Genomic characterization of divergent haplotypes of large structural variants in the genus Helianthus
department or school: Science, Faculty of
data provider: DSpace
degree campus: UBCV
creator: Lande, Kathryn
issued: 2021-05-04T18:22:16Z
issued: 2021
related degree: Master of Science - MSc
degree grantor: University of British Columbia
description: Recent analyses of the genomes of three wild sunflower species (Helianthus annuus, H. petiolaris, H. argophyllus) have uncovered 37 non-recombining, highly divergent haploblocks, all of which are megabases long. The lack of recombination between alternate haplotypes of these regions has been shown to result from segregating chromosomal structural variants (SVs) in many cases. These SVs are distributed along environmental clines. Genome-Wide Association Studies (GWAS) and Genome-Environment Association (GEA) analyses indicate that the SVs are strongly associated with certain climate and soil conditions, as well as a wide range of phenotypic traits and ecotypes. They are also significant from an evolutionary standpoint by providing a potential explanation for how these species are able to maintain a wide variety of locally adapted ecotypes and ecospecies despite considerable gene flow between distinct populations. However, while substantial high-level work has been done to identify the phenotypic traits, habitat associations, and phylogenetic origins of these SVs, there had been little characterization of the genes housed within the SVs before now. Through the subsequent analyses, I characterize the haplotype-specific genetic and transcriptomic divergence between gene variants using a mix of genomic and transcriptomic data sets previously generated by the Rieseberg Lab and collaborators. In so doing, I find that alternate haplotypes of these SVs demonstrate remarkable divergence in genes potentially related to local adaptation and the functions predicted in previous studies. I also investigate the evolutionary forces acting on each SV to show that both haplotype-specific positive and negative selection appear abundant. Finally, through population genetics I provide evidence that these SVs had introgressive origins.
aggregated CHO: https://circle.library.ubc.ca/rest/handle/2429/78091
note: Genomic Characterization of DivergentHaplotypes of Large Structural Variants in theGenus HelianthusbyKathryn LandeB.Sc, McGill University, 2018A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THEREQUIREMENTS FOR THE DEGREE OFMASTER OF SCIENCEinThe Faculty of Graduate and Postdoctoral Studies(Genome Science and Technology)THE UNIVERSITY OF BRITISH COLUMBIA(Vancouver)April 2021© Kathryn Lande, 2021The following individuals certify that they have read, and recommend to the Faculty of Graduate and Postdoctoral Studies for acceptance, the thesis entitled: Genomic Characterization of Divergent Haplotypes of Large Structural Variants in the Genus Helianthus submitted by Kathryn Lande in partial fulfillment of the requirements for the degree of Master of Science in Genome Science and Technology Examining Committee: Dr. Loren Rieseberg, Department of Botany Supervisor Dr. Judith Mank, Department of Zoology Supervisory Committee Member Dr. Joerg Bohlmann, Department of Forestry Supervisory Committee Member Dr. Peter Stirling, Department of Medical Genetics Additional Examiner Additional Supervisory Committee Members: Supervisory Committee Member Supervisory Committee Member ii, UBC, UBC, UBC, UBCAbstractRecent analyses of the genomes of three wild sunflower species (Helianthus annuus, H.petiolaris, H. argophyllus) have uncovered 37 non-recombining, highly divergenthaploblocks, all of which are megabases long. The lack of recombination betweenalternate haplotypes of these regions has been shown to result from segregatingchromosomal structural variants (SVs) in many cases.These SVs are distributed along environmental clines. Genome-Wide AssociationStudies (GWAS) and Genome-Environment Association (GEA) analyses indicate that theSVs are strongly associated with certain climate and soil conditions, as well as a widerange of phenotypic traits and ecotypes. They are also significant from an evolutionarystandpoint by providing a potential explanation for how these species are able tomai…
has type: Thesis/Dissertation
date issued: 2021-11
is shown at: 10.14288/1.0397228
language: eng
degree discipline: Genome Science and Technology
provider: Vancouver : University of British Columbia Library
publisher: University of British Columbia
rights: Attribution-NonCommercial-NoDerivatives 4.0 International
rights URI: http://creativecommons.org/licenses/by-nc-nd/4.0/
scholar level: Graduate
contributor: Rieseberg, Loren H.
type: Text
identifier URI: http://hdl.handle.net/2429/78091