Characteristics of the spiny dogfish (Squalus acanthias) nuclear genome
Sequenced shark nuclear genomes are underrepresented, with reference genomes available for only four out of nine orders so far. Here, we present the nuclear genome, with annotations, of the spiny dogfish (Squalus acanthias), a shark of interest to biomedical and conservation efforts, and the first r...
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ftpubmed:oai:pubmedcentral.nih.gov:10468316 2023-10-01T04:00:11+02:00 Characteristics of the spiny dogfish (Squalus acanthias) nuclear genome Wagner, C Isabel Kopp, Martina E L Thorburn, James Jones, Catherine S Hoarau, Galice Noble, Leslie R 2023-07-03 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10468316/ http://www.ncbi.nlm.nih.gov/pubmed/37395764 https://doi.org/10.1093/g3journal/jkad146 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10468316/ http://www.ncbi.nlm.nih.gov/pubmed/37395764 http://dx.doi.org/10.1093/g3journal/jkad146 © The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. G3 (Bethesda) Genome Report Text 2023 ftpubmed https://doi.org/10.1093/g3journal/jkad146 2023-09-03T01:31:23Z Sequenced shark nuclear genomes are underrepresented, with reference genomes available for only four out of nine orders so far. Here, we present the nuclear genome, with annotations, of the spiny dogfish (Squalus acanthias), a shark of interest to biomedical and conservation efforts, and the first representative of the second largest order of sharks (Squaliformes) with nuclear genome annotations available. Using Pacific Biosciences Continuous Long Read data in combination with Illumina paired-end and Hi-C sequencing, we assembled the genome de novo, followed by RNA-Seq-supported annotation. The final chromosome-level assembly is 3.7 Gb in size, has a BUSCO completeness score of 91.6%, and an error rate of less than 0.02%. Annotation predicted 33,283 gene models in the spiny dogfish's genome, of which 31,979 are functionally annotated. Text spiny dogfish Squalus acanthias PubMed Central (PMC) Pacific G3: Genes, Genomes, Genetics 13 9 |
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ftpubmed |
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English |
topic |
Genome Report |
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Genome Report Wagner, C Isabel Kopp, Martina E L Thorburn, James Jones, Catherine S Hoarau, Galice Noble, Leslie R Characteristics of the spiny dogfish (Squalus acanthias) nuclear genome |
topic_facet |
Genome Report |
description |
Sequenced shark nuclear genomes are underrepresented, with reference genomes available for only four out of nine orders so far. Here, we present the nuclear genome, with annotations, of the spiny dogfish (Squalus acanthias), a shark of interest to biomedical and conservation efforts, and the first representative of the second largest order of sharks (Squaliformes) with nuclear genome annotations available. Using Pacific Biosciences Continuous Long Read data in combination with Illumina paired-end and Hi-C sequencing, we assembled the genome de novo, followed by RNA-Seq-supported annotation. The final chromosome-level assembly is 3.7 Gb in size, has a BUSCO completeness score of 91.6%, and an error rate of less than 0.02%. Annotation predicted 33,283 gene models in the spiny dogfish's genome, of which 31,979 are functionally annotated. |
format |
Text |
author |
Wagner, C Isabel Kopp, Martina E L Thorburn, James Jones, Catherine S Hoarau, Galice Noble, Leslie R |
author_facet |
Wagner, C Isabel Kopp, Martina E L Thorburn, James Jones, Catherine S Hoarau, Galice Noble, Leslie R |
author_sort |
Wagner, C Isabel |
title |
Characteristics of the spiny dogfish (Squalus acanthias) nuclear genome |
title_short |
Characteristics of the spiny dogfish (Squalus acanthias) nuclear genome |
title_full |
Characteristics of the spiny dogfish (Squalus acanthias) nuclear genome |
title_fullStr |
Characteristics of the spiny dogfish (Squalus acanthias) nuclear genome |
title_full_unstemmed |
Characteristics of the spiny dogfish (Squalus acanthias) nuclear genome |
title_sort |
characteristics of the spiny dogfish (squalus acanthias) nuclear genome |
publisher |
Oxford University Press |
publishDate |
2023 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10468316/ http://www.ncbi.nlm.nih.gov/pubmed/37395764 https://doi.org/10.1093/g3journal/jkad146 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
spiny dogfish Squalus acanthias |
genre_facet |
spiny dogfish Squalus acanthias |
op_source |
G3 (Bethesda) |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10468316/ http://www.ncbi.nlm.nih.gov/pubmed/37395764 http://dx.doi.org/10.1093/g3journal/jkad146 |
op_rights |
© The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
op_doi |
https://doi.org/10.1093/g3journal/jkad146 |
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G3: Genes, Genomes, Genetics |
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13 |
container_issue |
9 |
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