Transposable elements in the salmonid genome

Salmonids are a diverse group of fishes whose common ancestor experienced an evolutionarily important whole genome duplication (WGD) event approximately 90 MYA. This event has shaped the evolutionary trajectory of salmonids, and may have contributed to a proliferation of the repeated DNA sequences k...

Full description

Bibliographic Details
Published in:Nature
Main Author: Minkley, David Richard
Other Authors: Koop, Benjamin F
Format: Thesis
Language:English
Published: 2018
Subjects:
Transposable elements
Salmon
Genome annotation
Repeats
Genome evolution
Bioinformatics
Speciation
Evolution
Tc1-Mariner
Whole genome duplication
Polyploidy
Fish
Rainbow trout
Arctic char
Atlantic salmon
Coho salmon
Chinook salmon
Salmo salar
Salvelinus alpinus
Oncorhynchus mykiss
Oncorhynchus kisutch
Oncorhynchus tshawytscha
Arctic
Online Access:https://dspace.library.uvic.ca//handle/1828/9287
id ftuvicpubl:oai:dspace.library.uvic.ca:1828/9287
record_format openpolar
spelling ftuvicpubl:oai:dspace.library.uvic.ca:1828/9287 2023-05-15T15:05:42+02:00 Transposable elements in the salmonid genome Minkley, David Richard Koop, Benjamin F 2018-04-30 application/pdf https://dspace.library.uvic.ca//handle/1828/9287 English en eng https://dspace.library.uvic.ca//handle/1828/9287 Lien, S., Koop, B.F., Sandve, S.R., Miller, J.R., Kent, M.P., Nome, T., Hvidsten, T.R., Leong, J.S., Minkley, D.R., Zimin, A., Grammes, F., Grove, H., Gjuvsland, A., Walenz, B., Hermansen, R.A., von Schalburg, K., Rondeau, E.B., Di Genova, A., Samy, J.K.A., Olav Vik, J., Vigeland, M.D., Caler, L., Grimholt, U., Jentoft, S., Inge Våge, D., de Jong, P., Moen, T., Baranski, M., Palti, Y., Smith, D.R., Yorke, J.A., Nederbragt, A.J., Tooming-Klunderud, A., Jakobsen, K.S., Jiang, X., Fan, D., Hu, Y., Liberles, D.A., Vidal, R., Iturra, P., Jones, S.J.M., Jonassen, I., Maass, A., Omholt, S.W., and Davidson, W.S. 2016. The Atlantic salmon genome provides insights into rediploidization. Nature 533: 200-205. Nature Publishing Group. doi:10.1038/nature17164. Christensen, K.A., Leong, J.S., Sakhrani, D., Biagi, C.A., Minkley, D.R., Withler, R.E., Rondeau, E.B., Koop, B.F., Devlin, R.H. 2018. Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome. PLoS One 13(4):e0195461 Available to the World Wide Web Transposable elements Salmon Genome annotation Repeats Genome evolution Bioinformatics Speciation Evolution Tc1-Mariner Whole genome duplication Polyploidy Fish Rainbow trout Arctic char Atlantic salmon Coho salmon Chinook salmon Salmo salar Salvelinus alpinus Oncorhynchus mykiss Oncorhynchus kisutch Oncorhynchus tshawytscha Thesis 2018 ftuvicpubl https://doi.org/10.1038/nature17164 2022-05-19T06:10:23Z Salmonids are a diverse group of fishes whose common ancestor experienced an evolutionarily important whole genome duplication (WGD) event approximately 90 MYA. This event has shaped the evolutionary trajectory of salmonids, and may have contributed to a proliferation of the repeated DNA sequences known as transposable elements (TEs). In this work I characterized repeated DNA in five salmonid genomes. I found that over half of the DNA within each of these genomes was derived from repeats, a value which is amongst the highest of all vertebrates. I investigated repeats of the most abundant TE superfamily, Tc1-Mariner, and found that large proliferative bursts of this element occurred shortly after the WGD and continued during salmonid speciation, where they have produced dramatic differences in TE content among extant salmonid lineages. This work provides important resources for future studies of salmonids, and advances the understanding of two important evolutionary forces: TEs and WGDs. Graduate 2019-04-19 Thesis Arctic Atlantic salmon Salmo salar Salvelinus alpinus University of Victoria (Canada): UVicDSpace Arctic Nature 533 7602 200 205
institution Open Polar
collection University of Victoria (Canada): UVicDSpace
op_collection_id ftuvicpubl
language English
topic Transposable elements
Salmon
Genome annotation
