KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba)

PLOS ONE, Dec 2019

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.

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KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba)

February KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba) Gabriele Sales 0 1 2 Bruce E. Deagle 0 2 Enrica Calura 0 1 2 Paolo Martini 0 1 2 Alberto Biscontin 0 1 2 Cristiano De Pittà 0 1 2 So Kawaguchi 0 2 Chiara Romualdi 0 1 2 Bettina Meyer 0 2 Rodolfo Costa 0 1 2 Simon Jarman 0 2 0 Data Availability Statement: Raw data are accessible on the National Center for Biotechnology Information Short Read Archive (SRA BioProject Accession PRJNA362526) at the URL: 1 Department of Biology, University of Padova , Padova , Italy , 2 Australian Antarctic Division , Kingston, Tasmania , Australia , 3 Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research , Bremerhaven, Germany , 4 Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University Oldenburg , Oldenburg , Germany 2 Editor: Cristiano Bertolucci, University of Ferrara , ITALY 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 largescale 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. - Funding: This work was supported by the following: the Helmholtz Virtual Institute ªPolarTimeº (VH-VI-500: Biological timing in a changing marine environment Ð clocks and rhythms in polar pelagic organisms, www. polartime.org), to BM; the Italian Programma Nazionale di Ricerche in Antartide Ð PNRA (grant Introduction Antarctic krill (Euphausia superba) is a key species in the Southern Ocean with an estimated biomass between 100 and 500 million tons. The species provides a critical ecological link between primary producers and apex predators and supports commercial fisheries [ 1 ]. 2013/C1.05, http://www.pnra.it/) to RC; the Australian Antarctic Science Program (AAS Project 4015, http://www.antarctica.gov.au/science/ information-for-scientists/research-guidelines/ AASP-guidelines) to SJ; the Alfred Wegener Institute through the research programme PACES II (topic 1, workpackage 5, https://www.awi.de/en. html) to BM. Changes in krill population viability would have catastrophic effect on the Antarctic ecosystem [ 1,2 ]. One looming threat is ocean acidification (OA)±this is lowering of sea water pH due to elevated levels of anthropogenic atmospheric carbon dioxide (CO2) dissolving into the oceans [3]. This threat is recognized to be a global issue for the marine environment, but cold southern ocean waters are particularly susceptible due to high solubility of CO2 [ 4 ]. Recent experimental work has documented the impact of increased CO2 levels on krill development [ 2,5,6 ]. There has long been interest in the ecological genetics of Antarctic krill both for the analysis of population structure [ 7,8 ] and analysis of functional genetics [9±12]. However, the genetic resources available for this species are relatively modest. The genome size of the species is exceptionally large [13]; at 48.53 pg, it is more than 15 times larger than the human genome. Arthropods are the most diverse animal phylum, but their genomic resources have a relatively narrow taxonomic focus and little insight into the krill genome can be obtained from related species [ 14 ]. Even with rapid advance in DNA sequencing technology the current prospects for ca (...truncated)


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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), PLOS ONE, 2017, Volume 12, Issue 2, DOI: 10.1371/journal.pone.0171908