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
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.
Additional details
Read the peer-reviewed publication(s):
(PubMed: 29126158)
Accessions (data generated as part of this study):
BioProject:
PRJNA384295
Sample ID | Taxonomic ID | Common Name | Genbank Name | Scientific Name | Sample Attributes |
---|---|---|---|---|---|
F1 | 41447 | greater amberjack | Seriola dumerili | Description:RNA extracted from female gonad Alternative accession-BioSample:SRS2150694 Tissue:gonad [UBERON:0000991] ... + | |
F2 | 41447 | greater amberjack | Seriola dumerili | Description:RNA extracted from female gonad Alternative accession-BioSample:SRS2150695 Tissue:gonad [UBERON:0000991] ... + | |
F3 | 41447 | greater amberjack | Seriola dumerili | Description:RNA extracted from female gonad Alternative accession-BioSample:SRS2150696 Tissue:gonad [UBERON:0000991] ... + | |
F4 | 41447 | greater amberjack | Seriola dumerili | Description:RNA extracted from female gonad Alternative accession-BioSample:SRS2150698 Tissue:gonad [UBERON:0000991] ... + | |
Fast1 | 41447 | greater amberjack | Seriola dumerili | Description:RNA extracted from muscle of fast grow... Alternative accession-BioSample:SRS2150705 Tissue:muscle structure [UBERON:0005090] ... + | |
Fast2 | 41447 | greater amberjack | Seriola dumerili | Description:RNA extracted from muscle of fast grow... Alternative accession-BioSample:SRS2150704 Tissue:muscle structure [UBERON:0005090] ... + | |
Fast3 | 41447 | greater amberjack | Seriola dumerili | Description:RNA extracted from muscle of fast grow... Alternative accession-BioSample:SRS2150703 Tissue:muscle structure [UBERON:0005090] ... + | |
Fast4 | 41447 | greater amberjack | Seriola dumerili | Description:RNA extracted from muscle of fast grow... Alternative accession-BioSample:SRS2150702 Tissue:muscle structure [UBERON:0005090] ... + | |
Female DNA sample | 41447 | greater amberjack | Seriola dumerili | Description:DNA extracted from blood of adult fema... Alternative accession-BioSample:SRS2150711 Tissue:blood [UBERON:0000178] ... + | |
M1 | 41447 | greater amberjack | Seriola dumerili | Description:RNA extracted from male gonad Alternative accession-BioSample:SRS2150701 Tissue:gonad [UBERON:0000991] ... + |