Repeats
Genome evolution
Bioinformatics
Speciation
Evolution
Tc1-Mariner
Whole genome duplication
Polyploidy
Fish
Rainbow trout
Arctic char
Atlantic salmon
Coho salmon
Chinook salmon
Salmo salar
Salvelinus alpinus
Oncorhynchus mykiss
Oncorhynchus kisutch
Oncorhynchus tshawytscha
spellingShingle Transposable elements
Salmon
Genome annotation
Repeats
Genome evolution
Bioinformatics
Speciation
Evolution
Tc1-Mariner
Whole genome duplication
Polyploidy
Fish
Rainbow trout
Arctic char
Atlantic salmon
Coho salmon
Chinook salmon
Salmo salar
Salvelinus alpinus
Oncorhynchus mykiss
Oncorhynchus kisutch
Oncorhynchus tshawytscha
Minkley, David Richard
Transposable elements in the salmonid genome
topic_facet Transposable elements
Salmon
Genome annotation
Repeats
Genome evolution
Bioinformatics
Speciation
Evolution
Tc1-Mariner
Whole genome duplication
Polyploidy
Fish
Rainbow trout
Arctic char
Atlantic salmon
Coho salmon
Chinook salmon
Salmo salar
Salvelinus alpinus
Oncorhynchus mykiss
Oncorhynchus kisutch
Oncorhynchus tshawytscha
description Salmonids are a diverse group of fishes whose common ancestor experienced an evolutionarily important whole genome duplication (WGD) event approximately 90 MYA. This event has shaped the evolutionary trajectory of salmonids, and may have contributed to a proliferation of the repeated DNA sequences known as transposable elements (TEs). In this work I characterized repeated DNA in five salmonid genomes. I found that over half of the DNA within each of these genomes was derived from repeats, a value which is amongst the highest of all vertebrates. I investigated repeats of the most abundant TE superfamily, Tc1-Mariner, and found that large proliferative bursts of this element occurred shortly after the WGD and continued during salmonid speciation, where they have produced dramatic differences in TE content among extant salmonid lineages. This work provides important resources for future studies of salmonids, and advances the understanding of two important evolutionary forces: TEs and WGDs. Graduate 2019-04-19
author2 Koop, Benjamin F
format Thesis
author Minkley, David Richard
author_facet Minkley, David Richard
author_sort Minkley, David Richard
title Transposable elements in the salmonid genome
title_short Transposable elements in the salmonid genome
title_full Transposable elements in the salmonid genome
title_fullStr Transposable elements in the salmonid genome
title_full_unstemmed Transposable elements in the salmonid genome
title_sort transposable elements in the salmonid genome
publishDate 2018
url https://dspace.library.uvic.ca//handle/1828/9287
geographic Arctic
geographic_facet Arctic
genre Arctic
Atlantic salmon
Salmo salar
Salvelinus alpinus
genre_facet Arctic
Atlantic salmon
Salmo salar
Salvelinus alpinus
op_relation https://dspace.library.uvic.ca//handle/1828/9287
Lien, S., Koop, B.F., Sandve, S.R., Miller, J.R., Kent, M.P., Nome, T., Hvidsten, T.R., Leong, J.S., Minkley, D.R., Zimin, A., Grammes, F., Grove, H., Gjuvsland, A., Walenz, B., Hermansen, R.A., von Schalburg, K., Rondeau, E.B., Di Genova, A., Samy, J.K.A., Olav Vik, J., Vigeland, M.D., Caler, L., Grimholt, U., Jentoft, S., Inge Våge, D., de Jong, P., Moen, T., Baranski, M., Palti, Y., Smith, D.R., Yorke, J.A., Nederbragt, A.J., Tooming-Klunderud, A., Jakobsen, K.S., Jiang, X., Fan, D., Hu, Y., Liberles, D.A., Vidal, R., Iturra, P., Jones, S.J.M., Jonassen, I., Maass, A., Omholt, S.W., and Davidson, W.S. 2016. The Atlantic salmon genome provides insights into rediploidization. Nature 533: 200-205. Nature Publishing Group. doi:10.1038/nature17164.
Christensen, K.A., Leong, J.S., Sakhrani, D., Biagi, C.A., Minkley, D.R., Withler, R.E., Rondeau, E.B., Koop, B.F., Devlin, R.H. 2018. Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome. PLoS One 13(4):e0195461
op_rights Available to the World Wide Web
op_doi https://doi.org/10.1038/nature17164
container_title Nature
container_volume 533
container_issue 7602
container_start_page 200
op_container_end_page 205
_version_ 1766337350802079744

Similar Items