The Arctic charr (Salvelinus alpinus) genome: An analysis of evolutionary change after whole genome duplication
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) chr...
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University of Guelph
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ftunivguelph:oai:atrium.lib.uoguelph.ca:10214/15993 2024-06-23T07:48:54+00:00 The Arctic charr (Salvelinus alpinus) genome: An analysis of evolutionary change after whole genome duplication Nugent, Cameron Ferguson, Moira Danzmann, Roy 2019-05-08 application/octet-stream application/pdf http://hdl.handle.net/10214/15993 en eng University of Guelph http://hdl.handle.net/10214/15993 All items in the Atrium are protected by copyright with all rights reserved unless otherwise indicated. genome diploidization bioinformatics genome wide association Arctic charr evolution Thesis 2019 ftunivguelph 2024-05-29T00:00:54Z 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 ... Thesis Arctic charr Arctic Salvelinus alpinus University of Guelph: DSpace digital archive Arctic |
institution |
Open Polar |
collection |
University of Guelph: DSpace digital archive |
op_collection_id |
ftunivguelph |
language |
English |
topic |
genome diploidization bioinformatics genome wide association Arctic charr evolution |
spellingShingle |
genome diploidization bioinformatics genome wide association Arctic charr evolution Nugent, Cameron The Arctic charr (Salvelinus alpinus) genome: An analysis of evolutionary change after whole genome duplication |
topic_facet |
genome diploidization bioinformatics genome wide association Arctic charr evolution |
description |
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 ... |
author2 |
Ferguson, Moira Danzmann, Roy |
format |
Thesis |
author |
Nugent, Cameron |
author_facet |
Nugent, Cameron |
author_sort |
Nugent, Cameron |
title |
The Arctic charr (Salvelinus alpinus) genome: An analysis of evolutionary change after whole genome duplication |
title_short |
The Arctic charr (Salvelinus alpinus) genome: An analysis of evolutionary change after whole genome duplication |
title_full |
The Arctic charr (Salvelinus alpinus) genome: An analysis of evolutionary change after whole genome duplication |
title_fullStr |
The Arctic charr (Salvelinus alpinus) genome: An analysis of evolutionary change after whole genome duplication |
title_full_unstemmed |
The Arctic charr (Salvelinus alpinus) genome: An analysis of evolutionary change after whole genome duplication |
title_sort |
arctic charr (salvelinus alpinus) genome: an analysis of evolutionary change after whole genome duplication |
publisher |
University of Guelph |
publishDate |
2019 |
url |
http://hdl.handle.net/10214/15993 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic charr Arctic Salvelinus alpinus |
genre_facet |
Arctic charr Arctic Salvelinus alpinus |
op_relation |
http://hdl.handle.net/10214/15993 |
op_rights |
All items in the Atrium are protected by copyright with all rights reserved unless otherwise indicated. |
_version_ |
1802639215206334464 |