The molecular evolution of spiggin nesting glue in sticklebacks.

Gene duplication and subsequent divergence can lead to the evolution of new functions and lineage-specific traits. In sticklebacks, the successive duplication of a mucin gene (MUC19) into a tandemly arrayed, multigene family has enabled the production of copious amounts of 'spiggin', a secreted adhesive protein essential for nest construction. Here, we examine divergence between spiggin genes among three-spined sticklebacks (Gasterosteus aculeatus) from ancestral marine and derived freshwater populations, and propose underpinning gene duplication mechanisms. Sanger sequencing revealed substantial diversity among spiggin transcripts, including alternatively spliced variants and interchromosomal spiggin chimeric genes. Comparative analysis of the sequenced transcripts and all other spiggin genes in the public domain support the presence of three main spiggin lineages (spiggin A, spiggin B and spiggin C) with further subdivisions within spiggin B (B1, B2) and spiggin C (C1, C2). Spiggin A had diverged least from the ancestral MUC19, while the spiggin C duplicates had diversified most substantially. In silico translations of the spiggin gene open reading frames predicted that spiggins A and B are secreted as long mucin-like polymers, while spiggins C1 and C2 are secreted as short monomers, with putative antimicrobial properties. We propose that diversification of duplicated spiggin genes has facilitated local adaptation of spiggin to a range of aquatic habitats.

Swarms of diversity at the gene cox1 in Antarctic krill.

The Antarctic krill, Euphausia superba, is an abundant and key species found in the Southern Ocean that forms dense, discrete swarms. Despite over three decades of research on Antarctic krill, the genetics of individual swarms is yet to be specifically investigated. In this study, we address the genetic diversity, population structure and demographic history of nine Antarctic krill swarms by sequencing 1173 bases of the gene cytochrome c oxidase subunit I (cox1, COI) from 504 individuals. Both haplotype diversity (h=0.9974-1.0000) and nucleotide diversity (pi=0.010275-0.011537) of Antarctic krill swarm samples was consistently high compared with populations of other species reported in the literature. Analysis of molecular variance did not show any significant genetic structure, thus implying that the sampled swarms do not appear to reflect discrete genetic units. Fu's Fs and Bayesian Skyride analyses provided strong evidence for a large increase in the population size of Antarctic krill, or selection favouring a particular mitochondrial lineage, within the last few 100,000 years (Pleistocene). The swarm-level results presented in this study not only further our understanding of Antarctic krill biology but, because of the economical importance of this species, also provide data to consider for future krill stock management.

Stability of RNA isolated from post-mortem tissues of Atlantic salmon (Salmo salar L.).

Studies of post-mortem interval on the stability of RNA from a number of various mammals have shown RNA to be stable for between 24 and 48 h following death. As yet there have been no studies looking at RNA stability in post-mortem tissues of poikilothermic fish. Brain, kidney, liver and muscle were collected from Atlantic salmon (Salmo salar) parr and samples of each tissue were placed into RNAlatertrade mark after 0-24 h post-mortem storage at room temperature. Electrophoretic analysis of the total RNA showed degradation of ribosomal RNA only in muscle from 8 h onwards. Probing of northern blots with beta-actin showed that, in the brain, beta-actin mRNA was stable for 24 h post-mortem but degradation of mRNA was observed after 8 h with the kidney and liver and after 4 h with the muscle. Expression of the weakly expressed thyroid hormone receptor beta (TRbeta) was detected by reverse transcriptase polymerase chain reaction (RT-PCR) in all tissues up to 24 h post-mortem although a reduction in PCR product was observed after 8 h with muscle and 24 h with kidney. Analysis with an Agilent 2100 Bioanalyzer showed that the RNA integrity number (RIN) of brain total RNA remained constant for 8 h post-mortem with only a small fall at 24 h post-mortem. The RINs of the remaining tissues indicated degradation at 8 h post-mortem with kidney and muscle and at 24 hours post-mortem with liver. Taken together these findings show that degradation of Atlantic salmon RNA is tissue dependent but stable for at least one hour post-mortem.

A description of the origins, design and performance of the TRAITS-SGP Atlantic salmon Salmo salar L. cDNA microarray.

The origins, design, fabrication and performance of an Atlantic salmon microarray are described. The microarray comprises 16 950 Atlantic salmon-derived cDNA features, printed in duplicate and mostly sourced from pre-existing expressed sequence tag (EST) collections [SALGENE and salmon genome project (SGP)] but also supplemented with cDNAs from suppression subtractive hybridization libraries and candidate genes involved in immune response, protein catabolism, lipid metabolism and the parr-smolt transformation. A preliminary analysis of a dietary lipid experiment identified a number of genes known to be involved in lipid metabolism. Significant fold change differences (as low as 1.2x) were apparent from the microarray analysis and were confirmed by quantitative real-time polymerase chain reaction analysis. The study also highlighted the potential for obtaining artefactual expression patterns as a result of cross-hybridization of similar transcripts. Examination of the robustness and sensitivity of the experimental design employed demonstrated the greater importance of biological replication over technical (dye flip) replication for identification of a limited number of key genes in the studied system. The TRAITS (TRanscriptome Analysis of Important Traits of Salmon)-salmon genome project microarray has been proven, in a number of studies, to be a powerful tool for the study of key traits of Atlantic salmon biology. It is now available for use by researchers in the wider scientific community.