Multi-tissue RNA-seq and transcriptome characterisation of the spiny dogfish shark (Squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation.
The spiny dogfish shark (Squalus acanthias) is one of the most commonly used cartilaginous fishes in biological research, especially in the fields of nitrogen metabolism, ion transporters and osmoregulation. Nonetheless, transcriptomic data for this organism is scarce. In the present study, a multi-...
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ftdoajarticles:oai:doaj.org/article:c85ef3a191df4876bf5dfcf9a000ee68 2023-05-15T18:51:06+02:00 Multi-tissue RNA-seq and transcriptome characterisation of the spiny dogfish shark (Squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation. Andres Chana-Munoz Agnieszka Jendroszek Malene Sønnichsen Rune Kristiansen Jan K Jensen Peter A Andreasen Christian Bendixen Frank Panitz 2017-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0182756 https://doaj.org/article/c85ef3a191df4876bf5dfcf9a000ee68 EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC5568229?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0182756 https://doaj.org/article/c85ef3a191df4876bf5dfcf9a000ee68 PLoS ONE, Vol 12, Iss 8, p e0182756 (2017) Medicine R Science Q article 2017 ftdoajarticles https://doi.org/10.1371/journal.pone.0182756 2022-12-31T05:38:46Z The spiny dogfish shark (Squalus acanthias) is one of the most commonly used cartilaginous fishes in biological research, especially in the fields of nitrogen metabolism, ion transporters and osmoregulation. Nonetheless, transcriptomic data for this organism is scarce. In the present study, a multi-tissue RNA-seq experiment and de novo transcriptome assembly was performed in four different spiny dogfish tissues (brain, liver, kidney and ovary), providing an annotated sequence resource. The characterization of the transcriptome greatly increases the scarce sequence information for shark species. Reads were assembled with the Trinity de novo assembler both within each tissue and across all tissues combined resulting in 362,690 transcripts in the combined assembly which represent 289,515 Trinity genes. BUSCO analysis determined a level of 87% completeness for the combined transcriptome. In total, 123,110 proteins were predicted of which 78,679 and 83,164 had significant hits against the SwissProt and Uniref90 protein databases, respectively. Additionally, 61,215 proteins aligned to known protein domains, 7,208 carried a signal peptide and 15,971 possessed at least one transmembrane region. Based on the annotation, 81,582 transcripts were assigned to gene ontology terms and 42,078 belong to known clusters of orthologous groups (eggNOG). To demonstrate the value of our molecular resource, we show that the improved transcriptome data enhances the current possibilities of osmoregulation research in spiny dogfish by utilizing the novel gene and protein annotations to investigate a set of genes involved in urea synthesis and urea, ammonia and water transport, all of them crucial in osmoregulation. We describe the presence of different gene copies and isoforms of key enzymes involved in this process, including arginases and transporters of urea and ammonia, for which sequence information is currently absent in the databases for this model species. The transcriptome assemblies and the derived annotations generated in this ... Article in Journal/Newspaper spiny dogfish Squalus acanthias Directory of Open Access Journals: DOAJ Articles PLOS ONE 12 8 e0182756 |
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Medicine R Science Q Andres Chana-Munoz Agnieszka Jendroszek Malene Sønnichsen Rune Kristiansen Jan K Jensen Peter A Andreasen Christian Bendixen Frank Panitz Multi-tissue RNA-seq and transcriptome characterisation of the spiny dogfish shark (Squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation. |
topic_facet |
Medicine R Science Q |
description |
The spiny dogfish shark (Squalus acanthias) is one of the most commonly used cartilaginous fishes in biological research, especially in the fields of nitrogen metabolism, ion transporters and osmoregulation. Nonetheless, transcriptomic data for this organism is scarce. In the present study, a multi-tissue RNA-seq experiment and de novo transcriptome assembly was performed in four different spiny dogfish tissues (brain, liver, kidney and ovary), providing an annotated sequence resource. The characterization of the transcriptome greatly increases the scarce sequence information for shark species. Reads were assembled with the Trinity de novo assembler both within each tissue and across all tissues combined resulting in 362,690 transcripts in the combined assembly which represent 289,515 Trinity genes. BUSCO analysis determined a level of 87% completeness for the combined transcriptome. In total, 123,110 proteins were predicted of which 78,679 and 83,164 had significant hits against the SwissProt and Uniref90 protein databases, respectively. Additionally, 61,215 proteins aligned to known protein domains, 7,208 carried a signal peptide and 15,971 possessed at least one transmembrane region. Based on the annotation, 81,582 transcripts were assigned to gene ontology terms and 42,078 belong to known clusters of orthologous groups (eggNOG). To demonstrate the value of our molecular resource, we show that the improved transcriptome data enhances the current possibilities of osmoregulation research in spiny dogfish by utilizing the novel gene and protein annotations to investigate a set of genes involved in urea synthesis and urea, ammonia and water transport, all of them crucial in osmoregulation. We describe the presence of different gene copies and isoforms of key enzymes involved in this process, including arginases and transporters of urea and ammonia, for which sequence information is currently absent in the databases for this model species. The transcriptome assemblies and the derived annotations generated in this ... |
format |
Article in Journal/Newspaper |
author |
Andres Chana-Munoz Agnieszka Jendroszek Malene Sønnichsen Rune Kristiansen Jan K Jensen Peter A Andreasen Christian Bendixen Frank Panitz |
author_facet |
Andres Chana-Munoz Agnieszka Jendroszek Malene Sønnichsen Rune Kristiansen Jan K Jensen Peter A Andreasen Christian Bendixen Frank Panitz |
author_sort |
Andres Chana-Munoz |
title |
Multi-tissue RNA-seq and transcriptome characterisation of the spiny dogfish shark (Squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation. |
title_short |
Multi-tissue RNA-seq and transcriptome characterisation of the spiny dogfish shark (Squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation. |
title_full |
Multi-tissue RNA-seq and transcriptome characterisation of the spiny dogfish shark (Squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation. |
title_fullStr |
Multi-tissue RNA-seq and transcriptome characterisation of the spiny dogfish shark (Squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation. |
title_full_unstemmed |
Multi-tissue RNA-seq and transcriptome characterisation of the spiny dogfish shark (Squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation. |
title_sort |
multi-tissue rna-seq and transcriptome characterisation of the spiny dogfish shark (squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2017 |
url |
https://doi.org/10.1371/journal.pone.0182756 https://doaj.org/article/c85ef3a191df4876bf5dfcf9a000ee68 |
genre |
spiny dogfish Squalus acanthias |
genre_facet |
spiny dogfish Squalus acanthias |
op_source |
PLoS ONE, Vol 12, Iss 8, p e0182756 (2017) |
op_relation |
http://europepmc.org/articles/PMC5568229?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0182756 https://doaj.org/article/c85ef3a191df4876bf5dfcf9a000ee68 |
op_doi |
https://doi.org/10.1371/journal.pone.0182756 |
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PLOS ONE |
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12 |
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8 |
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