An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar)

BACKGROUND: The Atlantic salmon is an important aquaculture species and a very interesting species biologically, since it spawns in fresh water and develops through several stages before becoming a smolt, the stage at which it migrates to the sea to feed. The dramatic change of habitat requires physiological, morphological and behavioural changes to prepare the salmon for its new environment. These changes are called the parr-smolt transformation or smoltification, and pre-adapt the salmon for survival and growth in the marine environment. The development of hypo-osmotic regulatory ability plays an important part in facilitating the transition from rivers to the sea. The physiological mechanisms behind the developmental changes are largely unknown. An understanding of the transformation process will be vital to the future of the aquaculture industry. A knowledge of which genes are expressed prior to the smoltification process is an important basis for further studies. RESULTS: In all, 2974 unique sequences, consisting of 779 contigs and 2195 singlets, were generated for Atlantic salmon from two cDNA libraries constructed from the gills and the intestine, accession numbers [Genbank: CK877169-CK879929, CK884015-CK886537 and CN181112-CN181464]. Nearly 50% of the sequences were assigned putative functions because they showed similarity to known genes, mostly from other species, in one or more of the databases used. The Swiss-Prot database returned significant hits for 1005 sequences. These could be assigned predicted gene products, and 967 were annotated using Gene Ontology (GO) terms for molecular function, biological process and/or cellular component, employing an annotation transfer procedure. CONCLUSION: This paper describes the construction of two cDNA libraries from pre-smolt Atlantic salmon (Salmo salar) and the subsequent EST sequencing, clustering and assigning of putative function to 1005 genes expressed in the gills and/or intestine

Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource

Background To identify as many different transcripts/genes in the Atlantic salmon genome as possible, it is crucial to acquire good cDNA libraries from different tissues and developmental stages, their relevant sequences (ESTs or full length sequences) and attempt to predict function. Such libraries allow identification of a large number of different transcripts and can provide valuable information on genes expressed in a particular tissue at a specific developmental stage. This data is important in constructing a microarray chip, identifying SNPs in coding regions, and for future identification of genes in the whole genome sequence. An important factor that determines the usefulness of generated data for biologists is efficient data access. Public searchable databases play a crucial role in providing such service. Description Twenty-three Atlantic salmon cDNA libraries were constructed from 15 tissues, yielding nearly 155,000 clones. From these libraries 58,109 ESTs were generated, of which 57,212 were used for contig assembly. Following deletion of mitochondrial sequences 55,118 EST sequences were submitted to GenBank. In all, 20,019 unique sequences, consisting of 6,424 contigs and 13,595 singlets, were generated. The Norwegian Salmon Genome Project Database has been constructed and annotation performed by the annotation transfer approach. Annotation was successful for 50.3% (10,075) of the sequences and 6,113 sequences (30.5%) were annotated with Gene Ontology terms for molecular function, biological process and cellular component. Conclusion We describe the construction of cDNA libraries from juvenile/pre-smolt Atlantic salmon (Salmo salar), EST sequencing, clustering, and annotation by assigning putative function to the transcripts. These sequences represents 97% of all sequences submitted to GenBank from the pre-smoltification stage. The data has been grouped into datasets according to its source and type of annotation. Various data query options are offered including searches on function assignments and Gene Ontology terms. Data delivery options include summaries for the datasets and their annotations, detailed self-explanatory annotations, and access to the original BLAST results and Gene Ontology annotation trees. Potential presence of a relatively high number of immune-related genes in the dataset was shown by annotation searches

Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon (<it>Salmo salar</it>) in a searchable data resource

Abstract Background To identify as many different transcripts/genes in the Atlantic salmon genome as possible, it is crucial to acquire good cDNA libraries from different tissues and developmental stages, their relevant sequences (ESTs or full length sequences) and attempt to predict function. Such libraries allow identification of a large number of different transcripts and can provide valuable information on genes expressed in a particular tissue at a specific developmental stage. This data is important in constructing a microarray chip, identifying SNPs in coding regions, and for future identification of genes in the whole genome sequence. An important factor that determines the usefulness of generated data for biologists is efficient data access. Public searchable databases play a crucial role in providing such service. Description Twenty-three Atlantic salmon cDNA libraries were constructed from 15 tissues, yielding nearly 155,000 clones. From these libraries 58,109 ESTs were generated, of which 57,212 were used for contig assembly. Following deletion of mitochondrial sequences 55,118 EST sequences were submitted to GenBank. In all, 20,019 unique sequences, consisting of 6,424 contigs and 13,595 singlets, were generated. The Norwegian Salmon Genome Project Database has been constructed and annotation performed by the annotation transfer approach. Annotation was successful for 50.3% (10,075) of the sequences and 6,113 sequences (30.5%) were annotated with Gene Ontology terms for molecular function, biological process and cellular component. Conclusion We describe the construction of cDNA libraries from juvenile/pre-smolt Atlantic salmon (Salmo salar), EST sequencing, clustering, and annotation by assigning putative function to the transcripts. These sequences represents 97% of all sequences submitted to GenBank from the pre-smoltification stage. The data has been grouped into datasets according to its source and type of annotation. Various data query options are offered including searches on function assignments and Gene Ontology terms. Data delivery options include summaries for the datasets and their annotations, detailed self-explanatory annotations, and access to the original BLAST results and Gene Ontology annotation trees. Potential presence of a relatively high number of immune-related genes in the dataset was shown by annotation searches.</p

Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon () in a searchable data resource-0

<p><b>Copyright information:</b></p><p>Taken from "Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon () in a searchable data resource"</p><p>http://www.biomedcentral.com/1471-2164/8/209</p><p>BMC Genomics 2007;8():209-209.</p><p>Published online 2 Jul 2007</p><p>PMCID:PMC1913521.</p><p></p> best annotation hits" is available for singlets. Other options are "Contigs length and number of reads" and "Distribution of average length and number of reads in contigs". The Clustered data summary provides a current snapshot of the SGP database

Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon () in a searchable data resource-3

<p><b>Copyright information:</b></p><p>Taken from "Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon () in a searchable data resource"</p><p>http://www.biomedcentral.com/1471-2164/8/209</p><p>BMC Genomics 2007;8():209-209.</p><p>Published online 2 Jul 2007</p><p>PMCID:PMC1913521.</p><p></p>ts, [GO: Molecular Function], [GO: Biological Process] and [GO: Cellular Component]. The annotation was performed for contig and singlet sequences. Complete SGP GO-GOA annotation is available at SGP data resource > Data and results > Annotations > SGP full annotation > GO term tables

Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon () in a searchable data resource-2

<p><b>Copyright information:</b></p><p>Taken from "Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon () in a searchable data resource"</p><p>http://www.biomedcentral.com/1471-2164/8/209</p><p>BMC Genomics 2007;8():209-209.</p><p>Published online 2 Jul 2007</p><p>PMCID:PMC1913521.</p><p></p>ptions, libraries and annotations. When a match occurs in any of these data, all three data categories are shown in results. The "Matches in datasets" display provides access to a subset of contigs, singlets and annotations selected in the search. The "Annotations best hits" display is the same for the Clustered data datasets menu and database search results. Clustered data datasets menu provides a current snapshot of the SGP database