A 44K microarray dataset of the changing transcriptome in developing Atlantic salmon (Salmo salar L.)

<p>Abstract</p> <p>Background</p> <p>Atlantic salmon (<it>Salmo salar </it>L.) is an environmentally and economically important organism and its gene content is reasonably well characterized. From a transcriptional standpoint, it is important to characterize the changes in gene expression over the course of unperturbed early development, from fertilization through to the parr stage.</p> <p>Findings</p> <p><it>S. salar </it>samples were taken at 17 time points from 2 to 89 days post fertilization. Total RNA was extracted and cRNA was synthesized and hybridized to a newly developed 44K oligo salmonid microarray platform. Quantified results were subjected to preliminary data analysis and submitted to NCBI's Gene Expression Omnibus (GEO). Data can be found under the GEO accession number GSE25938. <url>http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25938</url></p> <p>Conclusions</p> <p>Throughout the entire period of development, several thousand genes were found to be differentially regulated. This work represents the trancriptional characterization of a very large geneset that will be extremely valuable in further examination of the transcriptional changes in Atlantic salmon during the first few months of development. The expression profiles can help to annotate salmon genes in addition to being used as references against any number of experimental variables to which developing salmonids might be subjected.</p

Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome

<p>Abstract</p> <p>Background</p> <p>Salmonids are one of the most intensely studied fish, in part due to their economic and environmental importance, and in part due to a recent whole genome duplication in the common ancestor of salmonids. This duplication greatly impacts species diversification, functional specialization, and adaptation. Extensive new genomic resources have recently become available for Atlantic salmon (<it>Salmo salar</it>), but documentation of allelic versus duplicate reference genes remains a major uncertainty in the complete characterization of its genome and its evolution.</p> <p>Results</p> <p>From existing expressed sequence tag (EST) resources and three new full-length cDNA libraries, 9,057 reference quality full-length gene insert clones were identified for Atlantic salmon. A further 1,365 reference full-length clones were annotated from 29,221 northern pike (<it>Esox lucius</it>) ESTs. Pairwise d_N/d_Scomparisons within each of 408 sets of duplicated salmon genes using northern pike as a diploid out-group show asymmetric relaxation of selection on salmon duplicates.</p> <p>Conclusions</p> <p>9,057 full-length reference genes were characterized in <it>S. salar </it>and can be used to identify alleles and gene family members. Comparisons of duplicated genes show that while purifying selection is the predominant force acting on both duplicates, consistent with retention of functionality in both copies, some relaxation of pressure on gene duplicates can be identified. In addition, there is evidence that evolution has acted asymmetrically on paralogs, allowing one of the pair to diverge at a faster rate.</p

Genomic Resources for Sea Lice: Analysis of ESTs and Mitochondrial Genomes

Sea lice are common parasites of both farmed and wild salmon. Salmon farming constitutes an important economic market in North America, South America, and Northern Europe. Infections with sea lice can result in significant production losses. A compilation of genomic information on different genera of sea lice is an important resource for understanding their biology as well as for the study of population genetics and control strategies. We report on over 150,000 expressed sequence tags (ESTs) from five different species (Pacific Lepeophtheirus salmonis (49,672 new ESTs in addition to 14,994 previously reported ESTs), Atlantic L. salmonis (57,349 ESTs), Caligus clemensi (14,821 ESTs), Caligus rogercresseyi (32,135 ESTs), and Lernaeocera branchialis (16,441 ESTs)). For each species, ESTs were assembled into complete or partial genes and annotated by comparisons to known proteins in public databases. In addition, whole mitochondrial (mt) genome sequences of C. clemensi (13,440 bp) and C. rogercresseyi (13,468 bp) were determined and compared to L. salmonis. Both nuclear and mtDNA genes show very high levels of sequence divergence between these ectoparastic copepods suggesting that the different species of sea lice have been in existence for 37–113 million years and that parasitic association with salmonids is also quite ancient. Our ESTs and mtDNA data provide a novel resource for the study of sea louse biology, population genetics, and control strategies. This genomic information provides the material basis for the development of a 38K sea louse microarray that can be used in conjunction with our existing 44K salmon microarray to study host–parasite interactions at the molecular level. This report represents the largest genomic resource for any copepod species to date

GO Trimming: Systematically reducing redundancy in large Gene Ontology datasets

<p>Abstract</p> <p>Background</p> <p>The increased accessibility of gene expression tools has enabled a wide variety of experiments utilizing transcriptomic analyses. As these tools increase in prevalence, the need for improved standardization in processing and presentation of data increases, as does the need to guard against interpretation bias. Gene Ontology (GO) analysis is a powerful method of interpreting and summarizing biological functions. However, while there are many tools available to investigate GO enrichment, there remains a need for methods that directly remove redundant terms from enriched GO lists that often provide little, if any, additional information.</p> <p>Findings</p> <p>Here we present a simple yet novel method called GO Trimming that utilizes an algorithm designed to reduce redundancy in lists of enriched GO categories. Depending on the needs of the user, this method can be performed with variable stringency. In the example presented here, an initial list of 90 terms was reduced to 54, eliminating 36 largely redundant terms. We also compare this method to existing methods and find that GO Trimming, while simple, performs well to eliminate redundant terms in a large dataset throughout the depth of the GO hierarchy.</p> <p>Conclusions</p> <p>The GO Trimming method provides an alternative to other procedures, some of which involve removing large numbers of terms prior to enrichment analysis. This method should free up the researcher from analyzing overly large, redundant lists, and instead enable the concise presentation of manageable, informative GO lists. The implementation of this tool is freely available at: <url>http://lucy.ceh.uvic.ca/go_trimming/cbr_go_trimming.py</url></p

Genomics of sablefish (Anoplopoma fimbria): expressed genes, mitochondrial phylogeny, linkage map and identification of a putative sex gene

Abstract Background The sablefish (order: Scorpaeniformes) is an economically important species in commercial fisheries of the North Pacific and an emerging species in aquaculture. Aside from a handful of sequences in NCBI and a few published microsatellite markers, little is known about the genetics of this species. The development of genetic tools, including polymorphic markers and a linkage map will allow for the successful development of future broodstock and mapping of phenotypes of interest. The significant sexual dimorphism between females and males makes a genetic test for early identification of sex desirable. Results A full mitochondrial genome is presented and the resulting phylogenetic analysis verifies the placement of the sablefish within the Scorpaeniformes. Nearly 35,000 assembled transcript sequences are used to identify genes and obtain polymorphic SNP and microsatellite markers. 360 transcribed polymorphic loci from two sablefish families produce a map of 24 linkage groups. The sex phenotype maps to sablefish LG14 of the male map. We show significant conserved synteny and conservation of gene-order between the threespine stickleback Gasterosteus aculeatus and sablefish. An additional 1843 polymorphic SNP markers are identified through next-generation sequencing techniques. Sex-specific markers and sequence insertions are identified immediately upstream of the gene gonadal-soma derived factor (gsdf), the master sex determinant locus in the medaka species Oryzias luzonensis. Conclusions The first genomic resources for sablefish provide a foundation for further studies. Over 35,000 transcripts are presented, and the genetic map represents, as far as we can determine, the first linkage map for a member of the Scorpaeniformes. The observed level of conserved synteny and comparative mapping will allow the use of the stickleback genome in future genetic studies on sablefish and other related fish, particularly as a guide to whole-genome assembly. The identification of sex-specific insertions immediately upstream of a known master sex determinant implicates gsdf as an excellent candidate for the master sex determinant for sablefish