Supporting data for "Full Genome Survey and Dynamics of Gene Expression in the Greater Amberjack, Seriola dumerili"

Dataset type: Genomic, Transcriptomic
Data released on November 07, 2017

Sarropoulou E; Sundaram AYM; Kaitetzidou E; Kotoulas G; Gilfillan GD; Papandroulakis N; Mylonas CC; Magoulas A (2017): Supporting data for "Full Genome Survey and Dynamics of Gene Expression in the Greater Amberjack, Seriola dumerili" GigaScience Database. http://dx.doi.org/10.5524/100362

DOI10.5524/100362

Teleosts of the genus Seriola, commonly known as amberjacks, are of high commercial value in international markets due to their flesh quality and worldwide distribution. The species of interest to the Mediterranean aquaculture within the genus Seriola, is the greater amberjack (Seriola dumerili). This species holds great potential for the aquaculture industry, but reproduction in captivity has proven to be challenging and unreliable presumably due to its large size and pelagic migratory nature. Investigations to unravel the molecular background of Seriola species have only recently begun, and consequently molecular data are scarce. Illumina HiSeq sequencing generated a high coverage genome sequence comprising 45,909 scaffolds. Comparative mapping to the congener Japanese yellowtail (Seriola quinqueriadiata) and to the model species medaka (Oryzias latipes) allowed the generation of in silico groups. Transcriptome sequencing of male and female gonads identified significantly differentially expressed transcripts, comprising known sex determining and sex differentiation genes. Investigations in the muscle transcriptome of slow growing individuals, showed that transcripts involved in the biological processes of oxygen and gas transport were differentially expressed compared to fast/normal growing amberjacks, while transcripts involved in muscle functions were found to be enriched in fast/normal growing individuals. Valuable molecular resources have been generated for the greater amberjack in form of a first draft genome and a reference transcriptome. In addition, genes which may have roles in sex determination or differentiation, and genes that may be responsible for slow growth are suggested.

Keywords:

Additional details

Read the peer-reviewed publication(s):

(PubMed: 29126158)

Accessions (data generated as part of this study):

BioProject: PRJNA384295





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
F141447 greater amberjackSeriola dumerili Description:RNA extracted from female gonad
Alternative accession-BioSample:SRS2150694
Tissue:gonad [UBERON:0000991]
...
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F241447 greater amberjackSeriola dumerili Description:RNA extracted from female gonad
Alternative accession-BioSample:SRS2150695
Tissue:gonad [UBERON:0000991]
...
+
F341447 greater amberjackSeriola dumerili Description:RNA extracted from female gonad
Alternative accession-BioSample:SRS2150696
Tissue:gonad [UBERON:0000991]
...
+
F441447 greater amberjackSeriola dumerili Description:RNA extracted from female gonad
Alternative accession-BioSample:SRS2150698
Tissue:gonad [UBERON:0000991]
...
+
Fast141447 greater amberjackSeriola dumerili Description:RNA extracted from muscle of fast grow...
Alternative accession-BioSample:SRS2150705
Tissue:muscle structure [UBERON:0005090]
...
+
Fast241447 greater amberjackSeriola dumerili Description:RNA extracted from muscle of fast grow...
Alternative accession-BioSample:SRS2150704
Tissue:muscle structure [UBERON:0005090]
...
+
Fast341447 greater amberjackSeriola dumerili Description:RNA extracted from muscle of fast grow...
Alternative accession-BioSample:SRS2150703
Tissue:muscle structure [UBERON:0005090]
...
+
Fast441447 greater amberjackSeriola dumerili Description:RNA extracted from muscle of fast grow...
Alternative accession-BioSample:SRS2150702
Tissue:muscle structure [UBERON:0005090]
...
+
Female DNA sample41447 greater amberjackSeriola dumerili Description:DNA extracted from blood of adult fema...
Alternative accession-BioSample:SRS2150711
Tissue:blood [UBERON:0000178]
...
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M141447 greater amberjackSeriola dumerili Description:RNA extracted from male gonad
Alternative accession-BioSample:SRS2150701
Tissue:gonad [UBERON:0000991]
...
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Displaying 1-10 of 18 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
TextTEXT1.68 KB2017-10-23
OtherTEXT3.38 KB2017-10-23
Genome sequenceFASTA648.11 MB2017-10-23
Genome sequenceFASTA648.55 MB2017-10-23
Protein sequenceFASTA23.97 MB2017-10-23
Transcriptome sequenceFASTA86.26 MB2017-10-23
ReadmeTEXT3.97 KB2017-10-23
Tabular dataCSV3.34 MB2017-10-23
TextTEXT1.39 KB2017-10-23
TextTEXT1.43 MB2017-10-23
Displaying 1-10 of 18 File(s).
Funding body Awardee Award ID Comments
Ministry of Education and Religious Affairs, Sport and Culture Antonios Magoulas MIS 453278 NSRF 2007-2013 Program (Project MBBC, Development Proposals from Research Institutions - KRIPIS)
European Commission B Kloareg 654008 European Union Horizon 2020 Research and Innovation Program European Marine Biological Research Infrastructure Cluster (EMBRIC)
Date Action
November 7, 2017 Dataset publish
November 8, 2017 Manuscript Link added : 10.1093/gigascience/gix108
May 5, 2020 File readme.txt updated
May 5, 2020 File removed : Two_coloumn_file_maker2.txt. This file was never uploaded to our FTP server.
May 5, 2020 SD-seq_based_on_scaffolds.fasta: MD5sum file attribute added (somehow was missed at point of submission)
November 9, 2022 Manuscript Link updated : 10.1093/gigascience/gix108
November 15, 2022 Data type for File SD-seq_based_on_scaffolds.fasta updated
November 15, 2022 Data type for File Genome.scf.fasta.stats updated