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Data released on November 07, 2017

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

Sarropoulou, E; Sundaram, A, Y; Kaitetzidou, E; Kotoulas, G; Gilfillan, G, D; Papandroulakis, N; Mylonas, C, C; 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 RIS BibTeX Text

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.

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Read the peer-reviewed publication(s):

Sarropoulou, E., Sundaram, A. Y. M., Kaitetzidou, E., Kotoulas, G., Gilfillan, G. D., Papandroulakis, N., … Magoulas, A. (2017). Full genome survey and dynamics of gene expression in the greater amberjack Seriola dumerili. GigaScience, 6(12), 1–13. doi:10.1093/gigascience/gix108

Accessions (data included in GigaDB):

BioProject: PRJNA384295

Keywords:

Genomic, Transcriptomic

http://gigadb.org/images/data/cropped/100362.jpg

Funding:

  • Funding body - Ministry of Education and Religious Affairs, Sport and Culture
  • Award ID - MIS 453278
  • Comment - NSRF 2007-2013 Program (Project MBBC, Development Proposals from Research Institutions - KRIPIS)
  • Awardee - Antonios Magoulas
  • Funding body - European Commission
  • Award ID - 654008
  • Comment - European Union Horizon 2020 Research and Innovation Program European Marine Biological Research Infrastructure Cluster (EMBRIC)
  • Awardee - B Kloareg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

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]
... +
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]
... +
M141447 greater amberjackSeriola dumerili Description:RNA extracted from male gonad
Alternative accession-BioSample:SRS2150701
Tissue:gonad [UBERON:0000991]
... +
Displaying 1-10 of 18 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
Data Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDData TypeFile FormatSizeRelease Date 
TextTEXT-0 KB2017-10-23
TextTEXT1.39 KB2017-10-23
TextTEXT1.39 KB2017-10-23
TextTEXT1.41 KB2017-10-23
TextTEXT1.51 KB2017-10-23
TextTEXT1.68 KB2017-10-23
ReadmeTEXT2.88 KB2017-10-23
file_typeFASTA3.38 KB2017-10-23
TextTEXT14.16 KB2017-10-23
TextTEXT16.12 KB2017-10-23
Displaying 1-10 of 19 File(s).

History:

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