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Статті в журналах з теми "Séquençage long-Read":
Chikhaoui, Lies. "Étude du transcriptome circadian chez la souris à l’aide de séquençage long read Oxford Nanopore." Médecine du Sommeil 18, no. 4 (December 2021): 192. http://dx.doi.org/10.1016/j.msom.2021.10.019.
Chaudieu, Gilles, and Pascale Quignon. "La rétinopathie du Border collie, une maladie héréditaire mais un gène difficile à isoler." Bulletin de l'Académie vétérinaire de France 175 (2022). http://dx.doi.org/10.3406/bavf.2022.71001.
Дисертації з теми "Séquençage long-Read":
Marijon, Pierre. "Novel components at the periphery of long read genome assembly tools." Thesis, Lille 1, 2019. http://www.theses.fr/2019LIL1I087.
The sequencing of genetic information provides better understanding for a large number of biolog-ical phenomena: e.g. genetic diseases, speciation events, fundamental mechanisms of cell function.Sequencing techniques have considerably evolved since the Sanger method (1977). Nowadays third-generation sequencing technologies greatly reduce the costs of sequencing complete genomes. Theyproduce longer reads (sequence fragments), but require the design of specific assembly tools that takeinto account the high error rates in the produced fragments.The study of methods used by third-generation read assembly pipelines has revealed that im-provements in assembly were possible without modifying assembly tools themselves. Some improve-ments are thus proposed in this thesis work, and were implemented through publicly available tools.yacrd and fpa pre-process the set of reads prior to assembly, in order to improve efficiency and qualityof the assembly process. KNOT combines information from both the input reads and an assembly, inorder to provide insights on how to improve the contiguity of an assembly
Zhang, Panpan. "Étude du paysage des éléments transposables sous forme d'ADN circulaire extrachromosomique et dans l'assemblage des génomes de plantes à l'aide du séquençage en lectures longues." Thesis, Université de Montpellier (2022-….), 2022. http://www.theses.fr/2022UMONG016.
Transposable elements (TEs) are repetitive DNA sequences with the intrinsic ability to move and amplify in genomes. Active transposition of TEs is linked to the formation of extrachromosomal circular DNA (eccDNA). However, the complete landscape of this eccDNA compartment and its interactions with the genome were not well defined. In addition, at the beginning of my thesis, there were no bioinformatics tools available to identify eccDNAs from long-read sequencing data.To address these questions during my PhD, we first developed a tool, called ecc_finder, to automate eccDNA detection from long-read sequencing and optimized detection from short-read sequences to characterize TE mobility. By applying ecc_finder to Arabidopsis, human and wheat eccDNA-seq data (with genome sizes ranging from 120 Mb to 17 Gb), we documented the broad applicability of ecc_finder as well as optimization of computational time, sensitivity and accuracy.In the second project, we developed a meta-assembly tool called SASAR to reconcile the results of different genome assemblies from long-read sequencing data. For different plant species, SASAR obtained high quality genome assemblies in an efficient time and resolved structural variations caused by TEs.In the last project, we used SASAR-assembled genome and ecc_finder-detected eccDNA to characterize eccDNA-genome interactions. In Arabidopsis hypomethylated epigenetic mutants, we highlighted the role of the epigenome in protecting genome stability not only from TE mobility but also from genomic rearrangements and gene chimerism. Overall, our findings on eccDNA, genome assembly and their interactions, as well as the development of tools, offer new insights into the role of TEs in the adaptive evolution of plants to rapid environmental change
Fruchard, Cécile. "Étude des chromosomes sexuels et du déterminisme du sexe chez les plantes : comparaison des systèmes Silene et Coccinia." Thesis, Lyon, 2018. http://www.theses.fr/2018LYSE1108/document.
Although rarer than in animals, separate sexes (dioecy) have evolved in ∼15,600 angiosperm species (∼6% of all angiosperm species). How sex is controlled is a central question in plant sciences and also in agronomy as many crops are dioecious (∼20% of crops) with only one useful sex (usually female). Only three master sex-determining genes have been identified in dioecious plants so far, namely in persimmons, asparagus and strawberry. Dioecy likely evolved several times independently in angiosperms, suggesting that sex-determining genes are of diverse origins. Hermaphroditism is the predicted ancestral state of the angiosperm flower. Two main pathways have been identified that explain the evolution of hermaphroditism towards dioecy: either through a monoecious state (with both unisexual male and female flowers on the same individual) or a gynodioecious state (with females and individuals having hermaphroditic flowers). My aim is to compare two plant systems representing each one of these two pathways. In Coccinia grandis, a Cucurbitaceae with an XY chromosome system, dioecy evolved through monoecy. In Silene latifolia, a well-studied dioecious plant with XY sex chromosomes, dioecy evolved through gynodioecy. Three genes controlling monoecy have been identified in melon, and it was suggested that these genes act as sex-determining genes in closely related dioecious species such as C. grandis. I therefore chose a candidate gene approach in this species. Very few genetic and genomic data are available in C. grandis, and we chose to use SEX-DETector, a probabilistic method that uses RNA-seq data to genotype parents and their offspring, and infers sex-linked genes with no need for a reference genome. This method allowed me to identify 1,364 genes that are present on the sex chromosomes of C. grandis. I found that the sex chromosomes are enriched in sex-biasedgenes when compared to autosomes and I characterized Y chromosome degeneration in terms of decreased expression and gene loss. Finally, I showed that dosage compensation occurs in C. grandis. Testing for the three candidates genes is ongoing. In S. latifolia 3 regions involved in sex determination have already been identified on the Y chromosome. We chose to sequence this chromosome to identify sex-determining genes. The sequencing of Y chromosomes remains one of the greatest challenges of current genomics. The assembly step is very difficult because of their highly repeated content. Consequently, fully sequenced Y chromosomes are rare and mainly available for research in animals. To overcome the difficulty of assembling reads with many repeats, I used third generation sequencing (TGS, producing long reads). I produced a dataset using the Oxford Nanopore MinION sequencer with Y chromosome DNA. Assembling was performed using a combination of Illumina, MinION and PacBio sequencing data. The final assembly had a total length of 563 Mb with a scaffold N50 of 6,114 bp, and contained 16,219 de novo annotated genes