Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 39 for “"synteny"”.
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Conservation and synteny of long non-coding RNAs invertebrate genomes and their identification in novel transcriptomes
Long non-coding RNAs (IncRNAs) are a biological entity defined by <i>what they are not</i>, rather than by <i>what they are</i>. This indicates that our knowledge about them is sensibly limited. The aim of my PhD is to gain insights into the evolution and the functions of IncRNAs through …
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Methods for Analysis of Prokaryotic Genome Architecture
… representation of genomes and their alignments, synteny block analysis, whole genome sequence alignment, pan-genome analysis, multiple sequence alignment, and genome rearrangement analysis. Though our approach was originally developed from a pan-genome perspective for prokaryotes, the methods …
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Chromosomal assembly and comparative analysis of the red fox (Vulpes vulpes) genome
… and the X) based both on nucleotide-level synteny among the fox, dog, and cat identified through pairwise alignment of the reference genomes and on interspecies synteny reported in previously developed comparative maps. The result of the current analysis is the development of a new version …
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Probabilistic framework for genome-wide phylogeny and ortholog determination
… for any set of the genes. In a novel technique, synteny maps are used to train and evaluate the evolutionary model on both simulated and real sequence data. SINDIR avoids errors commonly committed by current methods and achieves a significantly improved accuracy of orthology determination.
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Efficient Algorithms for Prokaryotic Whole Genome Assembly and Finishing
… computationally resolved repeat structures and synteny with one or more reference organisms. The CARP tool requires a set of repeat sequences such as insertion sequences (IS) that can be found computationally found without assembling the genome. Development of methods to identify such repeating …
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Magnaporthe Oryzae Telomeric Retrotransposon (moter) Relics Further Highlight Telomere Dynamics In A Rapidly Evolving Fungal Pathogen
… MoTeR relics revealed several regions of shared synteny among distantly related strains that points towards their existence within ancestral strains, as well as seemingly strain- and lineage-specific relics that may be the result of more recent rearrangements. MoTeR relics serve as markers for …
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On the molecular diversity of dimethylsulphoniopropionate catabolism by marine bacteria
… bioinformatics analysis of the occurrence and synteny of genes associated with DMSP catabolism within sequenced members of the abundant Roseobacter clade, revealing some interesting patterns which warrant further experimental investigation. Finally, I have shown that the model marine …
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Linkage mapping in prairie cordgrass (Spartina pectinata Link) using genotyping-by-sequencing markers
… sorghum genome, providing a first glimpse into synteny between Chloridoids and other grasses. Genotyping-by-sequencing enabled rapid generation of a linkage map that will aid in future breeding and genomics efforts in prairie cordgrass.
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Genomic Conservation of the Outer Hair Cell Motility Protein, Prestin in the Monotreme: Ornithorhyncus anatinus (Platypus)
… identification based on 1) gene organization, 2) synteny, 3) structural motifs and 4) nucleotide and amino acid homology. A prestin ortholog was identified in the platypus with a great identity to the mammalian mouse prestin. The eutherian branches have a 96% identity and 98% shared similarity in …
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Analysis and Characterization of Vitamin B Biosynthesis Pathways in the Phytoparasitic Nematode Heterodera Glycines
… to SCN. HGT was further supported by gene synteny of the two genes HgSNZ and HgSNO. These two genes also were shown to form a complete, functional pathway for vitamin B6 biosynthesis, representing the first example the HGT of a complete functional pathway from bacteria into nematodes. The …
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Preliminary quantitative trait loci analysis for biomass traits in Miscanthus sinensis
… effect increased the power to detect QTLs. Synteny between sorghum and Miscanthus has been utilized to identify a plausible gene candidate underlying a flowering time QTL. This analysis sets the foundation for fine mapping, positional cloning, and the development of a marker assisted …
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Towards Cloning the Leaf Rust Resistance Gene Rph5
… C970 in the Bowman x Magnif 102 population. Synteny between rice chromosome 1 and barley chromosome 3 was employed to saturate the region within the sub-centimorgan region around Rph5 using sequence-tagged site (STS) markers that were developed based on barley expressed sequence tags (ESTs) …
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Evolutionary and Developmental Survey of Genes Involved in Chordate Pigmentation
… cnidarians to human. Phylogeny, intron code and synteny conservation prompted me to depict Rab evolution, with a special focus on chordates that exhibit a highly dynamic evolutionary pattern. <br></br><br></br> I clarified the evolution of Rab32/38 subfamily, fundamental in regulation of …
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Investigations of self-incompatibility (SI) in perennial ryegrass (Lolium perenne L.)
… regions on rice chromosomes 5 (R5) and 4 with synteny to regions of L. perenne genome containing the S and Z loci, respectively. Markers were developed from the syntenic rice genomic region to refine the S and Z maps. The closest flanking markers had a map distance of 2 cM from S and 0.2 cM …
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The genetic determinants of vigour control and precocity by pear (Pyrus communis L.) rootstocks
… of the QTL loci of apple and pear showed a high synteny between both loci and may help to identify candidate genes in both genera. The ease of vegetative propagation, a crucial trait for rootstock breeding, was assessed in rooting experiments and small effect QTLs were identified. These results …
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Genetic and phenotypic analysis of novel South African Avian poxviruses
… level did not vary greatly, gene content and synteny between isolates/species at these identified regions were far more divergent than expected. The reasons for these large genomic rearrangements are yet to be elucidated and will need to be considered in future phylogenetic studies and vaccine …
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Biochemical and Functional Characterization of Induced Terpene Formation in Arabidopsis Roots
… infection. We provide evidence based on genome synteny and phylogenetic analysis that the arabidiol biosynthetic gene cluster containing the arabidiol synthase (ABDS) and CYP705A1 genes possibly emerged via local gene duplication followed by de novo neofunctionalization. Together, our studies …
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Homeobox gene and microRNA duplication in Chelicerata
… and several miRNA clusters, providing extensive synteny support for a WGD in this lineage. Furthermore, the expression patterns of homeobox paralogs have diverged during embryogenesis and may represent cases of sub- and neo-functionalisation. Additionally, the mir-3791 family in P. tepidariorum …
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Unravelling the Origins and Evolution of the Animal Kingdom using Genomics
… (e.g., gene loss/gain, non-coding regions, synteny, etc),gene family evolution, and their evolutionary relationships using genome-wide data. No study to date has compared all the wealth of genomic data available to understand theevolution of the Animal Kingdom. Using a core bioinformatics …
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QTL Mapping and Molecular Dissection of Meat Quality Traits in Swine
… Comparative analyses revealed 51 conserved synteny groups, including 173 conserved segments, and overall comparative coverage greater than 90%. This map was used, together with porcine linkage and bacterial artificial chromosome (BAC) physical maps, to fine-map a QTL affecting pork …
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