Medicago sativa (Alfalfa) is an important agricultural plant for animal forage and nitrogen fixation, and has potential value in ligno-cellulosic energy production. In the quest to understand the plant, I generated a draft genome sequence of M. sativa via two reduced representation sequencing approaches: methylation-dependent filtration, and high CoT filtration. Libraries created from each approach were sequenced on an Illumina next-generation sequencing platform yielding approximately 2.5Gb of raw data. A combination of reference-based genome assembly approaches using the closely related species, Medicago truncatula as a reference, and de novo genome assembly approaches were performed to assemble the draft genome. The reference-based assembly generated 312,011 contigs with weighted median contig length (N50) of 247 bases, whereas de novo assembly produced 547,304 contigs with N50 of 275 bases. The creation of the M. sativa draft genome is vital for downstream functional analyses such as genome wide gene mining and gene expression profiling.

Medicago sativa (Alfalfa) is an important agricultural plant for animal forage and nitrogen fixation, and has potential value in ligno-cellulosic energy production. In the quest to understand the plant, I generated a draft genome sequence of M. sativa via two reduced representation sequencing approaches: methylation-dependent filtration, and high CoT filtration. Libraries created from each approach were sequenced on an Illumina next-generation sequencing platform yielding approximately 2.5Gb of raw data. A combination of reference-based genome assembly approaches using the closely related species, Medicago truncatula as a reference, and de novo genome assembly approaches were performed to assemble the draft genome. The reference-based assembly generated 312,011 contigs with weighted median contig length (N50) of 247 bases, whereas de novo assembly produced 547,304 contigs with N50 of 275 bases. The creation of the M. sativa draft genome is vital for downstream functional analyses such as genome wide gene mining and gene expression profiling.

In this thesis, we build upon the work of Plate by advancing the theory and utility of Holographic Reduced Representations (HRRs). HRRs are a type of linear, associative memory developed by Plate and are an implementation of Hinton’s reduced representations. HRRs and HRR-like representations have been used to model human memory, to model understanding analogies, and to model the semantics of natural language. However, in previous research, HRRs are restricted to storing and retrieving vectors of random numbers, limiting both the ability of HRRs to model human performance in detail, and the potential applications of HRRs. We delve into the theory of HRRs and develop techniques to store and retrieve images, or other kinds of structured data, in an HRR. We also investigate square matrix representations as an alternative to HRRs, and use iterative training algorithms to improve HRR performance. This work provides a foundation for cognitive modellers and computer scientists to explore new applications of HRRs. / Thesis (Master, Computing) -- Queen's University, 2010-08-10 12:50:04.004

