The genome and linkage map of the northern pike (Esox lucius): conserved synteny revealed between the salmonid sister group and the Neoteleostei.
The northern pike is the most frequently studied member of the Esociformes, the closest order to the diverse and economically important Salmoniformes. The ancestor of all salmonids purportedly experienced a whole-genome duplication (WGD) event, making salmonid species ideal for studying the early im...
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ftdoajarticles:oai:doaj.org/article:7365d3d3e0b541d3a3075009953cf47e 2023-05-15T15:32:52+02:00 The genome and linkage map of the northern pike (Esox lucius): conserved synteny revealed between the salmonid sister group and the Neoteleostei. Eric B Rondeau David R Minkley Jong S Leong Amber M Messmer Johanna R Jantzen Kristian R von Schalburg Craig Lemon Nathan H Bird Ben F Koop 2014-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0102089 https://doaj.org/article/7365d3d3e0b541d3a3075009953cf47e EN eng Public Library of Science (PLoS) https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25069045/pdf/?tool=EBI https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0102089 https://doaj.org/article/7365d3d3e0b541d3a3075009953cf47e PLoS ONE, Vol 9, Iss 7, p e102089 (2014) Medicine R Science Q article 2014 ftdoajarticles https://doi.org/10.1371/journal.pone.0102089 2022-12-31T16:21:50Z The northern pike is the most frequently studied member of the Esociformes, the closest order to the diverse and economically important Salmoniformes. The ancestor of all salmonids purportedly experienced a whole-genome duplication (WGD) event, making salmonid species ideal for studying the early impacts of genome duplication while complicating their use in wider analyses of teleost evolution. Studies suggest that the Esociformes diverged from the salmonid lineage prior to the WGD, supporting the use of northern pike as a pre-duplication outgroup. Here we present the first genome assembly, reference transcriptome and linkage map for northern pike, and evaluate the suitability of this species to provide a representative pre-duplication genome for future studies of salmonid and teleost evolution. The northern pike genome sequence is composed of 94,267 contigs (N50 = 16,909 bp) contained in 5,688 scaffolds (N50 = 700,535 bp); the total scaffolded genome size is 878 million bases. Multiple lines of evidence suggest that over 96% of the protein-coding genome is present in the genome assembly. The reference transcriptome was constructed from 13 tissues and contains 38,696 transcripts, which are accompanied by normalized expression data in all tissues. Gene-prediction analysis produced a total of 19,601 northern pike-specific gene models. The first-generation linkage map identifies 25 linkage groups, in agreement with northern pike's diploid karyotype of 2N = 50, and facilitates the placement of 46% of assembled bases onto linkage groups. Analyses reveal a high degree of conserved synteny between northern pike and other model teleost genomes. While conservation of gene order is limited to smaller syntenic blocks, the wider conservation of genome organization implies the northern pike exhibits a suitable approximation of a non-duplicated Protacanthopterygiian genome. This dataset will facilitate future studies of esocid biology and empower ongoing examinations of the Atlantic salmon and rainbow trout genomes by ... Article in Journal/Newspaper Atlantic salmon Directory of Open Access Journals: DOAJ Articles PLoS ONE 9 7 e102089 |
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Medicine R Science Q |
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Medicine R Science Q Eric B Rondeau David R Minkley Jong S Leong Amber M Messmer Johanna R Jantzen Kristian R von Schalburg Craig Lemon Nathan H Bird Ben F Koop The genome and linkage map of the northern pike (Esox lucius): conserved synteny revealed between the salmonid sister group and the Neoteleostei. |
topic_facet |
Medicine R Science Q |
description |
The northern pike is the most frequently studied member of the Esociformes, the closest order to the diverse and economically important Salmoniformes. The ancestor of all salmonids purportedly experienced a whole-genome duplication (WGD) event, making salmonid species ideal for studying the early impacts of genome duplication while complicating their use in wider analyses of teleost evolution. Studies suggest that the Esociformes diverged from the salmonid lineage prior to the WGD, supporting the use of northern pike as a pre-duplication outgroup. Here we present the first genome assembly, reference transcriptome and linkage map for northern pike, and evaluate the suitability of this species to provide a representative pre-duplication genome for future studies of salmonid and teleost evolution. The northern pike genome sequence is composed of 94,267 contigs (N50 = 16,909 bp) contained in 5,688 scaffolds (N50 = 700,535 bp); the total scaffolded genome size is 878 million bases. Multiple lines of evidence suggest that over 96% of the protein-coding genome is present in the genome assembly. The reference transcriptome was constructed from 13 tissues and contains 38,696 transcripts, which are accompanied by normalized expression data in all tissues. Gene-prediction analysis produced a total of 19,601 northern pike-specific gene models. The first-generation linkage map identifies 25 linkage groups, in agreement with northern pike's diploid karyotype of 2N = 50, and facilitates the placement of 46% of assembled bases onto linkage groups. Analyses reveal a high degree of conserved synteny between northern pike and other model teleost genomes. While conservation of gene order is limited to smaller syntenic blocks, the wider conservation of genome organization implies the northern pike exhibits a suitable approximation of a non-duplicated Protacanthopterygiian genome. This dataset will facilitate future studies of esocid biology and empower ongoing examinations of the Atlantic salmon and rainbow trout genomes by ... |
format |
Article in Journal/Newspaper |
author |
Eric B Rondeau David R Minkley Jong S Leong Amber M Messmer Johanna R Jantzen Kristian R von Schalburg Craig Lemon Nathan H Bird Ben F Koop |
author_facet |
Eric B Rondeau David R Minkley Jong S Leong Amber M Messmer Johanna R Jantzen Kristian R von Schalburg Craig Lemon Nathan H Bird Ben F Koop |
author_sort |
Eric B Rondeau |
title |
The genome and linkage map of the northern pike (Esox lucius): conserved synteny revealed between the salmonid sister group and the Neoteleostei. |
title_short |
The genome and linkage map of the northern pike (Esox lucius): conserved synteny revealed between the salmonid sister group and the Neoteleostei. |
title_full |
The genome and linkage map of the northern pike (Esox lucius): conserved synteny revealed between the salmonid sister group and the Neoteleostei. |
title_fullStr |
The genome and linkage map of the northern pike (Esox lucius): conserved synteny revealed between the salmonid sister group and the Neoteleostei. |
title_full_unstemmed |
The genome and linkage map of the northern pike (Esox lucius): conserved synteny revealed between the salmonid sister group and the Neoteleostei. |
title_sort |
genome and linkage map of the northern pike (esox lucius): conserved synteny revealed between the salmonid sister group and the neoteleostei. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2014 |
url |
https://doi.org/10.1371/journal.pone.0102089 https://doaj.org/article/7365d3d3e0b541d3a3075009953cf47e |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
PLoS ONE, Vol 9, Iss 7, p e102089 (2014) |
op_relation |
https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25069045/pdf/?tool=EBI https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0102089 https://doaj.org/article/7365d3d3e0b541d3a3075009953cf47e |
op_doi |
https://doi.org/10.1371/journal.pone.0102089 |
container_title |
PLoS ONE |
container_volume |
9 |
container_issue |
7 |
container_start_page |
e102089 |
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1766363349826666496 |