The Euphausia superba transcriptome database, SuperbaSE: An online, open resource for researchers
Sequences of cloned circadian genes are available in GenBank under accessions KX238951, KX238952, KX238953, KX238954, and KX238955, as are the sequences of the total assembly under accession GFCS00000000. Read data were submitted to NCBI SRA under accession SRR4408478. Annotated coding and peptide a...
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Wiley, European Society for Evolutionary Biology (ESEB), Society for the Study of Evolution (SSE)
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Online Access: | http://onlinelibrary.wiley.com/doi/10.1002/ece3.3168/abstract http://hdl.handle.net/2381/40071 https://doi.org/10.1002/ece3.3168 |
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ftleicester:oai:lra.le.ac.uk:2381/40071 2023-05-15T13:31:55+02:00 The Euphausia superba transcriptome database, SuperbaSE: An online, open resource for researchers Hunt, Benjamin J. Özkaya, Özge Davies, Nathaniel J. Gaten, Edward Seear, Paul Kyriacou, Charalambos P. Tarling, Geraint Rosato, Ezio 2017-07-12T13:41:42Z http://onlinelibrary.wiley.com/doi/10.1002/ece3.3168/abstract http://hdl.handle.net/2381/40071 https://doi.org/10.1002/ece3.3168 en eng Wiley, European Society for Evolutionary Biology (ESEB), Society for the Study of Evolution (SSE) Ecology and Evolution, 2017, 7 (16), pp. 1–18. http://onlinelibrary.wiley.com/doi/10.1002/ece3.3168/abstract http://hdl.handle.net/2381/40071 doi:10.1002/ece3.3168 2045-7758 Copyright © the authors, 2017. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. CC-BY Antarctic circadian crustacean database krill transcriptome Journal Article Article in Press 2017 ftleicester https://doi.org/10.1002/ece3.3168 2019-03-22T20:23:35Z Sequences of cloned circadian genes are available in GenBank under accessions KX238951, KX238952, KX238953, KX238954, and KX238955, as are the sequences of the total assembly under accession GFCS00000000. Read data were submitted to NCBI SRA under accession SRR4408478. Annotated coding and peptide assembly sequences are available at www.krill.le.ac.uk. Antarctic krill (Euphausia superba) is a crucial component of the Southern Ocean ecosystem, acting as the major link between primary production and higher trophic levels with an annual predator demand of up to 470 million tonnes. It also acts as an ecosystem engineer, affecting carbon sequestration and recycling iron and nitrogen, and has increasing importance as a commercial product in the aquaculture and health industries. Here we describe the creation of a de novo assembled head transcriptome for E. superba. As an example of its potential as a molecular resource, we relate its exploitation in identifying and characterizing numerous genes related to the circadian clock in E. superba, including the major components of the central feedback loop. We have made the transcriptome openly accessible for a wider audience of ecologists, molecular biologists, evolutionary geneticists, and others in a user-friendly format at SuperbaSE, hosted at www.krill.le.ac.uk. This work was funded by the Natural Environment Research Council (NERC) UK through an Antarctic Funding Initiative grant NE/D008719/1 (ÖÖ, PS, EG, CPK, GT, ER) and a PhD studentship (BJH). This research used the ALICE High Performance Computing Facility at the University of Leicester. Peer-reviewed Publisher Version Article in Journal/Newspaper Antarc* Antarctic Antarctic Krill Euphausia superba Southern Ocean University of Leicester: Leicester Research Archive (LRA) Antarctic Southern Ocean Leicester ENVELOPE(-116.403,-116.403,55.717,55.717) Ecology and Evolution 7 16 6060 6077 |
institution |
Open Polar |
collection |
University of Leicester: Leicester Research Archive (LRA) |
op_collection_id |
ftleicester |
language |
English |
topic |
Antarctic circadian crustacean database krill transcriptome |
spellingShingle |
