The chromosome-level genome assembly of european grayling reveals aspects of a unique genome evolution process within salmonids
Supplemental material available at Figshare: https://doi.org/10.25387/g3.7728512 Salmonids represent an intriguing taxonomical group for investigating genome evolution in vertebrates due to their relatively recent last common whole genome duplication event, which occurred between 80 and 100 million...
Published in: | G3 Genes|Genomes|Genetics |
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Main Authors: | , , , , , , , , |
Other Authors: | , , , , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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HAL CCSD
2019
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Online Access: | https://hal.science/hal-02154636 https://hal.science/hal-02154636/document https://hal.science/hal-02154636/file/S%C3%A4vilammi_2019_3G_1.pdf https://doi.org/10.1534/g3.118.200919 |
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Open Polar |
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Portail HAL-ANR (Agence Nationale de la Recherche) |
op_collection_id |
ftanrparis |
language |
English |
topic |
karyotyping of the cells salmonids fish rétrotransposon caryotype séquençage du génome chromosome génomique fonctionnelle gène sdY structure chromosome évolution du génome évolution chromosomique reproduction ombre commun salmonidae poisson thymallus thymallus [SDV]Life Sciences [q-bio] |
spellingShingle |
karyotyping of the cells salmonids fish rétrotransposon caryotype séquençage du génome chromosome génomique fonctionnelle gène sdY structure chromosome évolution du génome évolution chromosomique reproduction ombre commun salmonidae poisson thymallus thymallus [SDV]Life Sciences [q-bio] Sävilammi, Tiina Primmer, Craig R. Varadharajan, Srinidhi Guyomard, René Guiguen, Yann Sandve, Simen R. Vøllestad, L. Asbjørn Papakostas, Spiros Lien, Sigbjørn The chromosome-level genome assembly of european grayling reveals aspects of a unique genome evolution process within salmonids |
topic_facet |
karyotyping of the cells salmonids fish rétrotransposon caryotype séquençage du génome chromosome génomique fonctionnelle gène sdY structure chromosome évolution du génome évolution chromosomique reproduction ombre commun salmonidae poisson thymallus thymallus [SDV]Life Sciences [q-bio] |
description |
Supplemental material available at Figshare: https://doi.org/10.25387/g3.7728512 Salmonids represent an intriguing taxonomical group for investigating genome evolution in vertebrates due to their relatively recent last common whole genome duplication event, which occurred between 80 and 100 million years ago. Here, we report on the chromosome-level genome assembly of European grayling (Thymallus thymallus), which represents one of the earliest diverged salmonid subfamilies. To achieve this, we first generated relatively long genomic scaffolds by using a previously published draft genome assembly along with long-read sequencing data and a linkage map. We then merged those scaffolds by applying synteny evidence from the Atlantic salmon (Salmo salar) genome. Comparisons of the European grayling genome assembly to the genomes of Atlantic salmon and Northern pike (Esox lucius), the latter used as a nonduplicated outgroup, detailed aspects of the characteristic chromosome evolution process that has taken place in European grayling. While Atlantic salmon and other salmonid genomes are portrayed by the typical occurrence of numerous chromosomal fusions, European grayling chromosomes were confirmed to be fusion-free and were characterized by a relatively large proportion of paracentric and pericentric inversions. We further reported on transposable elements specific to either the European grayling or Atlantic salmon genome, on the male-specific sdY gene in the European grayling chromosome 11A, and on regions under residual tetrasomy in the homeologous European grayling chromosome pairs 9A-9B and 25A-25B. The same chromosome pairs have been observed under residual tetrasomy in Atlantic salmon and in other salmonids, suggesting that this feature has been conserved since the subfamily split. |
author2 |
