Inversion breakpoints in Atlantic cod chromosomes – fixed or variable within and between individuals?
Genomic variation is the key to speciation and evolution. Genomic variants underlie how species change, adapt, and evolve and range from single-point mutations to large chromosomal rearrangements. Inversions are an example of the latter and can profoundly affect local adaptation, such as with the At...
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ftoslouniv:oai:www.duo.uio.no:10852/97603 2023-05-15T14:30:31+02:00 Inversion breakpoints in Atlantic cod chromosomes – fixed or variable within and between individuals? Daughton, Tara Jane 2022 http://hdl.handle.net/10852/97603 eng eng Daughton, Tara Jane. Inversion breakpoints in Atlantic cod chromosomes – fixed or variable within and between individuals?. Master thesis, University of Oslo, 2022 http://hdl.handle.net/10852/97603 Inversion cod Atlantic cod evolution Master thesis Masteroppgave 2022 ftoslouniv 2022-11-16T23:35:58Z Genomic variation is the key to speciation and evolution. Genomic variants underlie how species change, adapt, and evolve and range from single-point mutations to large chromosomal rearrangements. Inversions are an example of the latter and can profoundly affect local adaptation, such as with the Atlantic cod. The Atlantic cod that inhabit the northernmost coast of Norway consists of two ecotypes: the stationary Northern Coastal Cod (NCC) and the migratory Northeast Arctic Cod (NEAC), which feeds offshore in the Barents Sea and only returns to the Northern coast to breed. NCC and NEAC breed at the same time and locations along the coast of Norway, from Møre in the south to Sørøya in the north, with the largest spawning aggregation taking place around the Lofoten archipelago. Even though they spawn simultaneously, phenotypic, and genetic differences are maintained between the two populations. From previous studies, four megabase-scale supergenes have been linked to migratory lifestyle and environmental adaptations, and I set out to locate the breakpoints and determine if they vary between individuals. To do so, I developed a PCR protocol for amplifying both inverted and non-inverted alleles to sequence the breakpoint regions within the Atlantic cod. In total, 79 breakpoint regions were sequenced using HiFi-sequencing, which creates accurate long reads known as HiFi reads. In doing so, I could use multiple, accurate, HiFi sequencing reads to (1) align each breakpoint read to the gadmor3 and coastal reference genome and then (2) make de novo haplotype assemblies for the breakpoint regions for different individuals with the inverted and non-inverted allele. The haplotype assemblies were used in a multiple sequence alignment, and I could pinpoint where the breakpoints are and that they are conserved and fixed within and between populations. Master Thesis Arctic cod Arctic atlantic cod Barents Sea Lofoten Northeast Arctic cod Universitet i Oslo: Digitale utgivelser ved UiO (DUO) Arctic Barents Sea Lofoten Norway Sørøya ENVELOPE(7.942,7.942,63.352,63.352) |
institution |
Open Polar |
collection |
Universitet i Oslo: Digitale utgivelser ved UiO (DUO) |
op_collection_id |
ftoslouniv |
language |
English |
topic |
Inversion cod Atlantic cod evolution |
spellingShingle |
Inversion cod Atlantic cod evolution Daughton, Tara Jane Inversion breakpoints in Atlantic cod chromosomes – fixed or variable within and between individuals? |
topic_facet |
Inversion cod Atlantic cod evolution |
description |
Genomic variation is the key to speciation and evolution. Genomic variants underlie how species change, adapt, and evolve and range from single-point mutations to large chromosomal rearrangements. Inversions are an example of the latter and can profoundly affect local adaptation, such as with the Atlantic cod. The Atlantic cod that inhabit the northernmost coast of Norway consists of two ecotypes: the stationary Northern Coastal Cod (NCC) and the migratory Northeast Arctic Cod (NEAC), which feeds offshore in the Barents Sea and only returns to the Northern coast to breed. NCC and NEAC breed at the same time and locations along the coast of Norway, from Møre in the south to Sørøya in the north, with the largest spawning aggregation taking place around the Lofoten archipelago. Even though they spawn simultaneously, phenotypic, and genetic differences are maintained between the two populations. From previous studies, four megabase-scale supergenes have been linked to migratory lifestyle and environmental adaptations, and I set out to locate the breakpoints and determine if they vary between individuals. To do so, I developed a PCR protocol for amplifying both inverted and non-inverted alleles to sequence the breakpoint regions within the Atlantic cod. In total, 79 breakpoint regions were sequenced using HiFi-sequencing, which creates accurate long reads known as HiFi reads. In doing so, I could use multiple, accurate, HiFi sequencing reads to (1) align each breakpoint read to the gadmor3 and coastal reference genome and then (2) make de novo haplotype assemblies for the breakpoint regions for different individuals with the inverted and non-inverted allele. The haplotype assemblies were used in a multiple sequence alignment, and I could pinpoint where the breakpoints are and that they are conserved and fixed within and between populations. |
format |
Master Thesis |
author |
Daughton, Tara Jane |
author_facet |
Daughton, Tara Jane |
author_sort |
Daughton, Tara Jane |
title |
Inversion breakpoints in Atlantic cod chromosomes – fixed or variable within and between individuals? |
title_short |
Inversion breakpoints in Atlantic cod chromosomes – fixed or variable within and between individuals? |
title_full |
Inversion breakpoints in Atlantic cod chromosomes – fixed or variable within and between individuals? |
title_fullStr |
Inversion breakpoints in Atlantic cod chromosomes – fixed or variable within and between individuals? |
title_full_unstemmed |
Inversion breakpoints in Atlantic cod chromosomes – fixed or variable within and between individuals? |
title_sort |
inversion breakpoints in atlantic cod chromosomes – fixed or variable within and between individuals? |
publishDate |
2022 |
url |
http://hdl.handle.net/10852/97603 |
long_lat |
ENVELOPE(7.942,7.942,63.352,63.352) |
geographic |
Arctic Barents Sea Lofoten Norway Sørøya |
geographic_facet |
Arctic Barents Sea Lofoten Norway Sørøya |
genre |
Arctic cod Arctic atlantic cod Barents Sea Lofoten Northeast Arctic cod |
genre_facet |
Arctic cod Arctic atlantic cod Barents Sea Lofoten Northeast Arctic cod |
op_relation |
Daughton, Tara Jane. Inversion breakpoints in Atlantic cod chromosomes – fixed or variable within and between individuals?. Master thesis, University of Oslo, 2022 http://hdl.handle.net/10852/97603 |
_version_ |
1766304348367749120 |