We are generally interested in genome stability, from its mechanistic aspects to the global impact it has on evolution. Our work combines approaches from molecular biology, biochemistry, cytogenetics and genomics in an integrative framework. We strongly believe there is much to learn from a diversity of model systems.
Ongoing research
Genomic consequences of a transition to asexuality.
Genome content and organization are extremely dynamic across animals and deciphering the mechanisms underlying this variation is critical to understand evolution and how biodiversity is generated. Sexual reproduction is one of the most beneficial forces acting on animal genome evolution, but some animals nevertheless reproduce asexually. Asexual organisms do not benefit from the positive impact of sexual reproduction and are thus expected to accumulate deleterious mutations and eventually go extinct.
We work on two species of fish, the mummichog (Fundulus heteroclitus) and the Banded Killifish (Fundulus diaphanus) and their sexually and asexually reproducing hybrids. We will determine whether their asexual hybrids are temporarilly stable and then examine the genomes of sexual and asexual hybrids to investigate whether and how their genomes differ compared to the parental species. We will also determine whether asexual hybrids accumulate more deleterious mutations compared to sexually reproducing hybrids and parental species.
Together, these approaches will help us understand how genomes evolve, how sexual reproduction benefits organisms and why sexual reproduction is so widespread.
Dalziel AC, Tirbhowan S, Drapeau HF, Power C, Jonah LS, Gbotsyo YA, Dion-Côté AM (2020) Using asexual vertebrates to study genome evolution and animal physiology: Banded (Fundulus diaphanus) x Common Killifish (F. heteroclitus) hybrid lineages as a model system. Evolutionary Applications.
Current students: Fiona Ewart, Annabelle Fournier, Pascale Ouellette, Alexandre-James Roussel
Ongoing research
Genomic consequences of a transition to asexuality.
Genome content and organization are extremely dynamic across animals and deciphering the mechanisms underlying this variation is critical to understand evolution and how biodiversity is generated. Sexual reproduction is one of the most beneficial forces acting on animal genome evolution, but some animals nevertheless reproduce asexually. Asexual organisms do not benefit from the positive impact of sexual reproduction and are thus expected to accumulate deleterious mutations and eventually go extinct.
We work on two species of fish, the mummichog (Fundulus heteroclitus) and the Banded Killifish (Fundulus diaphanus) and their sexually and asexually reproducing hybrids. We will determine whether their asexual hybrids are temporarilly stable and then examine the genomes of sexual and asexual hybrids to investigate whether and how their genomes differ compared to the parental species. We will also determine whether asexual hybrids accumulate more deleterious mutations compared to sexually reproducing hybrids and parental species.
Together, these approaches will help us understand how genomes evolve, how sexual reproduction benefits organisms and why sexual reproduction is so widespread.
Dalziel AC, Tirbhowan S, Drapeau HF, Power C, Jonah LS, Gbotsyo YA, Dion-Côté AM (2020) Using asexual vertebrates to study genome evolution and animal physiology: Banded (Fundulus diaphanus) x Common Killifish (F. heteroclitus) hybrid lineages as a model system. Evolutionary Applications.
Current students: Fiona Ewart, Annabelle Fournier, Pascale Ouellette, Alexandre-James Roussel
Identifying the molecular basis of undiagnosed genetic diseases.
Several characteristics of the New Brunswick population, including founder effect and limited gene flow, render it susceptible to genetic diseases. In this context, many patients presenting clinical phenotypes compatible with Mendelian diseases remain undiagnosed despite extensive clinical instigations,. We are using whole-genome sequencing approaches in various families presenting a genetic condition that remains undiagnosed. These projects will allow accurate diagnoses and personalized medical follow-ups.
Several characteristics of the New Brunswick population, including founder effect and limited gene flow, render it susceptible to genetic diseases. In this context, many patients presenting clinical phenotypes compatible with Mendelian diseases remain undiagnosed despite extensive clinical instigations,. We are using whole-genome sequencing approaches in various families presenting a genetic condition that remains undiagnosed. These projects will allow accurate diagnoses and personalized medical follow-ups.
Stress marker development in snow crab.