Department of Biology University of Memphis Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences HiLIFE - Institute of Biotechnology Helsinki (BI) Helsinki Institute of Life Science (HiLIFE) Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsinki Institute of Life Science (HiLIFE) Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki Helsingin yliopisto = Helsingfors universitet = University of Helsinki Department of Biosciences University of Kent Canterbury Génétique Animale et Biologie Intégrative (GABI) Institut National de la Recherche Agronomique (INRA)-AgroParisTech Laboratoire de Physiologie et Génomique des Poissons (LPGP) Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ) Department of Animal and Aquacultural Sciences Faculty of Biosciences Norwegian University of Life Sciences (NMBU) Centre for Integrative Genetics (CIGENE) This work was supported by the Academy of Finland (project numbers 287342 and 302873). We thank the Finnish Centre for Scientific Computing for providing computational resources. SV and LAV are supported by Center for Computational Inference in Evolutionary Life Science (CELS) and the Department of Biosciences, University of Oslo. YG and RG contributions were supported by the Agence Nationale de la Recherche (ANR Blanc SVSE 7 2011, project SDS). ANR-15-CE37-0004,SmellBrain,Dissection fonctionnelle des circuits codant pour la récompense dans le système olfactif(2015) |
format |
Article in Journal/Newspaper |
author |
Sävilammi, Tiina Primmer, Craig R. Varadharajan, Srinidhi Guyomard, René Guiguen, Yann Sandve, Simen R. Vøllestad, L. Asbjørn Papakostas, Spiros Lien, Sigbjørn |
author_facet |
Sävilammi, Tiina Primmer, Craig R. Varadharajan, Srinidhi Guyomard, René Guiguen, Yann Sandve, Simen R. Vøllestad, L. Asbjørn Papakostas, Spiros Lien, Sigbjørn |
author_sort |
Sävilammi, Tiina |
title |
The chromosome-level genome assembly of european grayling reveals aspects of a unique genome evolution process within salmonids |
title_short |
The chromosome-level genome assembly of european grayling reveals aspects of a unique genome evolution process within salmonids |
title_full |
The chromosome-level genome assembly of european grayling reveals aspects of a unique genome evolution process within salmonids |
title_fullStr |
The chromosome-level genome assembly of european grayling reveals aspects of a unique genome evolution process within salmonids |
title_full_unstemmed |
The chromosome-level genome assembly of european grayling reveals aspects of a unique genome evolution process within salmonids |
title_sort |
chromosome-level genome assembly of european grayling reveals aspects of a unique genome evolution process within salmonids |
publisher |
HAL CCSD |
publishDate |
2019 |
url |
https://hal.science/hal-02154636 https://hal.science/hal-02154636/document https://hal.science/hal-02154636/file/S%C3%A4vilammi_2019_3G_1.pdf https://doi.org/10.1534/g3.118.200919 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
ISSN: 2160-1836 G3 https://hal.science/hal-02154636 G3, 2019, 9 (5), pp.1283-1294. ⟨10.1534/g3.118.200919⟩ https://www.g3journal.org/ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1534/g3.118.200919 info:eu-repo/semantics/altIdentifier/pmid/30833292 hal-02154636 https://hal.science/hal-02154636 https://hal.science/hal-02154636/document https://hal.science/hal-02154636/file/S%C3%A4vilammi_2019_3G_1.pdf doi:10.1534/g3.118.200919 PRODINRA: 472552 PUBMED: 30833292 WOS: 000467271400001 |
op_rights |
http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1534/g3.118.200919 |
container_title |
G3 Genes|Genomes|Genetics |
container_volume |
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container_issue |
5 |
container_start_page |
1283 |
op_container_end_page |
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spelling |
