Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats
Abstract Background Increased availability of genome assemblies for non-model organisms has resulted in invaluable biological and genomic insight into numerous vertebrates, including teleosts. Sequencing of the Atlantic cod (Gadus morhua) genome and the genomes of many of its relatives (Gadiformes)...
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ftdatacite:10.6084/m9.figshare.c.4065584.v1 2023-05-15T15:26:46+02:00 Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats Tørresen, Ole Brieuc, Marine Solbakken, Monica Sørhus, Elin Nederbragt, Alexander Kjetill Jakobsen Sonnich Meier Edvardsen, Rolf Jentoft, Sissel 2018 https://dx.doi.org/10.6084/m9.figshare.c.4065584.v1 https://figshare.com/collections/Genomic_architecture_of_haddock_Melanogrammus_aeglefinus_shows_expansions_of_innate_immune_genes_and_short_tandem_repeats/4065584/1 unknown Figshare https://dx.doi.org/10.1186/s12864-018-4616-y https://dx.doi.org/10.6084/m9.figshare.c.4065584 CC BY 4.0 https://creativecommons.org/licenses/by/4.0 CC-BY Genetics FOS Biological sciences Molecular Biology Evolutionary Biology Ecology Immunology FOS Clinical medicine 69999 Biological Sciences not elsewhere classified Marine Biology 60506 Virology Computational Biology Collection article 2018 ftdatacite https://doi.org/10.6084/m9.figshare.c.4065584.v1 https://doi.org/10.1186/s12864-018-4616-y https://doi.org/10.6084/m9.figshare.c.4065584 2021-11-05T12:55:41Z Abstract Background Increased availability of genome assemblies for non-model organisms has resulted in invaluable biological and genomic insight into numerous vertebrates, including teleosts. Sequencing of the Atlantic cod (Gadus morhua) genome and the genomes of many of its relatives (Gadiformes) demonstrated a shared loss of the major histocompatibility complex (MHC) II genes 100 million years ago. An improved version of the Atlantic cod genome assembly shows an extreme density of tandem repeats compared to other vertebrate genome assemblies. Highly contiguous assemblies are therefore needed to further investigate the unusual immune system of the Gadiformes, and whether the high density of tandem repeats found in Atlantic cod is a shared trait in this group. Results Here, we have sequenced and assembled the genome of haddock (Melanogrammus aeglefinus) – a relative of Atlantic cod – using a combination of PacBio and Illumina reads. Comparative analyses reveal that the haddock genome contains an even higher density of tandem repeats outside and within protein coding sequences than Atlantic cod. Further, both species show an elevated number of tandem repeats in genes mainly involved in signal transduction compared to other teleosts. A characterization of the immune gene repertoire demonstrates a substantial expansion of MCHI in Atlantic cod compared to haddock. In contrast, the Toll-like receptors show a similar pattern of gene losses and expansions. For the NOD-like receptors (NLRs), another gene family associated with the innate immune system, we find a large expansion common to all teleosts, with possible lineage-specific expansions in zebrafish, stickleback and the codfishes. Conclusions The generation of a highly contiguous genome assembly of haddock revealed that the high density of short tandem repeats as well as expanded immune gene families is not unique to Atlantic cod – but possibly a feature common to all, or most, codfishes. A shared expansion of NLR genes in teleosts suggests that the NLRs have a more substantial role in the innate immunity of teleosts than other vertebrates. Moreover, we find that high copy number genes combined with variable genome assembly qualities may impede complete characterization of these genes, i.e. the number of NLRs in different teleost species might be underestimates. Article in Journal/Newspaper atlantic cod Gadus morhua DataCite Metadata Store (German National Library of Science and Technology) |
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Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
unknown |
topic |
Genetics FOS Biological sciences Molecular Biology Evolutionary Biology Ecology Immunology FOS Clinical medicine 69999 Biological Sciences not elsewhere classified Marine Biology 60506 Virology Computational Biology |
spellingShingle |
