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The Euphausia superba transcriptome database, SuperbaSE: An online, open resource for researchers

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journal contribution
posted on 2017-07-12, 13:41 authored by Benjamin J. Hunt, Özge Özkaya, Nathaniel J. Davies, Edward Gaten, Paul Seear, Charalambos P. Kyriacou, Geraint Tarling, Ezio Rosato
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.

Funding

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.

History

Citation

Ecology and Evolution, 2017, 7 (16), pp. 1–18.

Author affiliation

/Organisation/COLLEGE OF MEDICINE, BIOLOGICAL SCIENCES AND PSYCHOLOGY/MBSP Non-Medical Departments/Department of Genetics

Version

  • VoR (Version of Record)

Published in

Ecology and Evolution

Publisher

Wiley, European Society for Evolutionary Biology (ESEB), Society for the Study of Evolution (SSE)

eissn

2045-7758

Acceptance date

2017-05-21

Copyright date

2017

Available date

2017-07-12

Publisher version

http://onlinelibrary.wiley.com/doi/10.1002/ece3.3168/abstract

Notes

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.

Language

en

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