Most staple food crops were domesticated thousands of years ago through independent processes across different regions of the world. Studies of the history of such crops have been essential to our understanding of plant domestication as a process that started with the collection of wild material and continued with subsequent propagation, cultivation, and selection under human care. Domestication often involves a complex genetic structure with contributions from multiple founder populations, interspecific hybridization, chromosomal introgressions, and polyploidization events that occurred hundreds to thousands of years earlier. Such intricate origins complicate the systematic study of the sources of phenotypic variation. The analysis of recently domesticated, non-traditional, non-model species, such as Sinningia speciosa (Gesneriaceae), can expand the knowledge that we have on phenotypic variation under domestication, and help us to comprehend modern patterns of plant domestication and to broaden our understanding of the general trends. S. speciosa is commonly known as the 'florist's gloxinia', and it has been cultivated for 200 years as an ornamental houseplant. In our genomic study of S. speciosa, we examined an extensive diversity panel consisting of 115 individuals that included different species in the genus, wild representatives, and cultivated accessions, as well as 150 individuals from an F2 segregating population. Our analyses revealed that all of the domesticated varieties are derived from a single founder population that originated in or near the city of Rio de Janeiro in Brazil. We identified two loci associated with domesticated traits (flower symmetry and color) and did not detect any major hybridization or polyploidization events that could have contributed to the rapid increase in phenotypic diversity. Our findings, in conjunction with other features such as a small, low-complexity genome, ease of cultivation, and rapid generation time, makes this species an attractive model for the study of genomic variation under domestication. Basic research on non-model organisms with low economic importance is uncommon but necessary to understand the world from a broader perspective. In such cases, reduced representation approaches like Genotyping-by-Sequencing (GBS) are efficient low-cost alternatives to whole genome resequencing. However, most of these technologies are subject to patent protection, licensing processes, and fees that constrain genomic research for small non-profit research organizations. We have designed a protocol to construct reduced representation libraries from genomic DNA. Our approach, called Targeted Amplification of Scattered Sites (TASS), deviates from the traditional digestion-ligation-amplification process that is the subject of intellectual property that protects most current methods. Instead, TASS relies on 1) targeting and duplicating scattered regions in the genome by annealing and expanding long tail primers with short annealing sites, and 2) amplifying these regions using primers that are complementary to the added overhangs. At the moment GBS is more consistent and delivers more variants than TASS. However, we have established a foundation on which further optimization can produce an accessible, easy to implement, high-throughput genotyping approach. / Doctor of Philosophy / Most staple food crops were domesticated thousands of years ago through unrelated processes that were initiated across different regions of the world. Studies of the history of such crops have been essential to our understanding of plant domestication, a process that started with the collection of wild material and continued with subsequent propagation and cultivation under human care. Plant domestication has often involved a complex combination of ancestral lineages that encompass multiple populations, crosses with other species, and large DNA reorganizations that occurred hundreds to thousands of years earlier. Such intricate origins make the systematic study of plant domestication very challenging. The analysis of recently domesticated plants such as the 'florist's gloxinia' (Sinningia speciosa), can help us to better understand some of the changes that have occurred during domestication, as well as to comprehend modern patterns of plant domestication and to broaden our understanding of general trends. Florist's gloxinias are ornamental plants that have been cultivated during the last 200 years. In this study we examined 115 specimens, including wild and cultivated types of florist's gloxinias, as well as closely related species in Sinningia. We also constructed and evaluated an artificial population of 150 individuals from the cross of a wild and a cultivated form. Our analyses revealed that all of the domesticated varieties are descendants from a single wild population that originated in or near the city of Rio de Janeiro in Brazil. We also identified two regions of DNA that are responsible for the changes in flower shape and color, and crosses with other species did not introduce such alterations. Our findings, in conjunction with other features such as its small nuclear DNA content, the ease of cultivation indoors, and a rapid generation time, makes the florists' gloxinia an attractive crop to the study the effects of plant domestication. Research on organisms with low economic importance is uncommon but necessary to understand the world from a broader perspective. In such cases, analyzing the entire genetic information that is stored as DNA may be cost-prohibitive. Instead, approaches that sample small portions of DNA from each individual can be utilized. Most of these technologies are currently patented and subject to licensing processes and fees that limit their implementation by small non-profit research organizations. In this study we designed a protocol to sample small portions of DNA, similarly to existing techniques. However, our approach, called Targeted Amplification of Scattered Sites (TASS), employs a sampling process that deviates from the traditional patented procedure that is used in most current methods. At present, TASS is not as consistent and delivers less information than traditional approaches. However, we have established a foundation on which further optimization can produce an accessible and easy to implement technique.

