ArticleBMC genomics2013
Deep sequencing for de novo construction of a marine fish (Sparus aurata) transcriptome database with a large coverage of protein-coding transcripts.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers, 1 of them a synthesis that pooled it.
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Who cites it
36 citing papers in PubMed, 1 synthesis or guideline pooled it, 82 citations in OpenAlex.
- Transcriptional assessment by microarray analysis and large-scale meta-analysis of the metabolic capacity of cardiac and skeletal muscle tissues to cope with reduced nutrient availability in Gilthead Sea Bream (Sparus aurata L.).Marine biotechnology (New York, N.Y.) · 2014Pooled it
- Gilthead seabream (Sparus aurata) response to three music stimuli (Mozart--"Eine Kleine Nachtmusik," Anonymous--"Romanza," Bach--"Violin Concerto No. 1") and white noise under recirculating water conditions.Fish physiology and biochemistry · 2015Trial
- Post-feeding Molecular Responses of Cobia (Rachycentron canadum): RNA-Sequencing as a Tool to Evaluate Postprandial Effects in Hepatic Lipid Metabolism.Marine biotechnology (New York, N.Y.) · 2023Article
- Comparative Transcriptome Analysis Identified Key Pathways and Genes Regulating Differentiated Stigma Color in Melon (International journal of molecular sciences · 2022Article
- Molecular Mechanism Based on Histopathology, Antioxidant System and Transcriptomic Profiles in Heat Stress Response in the Gills of Japanese Flounder.International journal of molecular sciences · 2022Article
- Transcriptomic Profiling and Microsatellite Identification in Cobia (Rachycentron canadum), Using High-Throughput RNA Sequencing.Marine biotechnology (New York, N.Y.) · 2022Article
- De novo assembly, transcriptome characterization and marker discovery in Indian major carp, Labeo rohita through pyrosequencing.Genetica · 2022Article
- Transcriptome analysis of flathead grey mullet (Frontiers in physiology · 2022Article
- Transcriptomic Analysis ofFrontiers in plant science · 2022Article
- Cross-Talk Between Intestinal Microbiota and Host Gene Expression in Gilthead Sea Bream (Frontiers in physiology · 2021Article
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- Hints on T cell responses in a fish-parasite model: Enteromyxum leei induces differential expression of T cell signature molecules depending on the organ and the infection status.Parasites & vectors · 2018Article
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- Ghrelin and Its Receptors in Gilthead Sea Bream: Nutritional Regulation.Frontiers in endocrinology · 2018Article
- Genetic Characterization of the FishFrontiers in genetics · 2018Article
- Article
- The circadian transcriptome of marine fish (Sparus aurata) larvae reveals highly synchronized biological processes at the whole organism level.Scientific reports · 2017Article
- Article
- Trans-omics approaches used to characterise fish nutritional biorhythms in leopard coral grouper (Plectropomus leopardus).Scientific reports · 2017Article
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Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe gilthead sea bream (Sparus aurata) is the main fish species cultured in the Mediterranean area and constitutes an interesting model of research. Nevertheless, transcriptomic and genomic data are still scarce for this highly valuable species. A transcriptome database was constructed by de novo assembly of gilthead sea bream sequences derived from public repositories of mRNA and collections of expressed sequence tags together with new high-quality reads from five cDNA 454 normalized libraries of skeletal muscle (1), intestine (1), head kidney (2) and blood (1).
resultsSequencing of the new 454 normalized libraries produced 2,945,914 high-quality reads and the de novo global assembly yielded 125,263 unique sequences with an average length of 727 nt. Blast analysis directed to protein and nucleotide databases annotated 63,880 sequences encoding for 21,384 gene descriptions, that were curated for redundancies and frameshifting at the homopolymer regions of open reading frames, and hosted at http://www.nutrigroup-iats.org/seabreamdb. Among the annotated gene descriptions, 16,177 were mapped in the Ingenuity Pathway Analysis (IPA) database, and 10,899 were eligible for functional analysis with a representation in 341 out of 372 IPA canonical pathways. The high representation of randomly selected stickleback transcripts by Blast search in the nucleotide gilthead sea bream database evidenced its high coverage of protein-coding transcripts.
conclusionsThe newly assembled gilthead sea bream transcriptome represents a progress in genomic resources for this species, as it probably contains more than 75% of actively transcribed genes, constituting a valuable tool to assist studies on functional genomics and future genome projects.
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