UBC Theses and Dissertations
Annotation of complex genomes for comparative genomics Gagalova, Kristina Kirilova
Advancements in whole-genome sequencing technologies have opened the use of genomic approaches to study a variety of organisms and allowed studies at the whole-genome scale in non-model organisms. In these studies, genome annotation is a fundamental step to extract diverse biological information from sequences that are otherwise strings of characters incomprehensible to humans. Here I assembled and annotated genomes of plant and insect species of applied interest. A common theme in my thesis is comparative and evolutionary genomics of the described organisms. The sequenced species I studied have complex genomic features, including large genome sizes and high repeat contents, which I described in detail. In Chapter 2, I investigate the protein-coding genes of four spruces (Picea, Pinaceae) native to North America. Comparison to other annotated conifers highlights changes in selection in gene families. Several gene families have a significantly expanded number of genes. Some genes are under positive selection: previous studies in spruce highlighted the same proteins as genetic markers for local adaptation. In Chapter 3, I characterize the genome of Pissodes strobi, a naturally occurring pest of the spruces described in Chapter 2. The genome of P. strobi is larger and more repetitive than other sequenced species in the same family (Curculionidae). In Chapter 4, I assemble and annotate the genome of a proprietary Cannabis sativa strain, and study the flavonoid/anthocyanin metabolic pathway, uncovering the upregulation of key metabolic genes involved in the regulation of leaf pigmentation. The presented genome annotations and comparative analyses provide insights into the biology and evolution of the described species. Comparative genome studies are important for generating hypotheses and open avenues of inquiry in future studies in population genomics. In the case of Picea gen. and P. strobi, such studies will enable us to understand the local adaptation of species and the genetic basis of regulatory processes, such as biotic stress mitigation and pest resistance.
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