNA in sex determination in DUI bivalve species.
Nadimi, Maryam. "Comparative mitochondrial genomics toward understanding genetics and evolution of arbuscular mycorrhizal fungi." Thèse, 2015. http://hdl.handle.net/1866/12376.
Повний текст джерелаArbuscular mycorrhizal fungi (AMF) are the most widespread eukaryotic symbionts, forming mutualistic associations known as Arbuscular Mycorrhizae with the majority of plantroots. AMF are obligate biotrophs belonging to an ancient fungal lineage of phylum Glomeromycota. Their mycelia are formed by a complex network made up of coenocytic hyphae, where nuclei and cell organelles can freely move from one compartment to another. AMF are commonly acknowledged to improve plant growth by enhancing mineral nutrient uptake, in particular phosphate and nitrate, and they confer tolerance to abiotic and biotic stressors for plants. Despite their significant roles in ecosystems, their genetics and evolution are not well understood. Studying AMF is challenging due to their obligate biotrophy, their slow growth, and their limited morphological criteria. In addition, intra-isolate genetic polymorphism of nuclear DNA brings another level of complexity to the investigation of the biology, ecology and function of AMF. Genetic polymorphism of nuclear DNA within a single isolate limits the development of efficient molecular markers mainly at lower taxonomic levels (i.e. the inter-isolate level). Instead, mitochondrial (mt) genomics have been used as an attractive alternative to study AMF. In AMF, mt genomes have been shown to be homogeneous, or at least much less polymorphic than nuclear DNA. However, by generating large mt sequence datasets we can investigate the efficiency and usefulness of developing molecular marker toolkits in order to study the dynamic and evolutionary mechanisms of AMF. This approach also elucidates the population genetics, community ecology and functions of Glomeromycota. Therefore, the objectives of my Ph.D. project were: 1) To investigate mitochondrial genome evolution using comparative mitogenomic analyses of closely related species and isolates as well as phylogenetically distant taxa of AMF; 2) To explore mt genome inheritance among compatible isolates of the model AMF Rhizophagus irregularis through anastomosis formation; and 3) To assess mtDNA and mt genes for marker development and phylogenetic analyses. We used whole genome shotgun, 454 pyrosequencing and HiSeq Illimina to sequence AMF taxa selected according to their importance and availability in our lab collections. De novo assemblies, Sanger sequencing, annotation and comparative genomics were then performed to characterize complete mtDNAs. We discovered interesting evolutionary mechanisms in Gigaspora rosea: 1) we found a fully reshuffled mt genome synteny compared to Rhizaphagus irregularis DAOM 197198; and 2) we discovered the presence of fragmented cox1 and rns genes. We demonstrated that two cox1 transcripts are joined by trans-splicing. We also reported an unusual mtDNA organization in Rhizophagus sp. DAOM 213198, whose mt genome consisted of two circular mtDNAs. In addition, we observed a considerably higher number of mt plasmidrelated sequences in Glomeraceae compared with Gigasporaceae, contributing a mechanism for faster evolution of mtDNA in Glomeromycota. We also sequenced other isolates of R. irregularis and Rhizophagus sp. in order to unravel their evolutionary relationships and to develop molecular toolkits for their discrimination. Comparative mitogenomic analyses of these mtDNAs revealed the occurrence of many mobile elements such as mobile open reading frames (mORFs), short inverted repeats (SIRs), and plasmid-related sequences (dpo) that impact mt genome synteny and mtDNA alteration. All together, these evolutionary mechanisms among closely related AMF isolates give us clues for designing reliable and efficient intra- and inter-specific markers to discriminate closely related AMF taxa and isolates. Data generated in my Ph.D. project advances our knowledge of mitochondrial genomes evolution not only in Glomeromycota, but also in the larger framework of the Fungal kingdom and Eukaryotes in general. Molecular toolkits developed in this project will offer new opportunities to study population genetics, genetic exchanges and ecology of AMF. In turn, this work will contribute to understanding the role of these fungi in nature, with potential applications in both agriculture and environmental protection.