The life cycle of the Atlantic salmon (Salmo salar) involves a period of 1 to 3 years in freshwater followed by migration to the sea where the salmon undergoes rapid growth. In preparation for the marine environment, while still in freshwater, the salmon undergo a transformation from a freshwater dwelling parr to a saltwater adapted smolt, a process known as smoltification. The Atlantic salmon Transcriptome Analysis of Important Traits of Salmon/Salmon Genome Project (TRAITS/SGP) cDNA microarray was used to investigate how gene expression alters during smoltification. Genes differentially expressed during smoltification were identified by comparing gene expression profiles in smolt brain, gill, and kidney tissue samples with those of parr. Of the three tissues investigated, the number of differentially expressed genes was the greatest in gill. Many of the differentially expressed genes could be assigned to one of four main categories: growth, metabolism, oxygen transport, and osmoregulation. Quantitative polymerase chain reaction successfully confirmed the differential expression of seven of the upregulated genes. The TRAITS/SGP cDNA microarray was used to successfully demonstrate for the first time how gene expression mediates smoltification in the Atlantic salmon. Changes in gene expression observed in this study reflected the physiological and biochemical changes recorded by previous studies describing the parr-smolt transformation. This study significantly increases our knowledge of smoltification and will benefit future studies in this area of research.

Adaptive gene flow is a consequential phenomenon across all kingdoms. Although recognition is increasing, there is no study showing that bidirectional gene flow mediates adaptation at loci that manage core processes. We previously discovered concerted molecular changes among interacting members of the meiotic machinery controlling crossover number upon adaptation to whole-genome duplication (WGD) in Arabidopsis arenosa. Here we conduct a population genomic study to test the hypothesis that adaptation to WGD has been mediated by adaptive gene flow between A. arenosa and A. lyrata. We find that A. lyrata underwent WGD more recently than A. arenosa, suggesting that pre-adapted alleles have rescued nascent A. lyrata, but we also detect gene flow in the opposite direction at functionally interacting loci under the most extreme levels of selection. These data indicate that bidirectional gene flow allowed for survival after WGD, and that the merger of these species is greater than the sum of their parts.

BackgroundAll crustaceans periodically moult to renew their exoskeleton. In krill this involves partial digestion and resorption of the old exoskeleton and synthesis of new cuticle. Molecular events that underlie the moult cycle are poorly understood in calcifying crustaceans and even less so in non-calcifying organisms such as krill. To address this we constructed an Antarctic krill cDNA microarray in order to generate gene expression profiles across the moult cycle and identify possible activation pathways.ResultsA total of 26 different cuticle genes were identified that showed differential gene expression across the moult cycle. Almost all cuticle genes were up regulated during premoult and down regulated during late intermoult. There were a number of transcripts with significant sequence homology to genes potentially involved in the synthesis, breakdown and resorption of chitin. During early premoult glutamine synthetase, a gene involved in generating an amino acid used in the synthesis of glucosamine, a constituent of chitin, was up regulated more than twofold. Mannosyltransferase 1, a member of the glycosyltransferase family of enzymes that includes chitin synthase was also up regulated during early premoult. Transcripts homologous to a β-N-acetylglucosaminidase (β-NAGase) precursor were expressed at a higher level during late intermoult (prior to apolysis) than during premoult. This observation coincided with the up regulation during late intermoult, of a coatomer subunit epsilon involved in the production of vesicles that maybe used to transport the β-NAGase precursors into the exuvial cleft. Trypsin, known to activate the β-NAGase precursor, was up regulated more than fourfold during premoult. The up regulation of a predicted oligopeptide transporter during premoult may allow the transport of chitin breakdown products across the newly synthesised epi- and exocuticle layers.ConclusionWe have identified many genes differentially expressed across the moult cycle of krill that correspond with known phenotypic structural changes. This study has provided a better understanding of the processes involved in krill moulting and how they may be controlled at the gene expression level.

Adaptive gene flow is a consequential evolutionary phenomenon across all kingdoms of life.While recognition of widespread gene flow is growing, examples lack of bidirectional gene flow mediating adaptations at specific loci that cooperatively manage core cellular processes.We previously described concerted molecular changes among physically interacting members of the meiotic machinery controlling crossover number and distribution upon adaptation to whole genome duplication (WGD) in Arabidopsis arenosa. Here we conduct a population genomic study to test the hypothesis that escape from extinction following the trauma of WGD was mediated by adaptive gene flow between A. arenosa and its congener Arabidopsis lyrata. We show that A. lyrata underwent WGD more recently than A. arenosa, indicating that specific pre-adapted alleles donated by A. arenosa underwent selection and rescued the nascent A. lyrata tetraploids from early extinction. At the same time, we detect specific signals of gene flow in the opposite direction at other functionally interacting gene coding loci that display dramatic signatures of selective sweep in both tetraploid species. Cytological analysis shows that A. lyrata tetraploids exhibit similar levels of meiotic stability as A. arenosa tetraploids. Taken together, these data indicate that bidirectional gene flow allowed for an escape from extinction of the young autopolyploids, especially the rare tetraploid A. lyrata, and suggest that the merger of these species is greater than the sum of their parts.

