KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba)
© 2017 Sales et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Antarctic krill (Euphausia superba) is a key...
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ftcurtin:oai:espace.curtin.edu.au:20.500.11937/71708 2023-06-11T04:04:28+02:00 KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba) Sales, G. Deagle, B. Calura, E. Martini, P. Biscontin, A. De Pittà, C. Kawaguchi, S. Romualdi, C. Meyer, B. Costa, R. Jarman, Simon 2017 fulltext https://hdl.handle.net/20.500.11937/71708 https://doi.org/10.1371/journal.pone.0171908 unknown Public Library of Science http://hdl.handle.net/20.500.11937/71708 doi:10.1371/journal.pone.0171908 http://creativecommons.org/licenses/by/4.0/ Journal Article 2017 ftcurtin https://doi.org/20.500.11937/7170810.1371/journal.pone.0171908 2023-05-30T19:54:36Z © 2017 Sales et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Antarctic krill (Euphausia superba) is a key species in the Southern Ocean with an estimated biomass between 100 and 500 million tonnes. Changes in krill population viability would have catastrophic effect on the Antarctic ecosystem. One looming threat due to elevated levels of anthropogenic atmospheric carbon dioxide (CO2) is ocean acidification (lowering of sea water pH by CO2 dissolving into the oceans). The genetics of Antarctic krill has long been of scientific interest for both for the analysis of population structure and analysis of functional genetics. However, the genetic resources available for the species are relatively modest. We have developed the most advanced genetic database on Euphausia superba, KrillDB, which includes comprehensive data sets of former and present transcriptome projects. In particular, we have built a de novo transcriptome assembly using more than 360 million Illumina sequence reads generated from larval krill including individuals subjected to different CO2levels. The database gives access to: 1) the full list of assembled genes and transcripts; 2) their level of similarity to transcripts and proteins from other species; 3) the predicted protein domains contained within each transcript; 4) their predicted GO terms; 5) the level of expression of each transcript in the different larval stages and CO2treatments. All references to external entities (sequences, domains, GO terms) are equipped with a link to the appropriate source database. Moreover, the software implements a full-text search engine that makes it possible to submit free-form queries. KrillDB represents the first largescale attempt at classifying and annotating the full krill transcriptome. For this reason, we believe it will constitute a cornerstone of future ... Article in Journal/Newspaper Antarc* Antarctic Antarctic Krill Euphausia superba Ocean acidification Southern Ocean Curtin University: espace Antarctic Southern Ocean The Antarctic PLOS ONE 12 2 e0171908 |
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© 2017 Sales et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Antarctic krill (Euphausia superba) is a key species in the Southern Ocean with an estimated biomass between 100 and 500 million tonnes. Changes in krill population viability would have catastrophic effect on the Antarctic ecosystem. One looming threat due to elevated levels of anthropogenic atmospheric carbon dioxide (CO2) is ocean acidification (lowering of sea water pH by CO2 dissolving into the oceans). The genetics of Antarctic krill has long been of scientific interest for both for the analysis of population structure and analysis of functional genetics. However, the genetic resources available for the species are relatively modest. We have developed the most advanced genetic database on Euphausia superba, KrillDB, which includes comprehensive data sets of former and present transcriptome projects. In particular, we have built a de novo transcriptome assembly using more than 360 million Illumina sequence reads generated from larval krill including individuals subjected to different CO2levels. The database gives access to: 1) the full list of assembled genes and transcripts; 2) their level of similarity to transcripts and proteins from other species; 3) the predicted protein domains contained within each transcript; 4) their predicted GO terms; 5) the level of expression of each transcript in the different larval stages and CO2treatments. All references to external entities (sequences, domains, GO terms) are equipped with a link to the appropriate source database. Moreover, the software implements a full-text search engine that makes it possible to submit free-form queries. KrillDB represents the first largescale attempt at classifying and annotating the full krill transcriptome. For this reason, we believe it will constitute a cornerstone of future ... |
format |
Article in Journal/Newspaper |
author |
Sales, G. Deagle, B. Calura, E. Martini, P. Biscontin, A. De Pittà, C. Kawaguchi, S. Romualdi, C. Meyer, B. Costa, R. Jarman, Simon |
spellingShingle |
Sales, G. Deagle, B. Calura, E. Martini, P. Biscontin, A. De Pittà, C. Kawaguchi, S. Romualdi, C. Meyer, B. Costa, R. Jarman, Simon KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba) |
author_facet |
Sales, G. Deagle, B. Calura, E. Martini, P. Biscontin, A. De Pittà, C. Kawaguchi, S. Romualdi, C. Meyer, B. Costa, R. Jarman, Simon |
author_sort |
Sales, G. |
title |
KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba) |
title_short |
KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba) |
title_full |
KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba) |
title_fullStr |
KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba) |
title_full_unstemmed |
KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba) |
title_sort |
krilldb: a de novo transcriptome database for the antarctic krill (euphausia superba) |
publisher |
Public Library of Science |
publishDate |
2017 |
url |
https://hdl.handle.net/20.500.11937/71708 https://doi.org/10.1371/journal.pone.0171908 |
geographic |
Antarctic Southern Ocean The Antarctic |
geographic_facet |
Antarctic Southern Ocean The Antarctic |
genre |
Antarc* Antarctic Antarctic Krill Euphausia superba Ocean acidification Southern Ocean |
genre_facet |
Antarc* Antarctic Antarctic Krill Euphausia superba Ocean acidification Southern Ocean |
op_relation |
http://hdl.handle.net/20.500.11937/71708 doi:10.1371/journal.pone.0171908 |
op_rights |
http://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/20.500.11937/7170810.1371/journal.pone.0171908 |
container_title |
PLOS ONE |
container_volume |
12 |
container_issue |
2 |
container_start_page |
e0171908 |
_version_ |
1768388056638816256 |