The snow crab (Chionocetes opilio) industry supports hundreds of jobs from harvesting to commercialization in New Brunswick. In its current state, this industry is more oriented toward quantity rather than quality, and most landings are in a state that does not allow to obtain the highest selling prices. Moreover, there is a growing interest in long term storing of live crabs for transportation and marketing off the fishing season, when market prices are high. For this to be successful, crabs that are in the best conditions must be selected.
Classical animal stress markers may prove useful, but crustaceans, and snow crab in particular, remain poorly studied; accurate physiological markers remain to be discovered. We are leveraging transcriptomic approaches to develop reliable and affordable biological markers of stress in snow crab to assess quality early in the commercialization chain. These markers will be validated on freshly harvested animals and contribute to increase yield and profitability.
Current students: Claude Power
The snow crab (Chionocetes opilio) industry supports hundreds of jobs from harvesting to commercialization in New Brunswick. In its current state, this industry is more oriented toward quantity rather than quality, and most landings are in a state that does not allow to obtain the highest selling prices. Moreover, there is a growing interest in long term storing of live crabs for transportation and marketing off the fishing season, when market prices are high. For this to be successful, crabs that are in the best conditions must be selected.
Classical animal stress markers may prove useful, but crustaceans, and snow crab in particular, remain poorly studied; accurate physiological markers remain to be discovered. We are leveraging transcriptomic approaches to develop reliable and affordable biological markers of stress in snow crab to assess quality early in the commercialization chain. These markers will be validated on freshly harvested animals and contribute to increase yield and profitability.
Current students: Claude Power
Past research
Genomic impacts of genetic conflicts on population structure and evolution.
Transposable elements (TEs) are selfish genetic elements that give rise to intragenomic conflicts due to their capacity to self-propagate to the detriment of their host. In Drosophila, the TEs HeT-A, TAHRE and TART (HTTs) form the telomere instead of telomerase-dependent repeats, as in most other eukaryotes. We are investigating the genomic determinants of telomere-length dynamics from TEs' perspective.
McGurk MP*, Dion-Côté AM*, Barbash DA (2021) Rapid evolution at the telomere: transposable elements dynamics at an intrinsically unstable locus. GENETICS 217(2):iyaa027.
Genomic impacts of genetic conflicts on population structure and evolution.
Transposable elements (TEs) are selfish genetic elements that give rise to intragenomic conflicts due to their capacity to self-propagate to the detriment of their host. In Drosophila, the TEs HeT-A, TAHRE and TART (HTTs) form the telomere instead of telomerase-dependent repeats, as in most other eukaryotes. We are investigating the genomic determinants of telomere-length dynamics from TEs' perspective.
McGurk MP*, Dion-Côté AM*, Barbash DA (2021) Rapid evolution at the telomere: transposable elements dynamics at an intrinsically unstable locus. GENETICS 217(2):iyaa027.
Evolutionary dynamics of a germline restricted chromosome.
Metazoans typically maintain identical genome copies in all cells, most of which undergo differentiation, while germ cells are devoted to maintain and transmit the genetic information to the next generation. However, some organisms undergo DNA elimination as a part of their development for unclear reasons. We are testing the hypothesis that DNA elimination is a strategy to minimize genomic conflict between the germline and the soma.
Kinsella CM*, Ruiz-Ruano FJ*, Dion-Côté AM, Charles AJ, Gossmann TI, Cabrero J, Kappei D, Hemmings N, Simons MJP, Camacho JPM, Forstmeier W, Suh A (2019) Programmed DNA elimination of germline development genes in songbirds. Nature Communications.
Metazoans typically maintain identical genome copies in all cells, most of which undergo differentiation, while germ cells are devoted to maintain and transmit the genetic information to the next generation. However, some organisms undergo DNA elimination as a part of their development for unclear reasons. We are testing the hypothesis that DNA elimination is a strategy to minimize genomic conflict between the germline and the soma.
Kinsella CM*, Ruiz-Ruano FJ*, Dion-Côté AM, Charles AJ, Gossmann TI, Cabrero J, Kappei D, Hemmings N, Simons MJP, Camacho JPM, Forstmeier W, Suh A (2019) Programmed DNA elimination of germline development genes in songbirds. Nature Communications.
