Abstract
BackgroundThe Atlantic cod is an ecologically and economically important North Atlantic fish species and also an emerging aquaculture species. To study gene expression in Atlantic cod embryonic stem (ES) cells, our goal was to generate and analyze expressed sequence tags (ESTs) from an ES cell cDNA library of mRNA consisting of approximately 3,900 ESTs.ResultsWe sequenced 3,935 EST clones using a directional cDNA library made from pooled ES cells harvested at the blastula stage. Quality filtering of these ESTs allowed identification of 2,719 high-quality sequences with an average length of 442 bp containing 368 contigs and 1,276 singletons (1,644 unique sequences). BLASTX searches produced 889 significant (E-value < 10-3) hits, of which 698 (42.5%) were annotated with Gene Ontology terms (E-value < 10-6). The number of unknown unique sequences was 946 (57.5%). All the high-quality EST sequences have been deposited in GenBank (GenBank: 2,719 sequences in UniGene library dbEST id: 22,021). Gene discovery and annotations are presented and discussed.ConclusionThis set of ESTs represents one of the first attempts to describe mRNA in ES cells from a marine cold-water fish species, and provides a basis for gene expression studies of Atlantic cod ES cells.
Highlights
The Atlantic cod is an ecologically and economically important North Atlantic fish species and an emerging aquaculture species
Sampling of cells RNA harvested from embryonic stem (ES) cells was used for cDNA library construction
Cluster analysis assembled the 2,719 high-quality expressed sequence tags (ESTs) into 368 contigs and 1,276 singletons (1,644 unique sequences). 42.5% (698) of the 1,644 unique sequences were annotated to known genes using BLASTX with an e-value cut-off of 10-3 and an annotation cut-off of 10-6 with the Blast2GO software
Summary
The Atlantic cod is an ecologically and economically important North Atlantic fish species and an emerging aquaculture species. To study gene expression in Atlantic cod embryonic stem (ES) cells, our goal was to generate and analyze expressed sequence tags (ESTs) from an ES cell cDNA library of mRNA consisting of approximately 3,900 ESTs. Embryonic stem (ES) cells in culture and their development into different lineages is a unique model system that provide means to identify extracellular factors that influence embryonic cell differentiation and proliferation. Specific transcription factors activate the expression of genes that are required for each cell lineage. ES and embryoid bodies (partly differentiated cells) can be utilized to identify and characterize factors or genes including nutrients, growth factors and hormones that may affect cell proliferation, lineage differentiation and the expression of specific genes and proteins during developmental differentiation. MRNA in oocytes and early blastocyte embryos are thought to be exclusively of maternal origin; expression of embryonic genes occurs later, at the late-blastula or gastrula stage, the exact time for this transition varies between species [2,3,4,5]
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call