Sardina pilchardus isolate:SPI-2018
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA481265 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR7535145_1.fastq.gz | Fastqsanger.gz | |||
| SRR7535145_2.fastq.gz | Fastqsanger.gz |
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Project description:RNA-Seq of ten tissues of Sardina pilchardus
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Project description:The European sardine (Sardina pilchardus Walbaum, 1792) is culturally and economically important throughout its distribution. Monitoring studies of sardine populations report an alarming decrease in stocks due to overfishing and environmental change, which has resulted in historically low captures along the Iberian Atlantic coast. Important biological and ecological features such as population diversity, structure, and migratory patterns can be addressed with the development and use of genomics resources. The genome of a single female individual was sequenced using Illumina HiSeq X Ten 10x Genomics linked reads, generating 113.8 gigabase pairs of data. Three draft genomes were assembled: 2 haploid genomes with a total size of 935 megabase pairs (N50 103 kilobase pairs) each, and a consensus genome of total size 950 megabase pairs (N50 97 kilobase pairs). The genome completeness assessment captured 84% of Actinopterygii Benchmarking Universal Single-Copy Orthologs. To obtain a more complete analysis, the transcriptomes of 11 tissues were sequenced to aid the functional annotation of the genome, resulting in 40,777 genes predicted. Variant calling on nearly half of the haplotype genome resulted in the identification of >2.3 million phased single-nucleotide polymorphisms with heterozygous loci. A draft genome was obtained, despite a high level of sequence repeats and heterozygosity, which are expected genome characteristics of a wild sardine. The reference sardine genome and respective variant data will be a cornerstone resource of ongoing population genomics studies to be integrated into future sardine stock assessment modelling to better manage this valuable resource.
| S-EPMC6528745 | biostudies-literature
Project description:European sardine or pilchard is a planktonic small pelagic fish present from the North Sea in Europe to the coast of Senegal in the North of Africa, and across the Mediterranean sea to the Black Sea. Ecologically, sardines are an intermediary link in the trophic network, preying on plankton and being predated by larger fishes, marine mammals, and seabirds. This species is of great nutritional and economic value as a cheap but rich source of protein and fat. It is either consumed directly by humans or fed as fishmeal for aquaculture and farm animals. Despite its importance in the food basket, little is known about the molecular mechanisms involved in protein and lipid synthesis in this species. We collected nine tissues of Sardina pilchardus and reconstructed the transcriptome. In all, 198,597 transcripts were obtained, from which 68,031 are protein-coding. Quality assessment of the transcriptome was performed by back-mapping reads to the transcriptome and by searching for Single Copy Orthologs. Additionally, Gene Ontology and KEGG annotations were retrieved for most of the protein-coding genes. Finally, each library was quantified in terms of Transcripts per Million to disclose their expression patterns.
| S-EPMC8609138 | biostudies-literature
Project description:Sardina pilchardus (sardine) genome assembly, fSarPil1
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Project description:Sardina pilchardus (sardine), genomic and transcriptomic data
| PRJEB67416 | ENA
Project description:Sardina pilchardus (sardine) genome assembly, fSarPil1, alternate haplotype
| PRJEB71084 | ENA
Project description:BackgroundWith the present difficulties in the conservation of sardines in the North Atlantic, it is important to investigate the local ecological knowledge (LEK) of fishermen about the biology and ecology of these fish. The ethnoecological data of European pilchard provided by local fishermen can be of importance for the management and conservation of this fishery resource. Thus, the present study recorded the ethnoecological knowledge of S. pilchardus in the traditional fishing community of Peniche, Portugal.MethodsThis study was based on 87 semi-structured interviews conducted randomly from June to September 2016 in Peniche. The interview script contained two main points: Profile of fishermen and LEK on European pilchard. The ethnoecological data of sardines were compared with the scientific literature following an emic-etic approach. Data collected also were also analysed following the union model of the different individual competences and carefully explored to guarantee the objectivity of the study.ResultsThe profile of the fishermen was investigated and measured. Respondents provided detailed informal data on the taxonomy, habitat, behaviour, migration, development, spawning and fat accumulation season of sardines that showed agreements with the biological data already published on the species. The main uses of sardines by fishermen, as well as beliefs and food taboos have also been mentioned by the local community.ConclusionsThe generated ethnoecological data can be used to improve the management of this fishery resource through an adaptive framework among the actors involved, in addition to providing data that can be tested in further ecological studies. Therefore, this local knowledge may have the capacity to contribute to more effective conservation actions for sardines in Portugal.
| S-EPMC5599890 | biostudies-literature