PhD Exit Seminar- Shalabh Thankur (Guttman lab)

PhD Exit Seminar

Wednesday, September 13, 2017 at 2:10 pm, Earth Sciences Building, Room 3087

Shalabh Thakur (Guttman Lab)

Comparative and Evolutionary Genomics of Pseudomonas syringae


The Pseudomonas syringae species complex comprises many genetically diverse strains ubiquitously found in both agricultural and non-agricultural environments. The species complex has a very broad host range; however, distinct strains show strong host specificity and are able to cause disease on limited crops. Although more popularly known as a plant pathogenic bacteria, many P. syringae strains are reported to be non-pathogenic and found in habitats linked to water sources, soil, and snow fields. Multi-locus sequence typing studies have sub-divided the P. syringae complex into at least 13 different subgroups referred as phylogroups. Given such extensive genetic and ecological diversity within the species complex, there is an ongoing debate over the species definition of P. syringae strains. My research work investigated whether strains within the P. syringae species complex belong to a single species population or if distinct phylogroups are in fact different species. We performed a whole-genome analysis of approximately 400 P. syringae strains using various comparative and evolutionary approaches to examine the extent of genetic cohesion within the P. syringae species complex due to various ecological and evolutionary mechanisms. The comparative genomics projects often face a computational challenge due to quadratic increase in time and the resources needed for the pairwise sequence comparisons with the increase in number of sequenced genomes. To overcome this challenge and facilitate large-scale sequence comparisons between hundreds of closely related prokaryotic genomes, we designed a novel comparative genomic pipeline named DeNoGAP. The DeNoGAP pipeline provides a robust computational pipeline for performing various comparative genomics tasks, such as gene prediction, ortholog prediction, functional annotation, and analysis of a pan-genome. DeNoGAP implements an iterative homolog clustering strategy to increase speed and accuracy for large-scale ortholog prediction analysis. Because of this strategy, DeNoGAP outperforms the efficiency of other ortholog prediction tools that implement traditional pairwise comparison algorithms. Our whole-genome comparative analysis of more than 400 strains shed insight into the P. syringae pan-genome. We found that the P. syringae pan-genome is big and diverse, comprising more than 79,000 gene families. We also found substantial diversity in the distribution of virulence-associated gene families, such as type III secreted effectors and toxins, across P. syringae strains. Evolutionary analyses of the gene families in the P. syringae pan-genome showed evidences of homologous recombination and positive selection across entire genomes of P. syringae strains. We found that the P. syringae strains in different phylogroups rarely exchange genes via homologous recombination. However, despite being rare, inter-phylogroup homologous recombination occurs disproportinately among virulence-associated and positively-selected genes that are essential for ecological adaptation and evolution of strains within the P. syringae species complex. Based on these findings, we hypothesized that P. syringae maintains genetic cohesion between its divergent strains due to an exchange of ecological and evolutionarily relevant genes. Together, my work provides a robust computational pipeline for large-scale comparative genomics projects and sheds insight into species definition of the P. syringae species complex based on strong evolutionary species concepts rather than molecular methods.


PhD Exit Seminar – Raphaël Brisset Di Roberto

PhD Exit Seminar

Tuesday August 29th, 1:10 pm – Ramsay Wright Building, Room 432

Raphaël Brisset Di Roberto (Peisajovich/ Chang lab)

Evolutionary alternatives on the road to a new specificity in a G protein-coupled receptor


Cells sense change in their external environment and react appropriately through the action of signaling pathways. This process is initiated by receptor proteins with a high degree of specificity for a particular stimulus. G protein-coupled receptors form the largest family of membrane protein receptors and their ability to sense a broad variety of ligands is unparalleled despite their common ancestral origin. How GPCRs evolved their unique specificities is unknown, although ligand binding affinity is often given a central role. The goal of this thesis was to assess the possible contributions of secondary mechanisms of specificity, namely ligand efficacy and downstream signaling regulation, to changes in ligand recognition. Through directed evolution, we generated a yeast pheromone receptor with an altered specificity in two steps. First, promiscuous receptors were obtained through either improved binding affinity or weaker molecular interaction with a negative regulator of signaling. Second, a ligand-discriminating receptor was obtained from a promiscuous variant solely by reducing the efficacy of the native pheromone. These findings demonstrate the importance of assessing GPCRs’ pharmacological profiles in their native context, where signaling trumps binding affinity in significance.

PhD Exit Seminar – Sophie St-Cyr (McGowan lab)

PhD Exit Seminar

Wednesday August 16th, 3:00 pm – SW 403 – University of Toronto at Scarborough

Sophie St-Cyr (McGowan lab)

“Maternal Programming of Adult Rodent Integrative Phenotype by Prenatal Exposure to Predator Odour”


Prenatal stress mediated through the mother can program the long-term phenotype of the offspring. The capacity for adaptation to adversity in early life depends in part on the life history of the animal. It is therefore likely that an early life ethologically relevant psychogenic stressor that has been present over evolutionary times could prime responses to an environment containing this stress via epigenetic mechanisms such as DNA methylation modifications. Pregnant C57BL/6 mice and, separately, Long-Evans rats were exposed daily to unpredictable and inescapable predator odors or distilled water control over the second half of pregnancy. I examined the effect of the prenatal predator odour exposure on the integrative phenotype of adult offspring at the level of behaviour, physiology, endocrinology, transcription and DNA methylation. Prenatally predator odour-exposed offspring exhibited an overall increase in stress-related behaviours on a variety of commonly-used and semi-naturalistic assessments of the response to stress, as well as modifications of energy consumption at baseline and under stress. These changes were accompanied by a sex-specific increase in endocrine responses to stress and an increase in circulating thyroid hormone. Additionally, I observed modifications in stress-related transcript abundance at birth and in adulthood accompanied by DNA methylation modifications in adulthood. Overall, assessments of the integrative phenotype of prenatal predator odour-exposed animals indicate a persistent increase in stress responsiveness across a variety of experimental conditions and phenotypic levels in the two rodent species. This phenotype supports the hypothesis that maternal programming allows developmental forecasting that shapes the individual developmental trajectory. Prenatal predator odour is therefore a potent programming stressor.