A Nanopore Based Chromosome-Level Assembly Representing Atlantic Cod from the Celtic Sea
Currently available genome assemblies for Atlantic cod (Gadus morhua) have been constructed from fish belonging to the Northeast Arctic Cod (NEAC) population; a migratory population feeding in the Barents Sea. These assemblies have been crucial for the development of genetic markers which have been...
Published in: | G3 Genes|Genomes|Genetics |
---|---|
Main Authors: | , , , , , , |
Format: | Text |
Language: | English |
Published: |
Genetics Society of America
2020
|
Subjects: | |
Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7466986/ http://www.ncbi.nlm.nih.gov/pubmed/32641450 https://doi.org/10.1534/g3.120.401423 |
id |
ftpubmed:oai:pubmedcentral.nih.gov:7466986 |
---|---|
record_format |
openpolar |
spelling |
ftpubmed:oai:pubmedcentral.nih.gov:7466986 2023-05-15T14:30:30+02:00 A Nanopore Based Chromosome-Level Assembly Representing Atlantic Cod from the Celtic Sea Kirubakaran, Tina Graceline Andersen, Øivind Moser, Michel Árnyasi, Mariann McGinnity, Philip Lien, Sigbjørn Kent, Matthew 2020-07-08 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7466986/ http://www.ncbi.nlm.nih.gov/pubmed/32641450 https://doi.org/10.1534/g3.120.401423 en eng Genetics Society of America http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7466986/ http://www.ncbi.nlm.nih.gov/pubmed/32641450 http://dx.doi.org/10.1534/g3.120.401423 Copyright © 2020 Kirubakaran et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. CC-BY G3 (Bethesda) Genome Report Text 2020 ftpubmed https://doi.org/10.1534/g3.120.401423 2020-09-20T00:22:01Z Currently available genome assemblies for Atlantic cod (Gadus morhua) have been constructed from fish belonging to the Northeast Arctic Cod (NEAC) population; a migratory population feeding in the Barents Sea. These assemblies have been crucial for the development of genetic markers which have been used to study population differentiation and adaptive evolution in Atlantic cod, pinpointing four discrete islands of genomic divergence located on linkage groups 1, 2, 7 and 12. In this paper, we present a high-quality reference genome from a male Atlantic cod representing a southern population inhabiting the Celtic sea. The genome assembly (gadMor_Celtic) was produced from long-read nanopore data and has a combined contig length of 686 Mb with an N50 of 10 Mb. Integrating contigs with genetic linkage mapping information enabled us to construct 23 chromosome sequences which mapped with high confidence to the latest NEAC population assembly (gadMor3) and allowed us to characterize, to an extent not previously reported large chromosomal inversions on linkage groups 1, 2, 7 and 12. In most cases, inversion breakpoints could be located within single nanopore contigs. Our results suggest the presence of inversions in Celtic cod on linkage groups 6, 11 and 21, although these remain to be confirmed. Further, we identified a specific repetitive element that is relatively enriched at predicted centromeric regions. Our gadMor_Celtic assembly provides a resource representing a ‘southern’ cod population which is complementary to the existing ‘northern’ population based genome assemblies and represents the first step toward developing pan-genomic resources for Atlantic cod. Text Arctic cod Arctic atlantic cod Barents Sea Gadus morhua Northeast Arctic cod PubMed Central (PMC) Arctic Barents Sea G3 Genes|Genomes|Genetics 10 9 2903 2910 |
institution |
Open Polar |
collection |
PubMed Central (PMC) |
op_collection_id |
ftpubmed |
language |
English |
topic |
Genome Report |
spellingShingle |
Genome Report Kirubakaran, Tina Graceline Andersen, Øivind Moser, Michel Árnyasi, Mariann McGinnity, Philip Lien, Sigbjørn Kent, Matthew A Nanopore Based Chromosome-Level Assembly Representing Atlantic Cod from the Celtic Sea |
topic_facet |
Genome Report |
description |
Currently available genome assemblies for Atlantic cod (Gadus morhua) have been constructed from fish belonging to the Northeast Arctic Cod (NEAC) population; a migratory population feeding in the Barents Sea. These assemblies have been crucial for the development of genetic markers which have been used to study population differentiation and adaptive evolution in Atlantic cod, pinpointing four discrete islands of genomic divergence located on linkage groups 1, 2, 7 and 12. In this paper, we present a high-quality reference genome from a male Atlantic cod representing a southern population inhabiting the Celtic sea. The genome assembly (gadMor_Celtic) was produced from long-read nanopore data and has a combined contig length of 686 Mb with an N50 of 10 Mb. Integrating contigs with genetic linkage mapping information enabled us to construct 23 chromosome sequences which mapped with high confidence to the latest NEAC population assembly (gadMor3) and allowed us to characterize, to an extent not previously reported large chromosomal inversions on linkage groups 1, 2, 7 and 12. In most cases, inversion breakpoints could be located within single nanopore contigs. Our results suggest the presence of inversions in Celtic cod on linkage groups 6, 11 and 21, although these remain to be confirmed. Further, we identified a specific repetitive element that is relatively enriched at predicted centromeric regions. Our gadMor_Celtic assembly provides a resource representing a ‘southern’ cod population which is complementary to the existing ‘northern’ population based genome assemblies and represents the first step toward developing pan-genomic resources for Atlantic cod. |
format |
Text |
author |
Kirubakaran, Tina Graceline Andersen, Øivind Moser, Michel Árnyasi, Mariann McGinnity, Philip Lien, Sigbjørn Kent, Matthew |
author_facet |
Kirubakaran, Tina Graceline Andersen, Øivind Moser, Michel Árnyasi, Mariann McGinnity, Philip Lien, Sigbjørn Kent, Matthew |
author_sort |
Kirubakaran, Tina Graceline |
title |
A Nanopore Based Chromosome-Level Assembly Representing Atlantic Cod from the Celtic Sea |
title_short |
A Nanopore Based Chromosome-Level Assembly Representing Atlantic Cod from the Celtic Sea |
title_full |
A Nanopore Based Chromosome-Level Assembly Representing Atlantic Cod from the Celtic Sea |
title_fullStr |
A Nanopore Based Chromosome-Level Assembly Representing Atlantic Cod from the Celtic Sea |
title_full_unstemmed |
A Nanopore Based Chromosome-Level Assembly Representing Atlantic Cod from the Celtic Sea |
title_sort |
nanopore based chromosome-level assembly representing atlantic cod from the celtic sea |
publisher |
Genetics Society of America |
publishDate |
2020 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7466986/ http://www.ncbi.nlm.nih.gov/pubmed/32641450 https://doi.org/10.1534/g3.120.401423 |
geographic |
Arctic Barents Sea |
geographic_facet |
Arctic Barents Sea |
genre |
Arctic cod Arctic atlantic cod Barents Sea Gadus morhua Northeast Arctic cod |
genre_facet |
Arctic cod Arctic atlantic cod Barents Sea Gadus morhua Northeast Arctic cod |
op_source |
G3 (Bethesda) |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7466986/ http://www.ncbi.nlm.nih.gov/pubmed/32641450 http://dx.doi.org/10.1534/g3.120.401423 |
op_rights |
Copyright © 2020 Kirubakaran et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1534/g3.120.401423 |
container_title |
G3 Genes|Genomes|Genetics |
container_volume |
10 |
container_issue |
9 |
container_start_page |
2903 |
op_container_end_page |
2910 |
_version_ |
1766304342935076864 |