ftanrparis:oai:HAL:hal-02154636v1 2023-12-03T10:19:17+01:00 The chromosome-level genome assembly of european grayling reveals aspects of a unique genome evolution process within salmonids Sävilammi, Tiina Primmer, Craig R. Varadharajan, Srinidhi Guyomard, René Guiguen, Yann Sandve, Simen R. Vøllestad, L. Asbjørn Papakostas, Spiros Lien, Sigbjørn Department of Biology University of Memphis Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences HiLIFE - Institute of Biotechnology Helsinki (BI) Helsinki Institute of Life Science (HiLIFE) Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsinki Institute of Life Science (HiLIFE) Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki Helsingin yliopisto = Helsingfors universitet = University of Helsinki Department of Biosciences University of Kent Canterbury Génétique Animale et Biologie Intégrative (GABI) Institut National de la Recherche Agronomique (INRA)-AgroParisTech Laboratoire de Physiologie et Génomique des Poissons (LPGP) Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ) Department of Animal and Aquacultural Sciences Faculty of Biosciences Norwegian University of Life Sciences (NMBU) Centre for Integrative Genetics (CIGENE) This work was supported by the Academy of Finland (project numbers 287342 and 302873). We thank the Finnish Centre for Scientific Computing for providing computational resources. SV and LAV are supported by Center for Computational Inference in Evolutionary Life Science (CELS) and the Department of Biosciences, University of Oslo. YG and RG contributions were supported by the Agence Nationale de la Recherche (ANR Blanc SVSE 7 2011, project SDS). ANR-15-CE37-0004,SmellBrain,Dissection fonctionnelle des circuits codant pour la récompense dans le système olfactif(2015) 2019-05-01 https://hal.science/hal-02154636 https://hal.science/hal-02154636/document https://hal.science/hal-02154636/file/S%C3%A4vilammi_2019_3G_1.pdf https://doi.org/10.1534/g3.118.200919 en eng HAL CCSD Genetics Society of America info:eu-repo/semantics/altIdentifier/doi/10.1534/g3.118.200919 info:eu-repo/semantics/altIdentifier/pmid/30833292 hal-02154636 https://hal.science/hal-02154636 https://hal.science/hal-02154636/document https://hal.science/hal-02154636/file/S%C3%A4vilammi_2019_3G_1.pdf doi:10.1534/g3.118.200919 PRODINRA: 472552 PUBMED: 30833292 WOS: 000467271400001 http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess ISSN: 2160-1836 G3 https://hal.science/hal-02154636 G3, 2019, 9 (5), pp.1283-1294. ⟨10.1534/g3.118.200919⟩ https://www.g3journal.org/ karyotyping of the cells salmonids fish rétrotransposon caryotype séquençage du génome chromosome génomique fonctionnelle gène sdY structure chromosome évolution du génome évolution chromosomique reproduction ombre commun salmonidae poisson thymallus thymallus [SDV]Life Sciences [q-bio] info:eu-repo/semantics/article Journal articles 2019 ftanrparis https://doi.org/10.1534/g3.118.200919 2023-11-04T22:30:55Z Supplemental material available at Figshare: https://doi.org/10.25387/g3.7728512 Salmonids represent an intriguing taxonomical group for investigating genome evolution in vertebrates due to their relatively recent last common whole genome duplication event, which occurred between 80 and 100 million years ago. Here, we report on the chromosome-level genome assembly of European grayling (Thymallus thymallus), which represents one of the earliest diverged salmonid subfamilies. To achieve this, we first generated relatively long genomic scaffolds by using a previously published draft genome assembly along with long-read sequencing data and a linkage map. We then merged those scaffolds by applying synteny evidence from the Atlantic salmon (Salmo salar) genome. Comparisons of the European grayling genome assembly to the genomes of Atlantic salmon and Northern pike (Esox lucius), the latter used as a nonduplicated outgroup, detailed aspects of the characteristic chromosome evolution process that has taken place in European grayling. While Atlantic salmon and other salmonid genomes are portrayed by the typical occurrence of numerous chromosomal fusions, European grayling chromosomes were confirmed to be fusion-free and were characterized by a relatively large proportion of paracentric and pericentric inversions. We further reported on transposable elements specific to either the European grayling or Atlantic salmon genome, on the male-specific sdY gene in the European grayling chromosome 11A, and on regions under residual tetrasomy in the homeologous European grayling chromosome pairs 9A-9B and 25A-25B. The same chromosome pairs have been observed under residual tetrasomy in Atlantic salmon and in other salmonids, suggesting that this feature has been conserved since the subfamily split. Article in Journal/Newspaper Atlantic salmon Salmo salar Portail HAL-ANR (Agence Nationale de la Recherche) G3 Genes|Genomes|Genetics 9 5 1283 1294 |