La propagation de bactéries intracellulaires invasives peut entrainer celle des génomes mitochondriaux qui leur sont liés génétiquement au sein du cytoplasme. Cette sélection par autostop peut conduire à une réduction de la taille efficace (Ne) pour le génome mitochondrial. Elle peut également favoriser l'introgression d'une mitochondrie introduite dans une espèce suite à une hybridation. Le principal objectif de ma thèse est de quantifier ces différents effets, de manière globale, au moyen d'un large échantillonnage d'Arthropodes de Polynésie française. Les événements d'introgressions mitochondriales sont à l'origine de discordances entre les histoires évolutives des génomes mitochondriaux et nucléaires. Afin de rechercher de telles discordances, nous avons développé des marqueurs génomiques nucléaires de type RADseq, permettant de reconstruire l'histoire des populations étudiées. J'ai pu montrer au moyen de simulations que ce type de données pouvait être utilisé pour inférer des relations phylogénétiques entre espèces (Cariou et al. 2013). Des améliorations du protocole RADseq nous ont également permis de démontrer l'applicabilité de cette méthode à de nombreux spécimens au sein de librairies hautement multiplexées (Henri et al. 2015). A partir d'analyses in silico, j'ai par ailleurs évalué l'importance de différents biais liés à l'utilisation de marqueurs RADseq pour estimer les diversités génétiques et proposé une méthode permettant de corriger certains d'entre eux. A partir de ces développements, j'ai pu démontrer que sur 30 espèces de Diptères et de Lépidoptères testées à ce jour, la proximité génétique mitochondriale est systématiquement confirmée par les marqueurs nucléaires, rejetant ainsi l'hypothèse d'une introgression mitochondriale récente. Sur un plus large échantillon, nous avons en revanche mis en évidence une réduction significative du Ne mitochondrial dans les lignées infectées par Wolbachia, suffisante pour réduire le polymorphisme, mais insuffisante pour générer une réduction notable de l'efficacité de la sélection naturelle / The spread of endosymbiotic bacteria can drive that of the linked mitochondrial genomes within the cytoplasm. This hitchhiking selection can lead to a reduction of the effective population size of the mitochondrial genomes (Ne). 1t can also facilitate mitochondrial introgression, following the introduction of exogenous mitochondria in a species by hybridization. The main objective of my thesis is to quantify these different effects, on a global scale, using a large sample of Arthropods. Mitochondrial introgressions can lead to discrepancies between the evolutionary histories of mitochondrial and nuclear genomes. To investigate such patterns, we used RADseq genomic markers, that allow reconstructing population histories, and developed improvements for the library preparation and data analysis. Using in silico experiments, 1 showed that RADseq data is suitable for phylogenetic inferences (Cariou et al. 2013). Adjustments in the RADseq protocol also allowed us to demonstrate the applicability of this method for highly multiplexed libraries (Henri et al. 2015). The impact of various biases related the estimation of population genetic diversity using RADseq was also investigated in silico, which lead me to propose an ABC method to correct some of them. Following these developments, 1 showed on 30 species of Diptera and Lepidoptera that nuclear markers always confirmed the mitochondrial genetic relatedness, ruling out the hypothesis of recent mitochondrial introgressions. On a larger sample, we detected a reduction of the mitochondrial Ne in Wolbachia infected lineages. This reduction caused a significant decrease in the polymorphism of infected populations, but appeared insufficient to reduce the efficacy of natural selection

Cotton has been a world-wide economic staple in textiles and oil production. There has been a concerted effort for cotton improvement to increase yield and quality to compete with non-natural man-made fibers. Unfortunately, cultivated cotton has limited genetic diversity; therefore finding new marketable traits within cultivated cotton has reached a plateau. To alleviate this problem, traditional breeding programs have been attempting to incorporate practical traits from wild relatives into cultivated lines. This incorporation has presented a new problem: uncultivated cotton hampered by photoperiodism. Traditionally, due to differing floral times, wild and cultivated cotton species were unable to be bred together in many commercial production areas world-wide. This worldwide breeding problem has inhibited new trait incorporation. Before favorable traits from undomesticated cotton could be integrated into cultivated elite lines using marker-assisted selection breeding, the markers associated with photoperiod independence needed to be discovered. In order to increase information about this debilitating trait, we set out to identify informative markers associated with photoperiodism. This study was segmented into four areas. First, we reviewed the history of cotton to highlight current problems in production. Next, we explored cotton’s floral development through a study of floral transition candidate genes. The third area was an in-depth analysis of Phytochrome C (previously linked to photoperiod independence in other crops). In the final area of study, we used Genotype-By-Sequencing (GBS), in a segregating population, was used to determine photoperiod independence associated with single nucleotide polymorphisms (SNPs). In short, this research reported SNP differences in thirty-eight candidate gene homologs within the flowering time network, including photoreceptors, light dependent transcripts, circadian clock regulators, and floral integrators. Also, our research linked other discrete SNP differences, in addition to those contained within candidate genes, to photoperiodicity within cotton. In conclusion, the SNP markers that our study found may be used in future marker assisted selection (MAS) breeding schemas to incorporate desirable traits into elite lines without the introgression of photoperiod sensitivity.