A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication
Abstract Genomic datasets continue to increase in number due to the ease of production for a wider selection of species including non-model organisms. For many of these species, especially those with large or polyploid genomes, highly contiguous and well-annotated genomes are still rare due to the c...
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Online Access: | http://dx.doi.org/10.1534/g3.118.200552 http://academic.oup.com/g3journal/article-pdf/8/12/3745/37190897/g3journal3745.pdf |
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croxfordunivpr:10.1534/g3.118.200552 2024-09-15T17:56:21+00:00 A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication De-Kayne, Rishi Feulner, Philine G D 2018 http://dx.doi.org/10.1534/g3.118.200552 http://academic.oup.com/g3journal/article-pdf/8/12/3745/37190897/g3journal3745.pdf en eng Oxford University Press (OUP) https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model G3 Genes|Genomes|Genetics volume 8, issue 12, page 3745-3755 ISSN 2160-1836 journal-article 2018 croxfordunivpr https://doi.org/10.1534/g3.118.200552 2024-08-12T04:24:14Z Abstract Genomic datasets continue to increase in number due to the ease of production for a wider selection of species including non-model organisms. For many of these species, especially those with large or polyploid genomes, highly contiguous and well-annotated genomes are still rare due to the complexity and cost involved in their assembly. As a result, a common starting point for genomic work in non-model species is the production of a linkage map. Dense linkage maps facilitate the analysis of genomic data in a variety of ways, from broad scale observations regarding genome structure e.g., chromosome number and type or sex-related structural differences, to fine scale patterns e.g., recombination rate variation and co-localization of differentiated regions. Here we present both sex-averaged and sex-specific linkage maps for Coregonus sp. “Albock”, a member of the European whitefish lineage (C. lavaretus spp. complex), containing 5395 single nucleotide polymorphism (SNP) loci across 40 linkage groups to facilitate future investigation into the genomic basis of whitefish adaptation and speciation. The map was produced using restriction-site associated digestion (RAD) sequencing data from two wild-caught parents and 156 F1 offspring. We discuss the differences between our sex-averaged and sex-specific maps and identify genome-wide synteny between C. sp. “Albock” and Atlantic Salmon (Salmo salar), which have diverged following the salmonid-specific whole genome duplication. Our analysis confirms that many patterns of synteny observed between Atlantic Salmon and Oncorhynchus and Salvelinus species are also shared by members of the Coregoninae subfamily. We also show that regions known for their species-specific rediploidization history can pose challenges for synteny identification since these regions have diverged independently in each salmonid species following the salmonid-specific whole genome duplication. The European whitefish map provided here will enable future studies to understand the distribution of ... Article in Journal/Newspaper Atlantic salmon Salmo salar Oxford University Press G3 Genes|Genomes|Genetics 8 12 3745 3755 |
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Oxford University Press |
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English |
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Abstract Genomic datasets continue to increase in number due to the ease of production for a wider selection of species including non-model organisms. For many of these species, especially those with large or polyploid genomes, highly contiguous and well-annotated genomes are still rare due to the complexity and cost involved in their assembly. As a result, a common starting point for genomic work in non-model species is the production of a linkage map. Dense linkage maps facilitate the analysis of genomic data in a variety of ways, from broad scale observations regarding genome structure e.g., chromosome number and type or sex-related structural differences, to fine scale patterns e.g., recombination rate variation and co-localization of differentiated regions. Here we present both sex-averaged and sex-specific linkage maps for Coregonus sp. “Albock”, a member of the European whitefish lineage (C. lavaretus spp. complex), containing 5395 single nucleotide polymorphism (SNP) loci across 40 linkage groups to facilitate future investigation into the genomic basis of whitefish adaptation and speciation. The map was produced using restriction-site associated digestion (RAD) sequencing data from two wild-caught parents and 156 F1 offspring. We discuss the differences between our sex-averaged and sex-specific maps and identify genome-wide synteny between C. sp. “Albock” and Atlantic Salmon (Salmo salar), which have diverged following the salmonid-specific whole genome duplication. Our analysis confirms that many patterns of synteny observed between Atlantic Salmon and Oncorhynchus and Salvelinus species are also shared by members of the Coregoninae subfamily. We also show that regions known for their species-specific rediploidization history can pose challenges for synteny identification since these regions have diverged independently in each salmonid species following the salmonid-specific whole genome duplication. The European whitefish map provided here will enable future studies to understand the distribution of ... |
format |
Article in Journal/Newspaper |
author |
De-Kayne, Rishi Feulner, Philine G D |
spellingShingle |
De-Kayne, Rishi Feulner, Philine G D A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication |
author_facet |
De-Kayne, Rishi Feulner, Philine G D |
author_sort |
De-Kayne, Rishi |
title |
A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication |
title_short |
A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication |
title_full |
A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication |
title_fullStr |
A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication |
title_full_unstemmed |
A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication |
title_sort |
european whitefish linkage map and its implications for understanding genome-wide synteny between salmonids following whole genome duplication |
publisher |
Oxford University Press (OUP) |
publishDate |
2018 |
url |
http://dx.doi.org/10.1534/g3.118.200552 http://academic.oup.com/g3journal/article-pdf/8/12/3745/37190897/g3journal3745.pdf |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
G3 Genes|Genomes|Genetics volume 8, issue 12, page 3745-3755 ISSN 2160-1836 |
op_rights |
https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model |
op_doi |
https://doi.org/10.1534/g3.118.200552 |
container_title |
G3 Genes|Genomes|Genetics |
container_volume |
8 |
container_issue |
12 |
container_start_page |
3745 |
op_container_end_page |
3755 |
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1810432558035369984 |