KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba).
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 atmosph...
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ftdoajarticles:oai:doaj.org/article:447a80053e764d89a1890242d5d885e2 2023-05-15T14:00:15+02:00 KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba). Gabriele Sales Bruce E Deagle Enrica Calura Paolo Martini Alberto Biscontin Cristiano De Pittà So Kawaguchi Chiara Romualdi Bettina Meyer Rodolfo Costa Simon Jarman 2017-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0171908 https://doaj.org/article/447a80053e764d89a1890242d5d885e2 EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC5302830?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0171908 https://doaj.org/article/447a80053e764d89a1890242d5d885e2 PLoS ONE, Vol 12, Iss 2, p e0171908 (2017) Medicine R Science Q article 2017 ftdoajarticles https://doi.org/10.1371/journal.pone.0171908 2022-12-31T02:51:22Z 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 CO2 levels. 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 CO2 treatments. 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 large-scale attempt at classifying and annotating the full krill transcriptome. For this reason, we believe it will constitute a cornerstone of future approaches devoted to physiological and molecular study of this key species in the Southern Ocean food web. Article in Journal/Newspaper Antarc* Antarctic Antarctic Krill Euphausia superba Ocean acidification Southern Ocean Directory of Open Access Journals: DOAJ Articles Antarctic Southern Ocean The Antarctic PLOS ONE 12 2 e0171908 |
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Directory of Open Access Journals: DOAJ Articles |
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language |
English |
topic |
Medicine R Science Q |
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Medicine R Science Q Gabriele Sales Bruce E Deagle Enrica Calura Paolo Martini Alberto Biscontin Cristiano De Pittà So Kawaguchi Chiara Romualdi Bettina Meyer Rodolfo Costa Simon Jarman KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba). |
topic_facet |
Medicine R Science Q |
description |
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 CO2 levels. 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 CO2 treatments. 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 large-scale attempt at classifying and annotating the full krill transcriptome. For this reason, we believe it will constitute a cornerstone of future approaches devoted to physiological and molecular study of this key species in the Southern Ocean food web. |
format |
Article in Journal/Newspaper |
author |
Gabriele Sales Bruce E Deagle Enrica Calura Paolo Martini Alberto Biscontin Cristiano De Pittà So Kawaguchi Chiara Romualdi Bettina Meyer Rodolfo Costa Simon Jarman |
author_facet |
Gabriele Sales Bruce E Deagle Enrica Calura Paolo Martini Alberto Biscontin Cristiano De Pittà So Kawaguchi Chiara Romualdi Bettina Meyer Rodolfo Costa Simon Jarman |
author_sort |
Gabriele Sales |
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 (PLoS) |
publishDate |
2017 |
url |
https://doi.org/10.1371/journal.pone.0171908 https://doaj.org/article/447a80053e764d89a1890242d5d885e2 |
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_source |
PLoS ONE, Vol 12, Iss 2, p e0171908 (2017) |
op_relation |
http://europepmc.org/articles/PMC5302830?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0171908 https://doaj.org/article/447a80053e764d89a1890242d5d885e2 |
op_doi |
https://doi.org/10.1371/journal.pone.0171908 |
container_title |
PLOS ONE |
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12 |
container_issue |
2 |
container_start_page |
e0171908 |
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1766269295450390528 |