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The Arctic charr (Salvelinus alpinus) genome: An analysis of evolutionary change after whole genome duplication

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Title: The Arctic charr (Salvelinus alpinus) genome: An analysis of evolutionary change after whole genome duplication
Author: Nugent, Cameron
Department: Department of Integrative Biology
Program: Integrative Biology
Advisor: Ferguson, MoiraDanzmann, Roy
Abstract: The genomic evolution of vertebrates has been influenced by the occurrence of whole genome duplications (WGD), which drastically alter the genomic landscape by producing duplicate copies of every chromosome. Diploidization is the fundamental process that follows WGD, during which duplicated (4N) chromosomes evolve into two distinct diploid (2N) pairs through mutations, deletions and rearrangements. The salmonid specific fourth round (Ss4R) of WGD occurred ~88-103 m.y.a. and the genomes of extant species have yet to fully diploidize. Salmonid diploidization is a variable and non-random process that is influenced by genomic architecture. Larger chromosomes (that have arisen through fusions) can form multivalents and undergo recombination, which stifles diploidization. The Ss4R’s effect on the evolution of duplicated fitness related loci is so far poorly characterized. I characterized the genomic architecture of Arctic charr (Salvelinus alpinus), a salmonid species whose genome is in the midst of diploidization and examined the relationship between genomic architecture and diploidization. An Arctic charr linkage map was constructed and chromosome arms sharing a pre-WGD ancestor (homeologous pairs) were identified. For homeologous pairs where neither arm has undergone a fusion event, diploidization has proceeded more rapidly. The evolution of quantitative trait loci (QTL, loci that correlate with variation in a quantitative trait in the phenotype of a population of organisms) in a diploidizing genome was explored through the development of an Arctic charr genotyping array. The array was used in genome-wide association analysis to identify the genetic basis of fork length, body mass and sexual maturation. Comparison with previous QTL studies showed that the genetic architecture of body mass is similar across divergent strains of Arctic charr. Comparison with body mass QTL from other salmonids suggested that conservation of QTL on duplicated chromosomes is not prevalent and that divergence of function may have occurred. Through characterization of the Arctic charr genome and investigating the evolutionary mechanisms that have shaped it, I have added to the understanding of the interplay of genomic architecture and diploidization and its effect on the evolution of phenotypes.
Date: 2019-05
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S2.1_AC-SNP-Sequences.csvuntranslated 490.0Kb Unknown View/Open Supplementary File S2.1
S2.2_AC_Linkage_Map.csvuntranslated 454.5Kb Unknown View/Open Supplementary File S2.2
S2.3_Blast_locations.csvuntranslated 1.385Mb Unknown View/Open Supplementary File S2.1
S2.4_Blastn_duplicates.csvuntranslated 59.66Kb Unknown View/Open Supplementary File S2.4
S3.1_Salp7K_array_markers.csvuntranslated 17.47Mb Unknown View/Open Supplementary File S3.1
S3.2_Salp87_array_SNP_NCBI_genome.csvuntranslated 9.060Mb Unknown View/Open Supplementary File S3.2
S4.1_AC_gene_positions_chromosomes.csvuntranslated 14.55Mb Unknown View/Open Supplementary File S4.1
S4.2_phenotype_family_summaries.csvuntranslated 22.06Kb Unknown View/Open Supplementary File S4.2
S4.3_manhattan_plots.pdfuntranslated 65.15Mb PDF View/Open Supplementary File S4.3
S4.4_gwas_significant_snps.csvuntranslated 641.8Kb Unknown View/Open Supplementary File S4.4
Nugent_Cameron_201905_PhD.pdfuntranslated 7.755Mb PDF View/Open Main article

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