Evolutionary impact of gene duplication
Gene duplication is thought to increase robustness of the protein-protein interaction network to perturbations. We tested this hypothesis at a large scale and systematically, leveraging the strengths of the yeast Saccharomyces cereviae as a model system. We found that some gene duplicates could indeed compensate for the loss of their cognate copy. However, we surprisingly found that gene duplication often increased fragility of the cell to perturbation, as many duplicates at least partially rely on their cognate copy to fulfill their function.
Diss G, Gagnon-Arsenault I, Dion-Côté AM, Vignaud H, Ascencio DI, Berger CM, Landry CR (2017) Gene duplication can impart fragility, not robustness, in the yeast protein interaction network. Science 355(6325): 630-634.
Gene duplication is thought to increase robustness of the protein-protein interaction network to perturbations. We tested this hypothesis at a large scale and systematically, leveraging the strengths of the yeast Saccharomyces cereviae as a model system. We found that some gene duplicates could indeed compensate for the loss of their cognate copy. However, we surprisingly found that gene duplication often increased fragility of the cell to perturbation, as many duplicates at least partially rely on their cognate copy to fulfill their function.
Diss G, Gagnon-Arsenault I, Dion-Côté AM, Vignaud H, Ascencio DI, Berger CM, Landry CR (2017) Gene duplication can impart fragility, not robustness, in the yeast protein interaction network. Science 355(6325): 630-634.
Molecular bases of reproductive isolation in a nascent species complex
The goal of my thesis was to understand the molecular bases of reproductive isolation at an early stage of speciation in the Lake Whitefish system.
I looked at the transcriptional impact of hybridization by an RNA-seq experiment in embryos. I found that transposable elements and ncRNAs are derepressed in unfit backcrosses. I then characterized the impact of hybridization at the chromosome scale. I found that reproductive isolation in the lake whitefish system is associated with mitosis and meiosis breakdown. Finally, I applied cytogenetic methods to three pairs of sympatric lake whitefish species and found that chromosome rearrangements appear to be associated with divergence. The work embedded in my thesis emphasizes the importance of molecular mechanisms to understand divergence and speciation.
Dion-Côté AM, Symonová R, Lamaze F, Ráb P, Bernatchez L (2017) Standing chromosomal variation in Lake Whitefish species pairs: the role of historical contingency and relevance for speciation. Molecular Ecology 26(1): 178-192.
Dion-Côté AM, Symonová R, Ráb P, Bernatchez L (2015) Reproductive isolation in a nascent species pair is associated with aneuploidy in hybrid offspring. Proceedings of the Royal Society B 282: 20142862.
Dion-Côté AM, Renaut S, Normandeau E, Bernatchez L (2014) RNA-seq reveals transcriptomic shock involving transposable elements reactivation in the offspring of incipient lake whitefish species. Molecular Biology and Evolution 31(5): 1188-99.
The goal of my thesis was to understand the molecular bases of reproductive isolation at an early stage of speciation in the Lake Whitefish system.
I looked at the transcriptional impact of hybridization by an RNA-seq experiment in embryos. I found that transposable elements and ncRNAs are derepressed in unfit backcrosses. I then characterized the impact of hybridization at the chromosome scale. I found that reproductive isolation in the lake whitefish system is associated with mitosis and meiosis breakdown. Finally, I applied cytogenetic methods to three pairs of sympatric lake whitefish species and found that chromosome rearrangements appear to be associated with divergence. The work embedded in my thesis emphasizes the importance of molecular mechanisms to understand divergence and speciation.
Dion-Côté AM, Symonová R, Lamaze F, Ráb P, Bernatchez L (2017) Standing chromosomal variation in Lake Whitefish species pairs: the role of historical contingency and relevance for speciation. Molecular Ecology 26(1): 178-192.
Dion-Côté AM, Symonová R, Ráb P, Bernatchez L (2015) Reproductive isolation in a nascent species pair is associated with aneuploidy in hybrid offspring. Proceedings of the Royal Society B 282: 20142862.
Dion-Côté AM, Renaut S, Normandeau E, Bernatchez L (2014) RNA-seq reveals transcriptomic shock involving transposable elements reactivation in the offspring of incipient lake whitefish species. Molecular Biology and Evolution 31(5): 1188-99.