Antarctic circadian crustacean database krill transcriptome Hunt, Benjamin J. Özkaya, Özge Davies, Nathaniel J. Gaten, Edward Seear, Paul Kyriacou, Charalambos P. Tarling, Geraint Rosato, Ezio The Euphausia superba transcriptome database, SuperbaSE: An online, open resource for researchers |
topic_facet |
Antarctic circadian crustacean database krill transcriptome |
description |
Sequences of cloned circadian genes are available in GenBank under accessions KX238951, KX238952, KX238953, KX238954, and KX238955, as are the sequences of the total assembly under accession GFCS00000000. Read data were submitted to NCBI SRA under accession SRR4408478. Annotated coding and peptide assembly sequences are available at www.krill.le.ac.uk. Antarctic krill (Euphausia superba) is a crucial component of the Southern Ocean ecosystem, acting as the major link between primary production and higher trophic levels with an annual predator demand of up to 470 million tonnes. It also acts as an ecosystem engineer, affecting carbon sequestration and recycling iron and nitrogen, and has increasing importance as a commercial product in the aquaculture and health industries. Here we describe the creation of a de novo assembled head transcriptome for E. superba. As an example of its potential as a molecular resource, we relate its exploitation in identifying and characterizing numerous genes related to the circadian clock in E. superba, including the major components of the central feedback loop. We have made the transcriptome openly accessible for a wider audience of ecologists, molecular biologists, evolutionary geneticists, and others in a user-friendly format at SuperbaSE, hosted at www.krill.le.ac.uk. This work was funded by the Natural Environment Research Council (NERC) UK through an Antarctic Funding Initiative grant NE/D008719/1 (ÖÖ, PS, EG, CPK, GT, ER) and a PhD studentship (BJH). This research used the ALICE High Performance Computing Facility at the University of Leicester. Peer-reviewed Publisher Version |
format |
Article in Journal/Newspaper |
author |
Hunt, Benjamin J. Özkaya, Özge Davies, Nathaniel J. Gaten, Edward Seear, Paul Kyriacou, Charalambos P. Tarling, Geraint Rosato, Ezio |
author_facet |
Hunt, Benjamin J. Özkaya, Özge Davies, Nathaniel J. Gaten, Edward Seear, Paul Kyriacou, Charalambos P. Tarling, Geraint Rosato, Ezio |
author_sort |
Hunt, Benjamin J. |
title |
The Euphausia superba transcriptome database, SuperbaSE: An online, open resource for researchers |
title_short |
The Euphausia superba transcriptome database, SuperbaSE: An online, open resource for researchers |
title_full |
The Euphausia superba transcriptome database, SuperbaSE: An online, open resource for researchers |
title_fullStr |
The Euphausia superba transcriptome database, SuperbaSE: An online, open resource for researchers |
title_full_unstemmed |
The Euphausia superba transcriptome database, SuperbaSE: An online, open resource for researchers |
title_sort |
euphausia superba transcriptome database, superbase: an online, open resource for researchers |
publisher |
Wiley, European Society for Evolutionary Biology (ESEB), Society for the Study of Evolution (SSE) |
publishDate |
2017 |
url |
http://onlinelibrary.wiley.com/doi/10.1002/ece3.3168/abstract http://hdl.handle.net/2381/40071 https://doi.org/10.1002/ece3.3168 |
long_lat |
ENVELOPE(-116.403,-116.403,55.717,55.717) |
geographic |
Antarctic Southern Ocean Leicester |
geographic_facet |
Antarctic Southern Ocean Leicester |
genre |
Antarc* Antarctic Antarctic Krill Euphausia superba Southern Ocean |
genre_facet |
Antarc* Antarctic Antarctic Krill Euphausia superba Southern Ocean |
op_relation |
Ecology and Evolution, 2017, 7 (16), pp. 1–18. http://onlinelibrary.wiley.com/doi/10.1002/ece3.3168/abstract http://hdl.handle.net/2381/40071 doi:10.1002/ece3.3168 2045-7758 |
op_rights |
Copyright © the authors, 2017. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1002/ece3.3168 |
container_title |
Ecology and Evolution |
container_volume |
7 |
container_issue |
16 |
container_start_page |
6060 |
op_container_end_page |
6077 |
_version_ |
1766022415914106880 |