Genetics FOS Biological sciences Molecular Biology Evolutionary Biology Ecology Immunology FOS Clinical medicine 69999 Biological Sciences not elsewhere classified Marine Biology 60506 Virology Computational Biology Tørresen, Ole Brieuc, Marine Solbakken, Monica Sørhus, Elin Nederbragt, Alexander Kjetill Jakobsen Sonnich Meier Edvardsen, Rolf Jentoft, Sissel Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats |
topic_facet |
Genetics FOS Biological sciences Molecular Biology Evolutionary Biology Ecology Immunology FOS Clinical medicine 69999 Biological Sciences not elsewhere classified Marine Biology 60506 Virology Computational Biology |
description |
Abstract Background Increased availability of genome assemblies for non-model organisms has resulted in invaluable biological and genomic insight into numerous vertebrates, including teleosts. Sequencing of the Atlantic cod (Gadus morhua) genome and the genomes of many of its relatives (Gadiformes) demonstrated a shared loss of the major histocompatibility complex (MHC) II genes 100 million years ago. An improved version of the Atlantic cod genome assembly shows an extreme density of tandem repeats compared to other vertebrate genome assemblies. Highly contiguous assemblies are therefore needed to further investigate the unusual immune system of the Gadiformes, and whether the high density of tandem repeats found in Atlantic cod is a shared trait in this group. Results Here, we have sequenced and assembled the genome of haddock (Melanogrammus aeglefinus) – a relative of Atlantic cod – using a combination of PacBio and Illumina reads. Comparative analyses reveal that the haddock genome contains an even higher density of tandem repeats outside and within protein coding sequences than Atlantic cod. Further, both species show an elevated number of tandem repeats in genes mainly involved in signal transduction compared to other teleosts. A characterization of the immune gene repertoire demonstrates a substantial expansion of MCHI in Atlantic cod compared to haddock. In contrast, the Toll-like receptors show a similar pattern of gene losses and expansions. For the NOD-like receptors (NLRs), another gene family associated with the innate immune system, we find a large expansion common to all teleosts, with possible lineage-specific expansions in zebrafish, stickleback and the codfishes. Conclusions The generation of a highly contiguous genome assembly of haddock revealed that the high density of short tandem repeats as well as expanded immune gene families is not unique to Atlantic cod – but possibly a feature common to all, or most, codfishes. A shared expansion of NLR genes in teleosts suggests that the NLRs have a more substantial role in the innate immunity of teleosts than other vertebrates. Moreover, we find that high copy number genes combined with variable genome assembly qualities may impede complete characterization of these genes, i.e. the number of NLRs in different teleost species might be underestimates. |
format |
Article in Journal/Newspaper |
author |
Tørresen, Ole Brieuc, Marine Solbakken, Monica Sørhus, Elin Nederbragt, Alexander Kjetill Jakobsen Sonnich Meier Edvardsen, Rolf Jentoft, Sissel |
author_facet |
Tørresen, Ole Brieuc, Marine Solbakken, Monica Sørhus, Elin Nederbragt, Alexander Kjetill Jakobsen Sonnich Meier Edvardsen, Rolf Jentoft, Sissel |
author_sort |
Tørresen, Ole |
title |
Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats |
title_short |
Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats |
title_full |
Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats |
title_fullStr |
Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats |
title_full_unstemmed |
Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats |
title_sort |
genomic architecture of haddock (melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats |
publisher |
Figshare |
publishDate |
2018 |
url |
https://dx.doi.org/10.6084/m9.figshare.c.4065584.v1 https://figshare.com/collections/Genomic_architecture_of_haddock_Melanogrammus_aeglefinus_shows_expansions_of_innate_immune_genes_and_short_tandem_repeats/4065584/1 |
genre |
atlantic cod Gadus morhua |
genre_facet |
atlantic cod Gadus morhua |
op_relation |
https://dx.doi.org/10.1186/s12864-018-4616-y https://dx.doi.org/10.6084/m9.figshare.c.4065584 |
op_rights |
CC BY 4.0 https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.c.4065584.v1 https://doi.org/10.1186/s12864-018-4616-y https://doi.org/10.6084/m9.figshare.c.4065584 |
_version_ |
1766357245180772352 |