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 1Á2Â) 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.

Secombes CJ. Interferon type I and type II responses in an Atlantic salmon (Salmo salar) SHK-1 cell line by the salmon TRAITS/SGP microarray. Physiol Genomics 32: [33][34][35][36][37][38][39][40][41][42][43][44] 2007. First published September 5, 2007; doi:10.1152/physiolgenomics.00064.2007 RNA was hybridized to an Atlantic salmon cDNA microarray (salmon 17K feature TRAITS/SGP array) in order to assess differential gene expression in response to IFN exposure. For IFN I and II, 47 and 72 genes were stimulated, respectively; most genes were stimulated by a single IFN type, but some were affected by both IFNs, indicating coregulation of the IFN response in fish. Real-time PCR analysis was employed to confirm the microarray results for selected differentially expressed genes in both a cell line and primary leukocyte cultures. transcriptome; immune; fish INTERFERONS (IFNs) are cytokines that have key roles in the regulation of both innate and adaptive immune responses. They exhibit a diverse range of activities including antiviral, antitumor, and immunomodulatory roles (4). There are three types of IFN known in mammals (I-III); however, to date only types I and II have been identified in fish. Type I consists of a large number of related proteins including the ␣-and ␤-IFNs, which function principally in the antiviral response (55). Type II IFN is a single protein (IFN-␥) that originally was described for its macrophage-activating activity (59). The two families of IFN molecules are not structurally related but share similarities in their receptors and mechanisms of gene activation (41, 55). Type I and II IFNs produce their effect via different heterodimer cell surface receptors. Once IFN is bound to the receptor, signal transduction leads to activation of IFN-responsive genes via conserved signal transduction pathways leading to change of function of the cell (53). It is estimated in mammals that up to 200 or more genes may be affected by IFN stimulation (13). IFN-␥ signal transduction is primarily via the Janus-activated kinase (JAK)-signal transducer and activator of transcription (STAT) pathway. Here JAK1 associates with JAK2 on stimulation and causes the phosphorylation of STAT1. Two STAT1 molecules dimerize to form a homodimer, which then binds to specific consensus sequences in the promoter of IFN-␥-responsive genes at specific ␥-IFN activation site (GAS) elements, resulting in initiation of transcription. Type I IFN molecules follow a similar pathway, but there are two different kinases that are associated with the receptor. In this case JAK1 and tyrosine kinase 2 (TYK2) are activated and phosphorylate both STAT1 and STAT2, which form a heterodimer that in combination with interferon regulatory factor 9 forms a trimer that binds to interferon-stimulated response elements (IRSE) and subsequently induces transcription (reviewed in Refs. 41, 55). In mammals IFN type I can stimulate genes via both IRSE and GAS elements in the promoter, whereas IFN-␥ does not usually act via IRSE (41, 55), although many IFN-respon...

In this study we performed a genotype-phenotype association analysis of meiotic stability in 10 autotetraploid Arabidopsis lyrata and A . lyrata/A . arenosa hybrid populations collected from the Wachau region and East Austrian Forealps. The aim was to determine the effect of eight meiosis genes under extreme selection upon adaptation to whole genome duplication. Individual plants were genotyped by high-throughput sequencing of the eight meiosis genes ( ASY1 , ASY3 , PDS5b , PRD3 , REC8 , SMC3 , ZYP1a/b ) implicated in synaptonemal complex formation and phenotyped by assessing meiotic metaphase I chromosome configurations. Our results reveal that meiotic stability varied greatly (20–100%) between individual tetraploid plants and associated with segregation of a novel ASYNAPSIS3 ( ASY3 ) allele derived from A . lyrata . The ASY3 allele that associates with meiotic stability possesses a putative in-frame tandem duplication (TD) of a serine-rich region upstream of the coiled-coil domain that appears to have arisen at sites of DNA microhomology. The frequency of multivalents observed in plants homozygous for the ASY3 TD haplotype was significantly lower than in plants heterozygous for ASY3 TD/ND (non-duplicated) haplotypes. The chiasma distribution was significantly altered in the stable plants compared to the unstable plants with a shift from proximal and interstitial to predominantly distal locations. The number of HEI10 foci at pachytene that mark class I crossovers was significantly reduced in a plant homozygous for ASY3 TD compared to a plant heterozygous for ASY3 ND/TD . Fifty-eight alleles of the 8 meiosis genes were identified from the 10 populations analysed, demonstrating dynamic population variability at these loci. Widespread chimerism between alleles originating from A . lyrata/A . arenosa and diploid/tetraploids indicates that this group of rapidly evolving genes may provide precise adaptive control over meiotic recombination in the tetraploids, the very process that gave rise to them.

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