The Atlantic salmon genome provides insights into rediploidization.

The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.

Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture.

We describe an emerging initiative - the 'Functional Annotation of All Salmonid Genomes' (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.

Chromosomal organization of four classes of repetitive DNA sequences in killifish Orestias ascotanensis Parenti, 1984 (Cyprinodontiformes, Cyprinodontidae).

Orestias Valenciennes, 1839 is a genus of freshwater fish endemic to the South American Altiplano. Cytogenetic studies of these species have focused on conventional karyotyping. The aim of this study was to use classical and molecular cytogenetic methods to identify the constitutive heterochromatin distribution and chromosome organization of four classes of repetitive DNA sequences (histone H3 DNA, U2 snRNA, 18S rDNA and 5S rDNA) in the chromosomes of O. ascotanensis Parenti, 1984, an endemic species restricted to the Salar de Ascotán in the Chilean Altiplano. All individuals analyzed had a diploid number of 48 chromosomes. C-banding identified constitutive heterochromatin mainly in the pericentromeric region of most chromosomes, especially a GC-rich heterochromatic block of the short arm of pair 3. FISH assay with an 18S probe confirmed the location of the NOR in pair 3 and revealed that the minor rDNA cluster occurs interstitially on the long arm of pair 2. Dual FISH identified a single block of U2 snDNA sequences in the pericentromeric regions of a subtelocentric chromosome pair, while histone H3 sites were observed as small signals scattered in throughout the all chromosomes. This work represents the first effort to document the physical organization of the repetitive fraction of the Orestias genome. These data will improve our understanding of the chromosomal evolution of a genus facing serious conservation problems.

RNA sequencing to study gene expression and SNP variations associated with growth in zebrafish fed a plant protein-based diet.

The objectives of this study were to measure gene expression in zebrafish and then identify SNP to be used as potential markers in a growth association study. We developed an approach where muscle samples collected from low- and high-growth fish were analyzed using RNA-Sequencing (RNA-seq), and SNP were chosen from the genes that were differentially expressed between the low and high groups. A population of 24 families was fed a plant protein-based diet from the larval to adult stages. From a total of 440 males, 5 % of the fish from both tails of the weight gain distribution were selected. Total RNA was extracted from individual muscle of 8 low-growth and 8 high-growth fish. Two pooled RNA-Seq libraries were prepared for each phenotype using 4 fish per library. Libraries were sequenced using the Illumina GAII Sequencer and analyzed using the CLCBio genomic workbench software. One hundred and twenty-four genes were differentially expressed between phenotypes (p value < 0.05 and FDR < 0.2). From these genes, 164 SNP were selected and genotyped in 240 fish samples. Marker-trait analysis revealed 5 SNP associated with growth in key genes (Nars, Lmod2b, Cuzd1, Acta1b, and Plac8l1). These genes are good candidates for further growth studies in fish and to consider for identification of potential SNPs associated with different growth rates in response to a plant protein-based diet.

Growth response and expression of muscle growth-related candidate genes in adult zebrafish fed plant and fishmeal protein-based diets.

The main objective of this study was to examine the effects of a plant protein- vs. fishmeal-based diet on growth response in a population of 24 families, as well as expression of growth-related genes in the muscle of adult zebrafish (Danio rerio). Each family was split to create two fish populations with similar genetic backgrounds, and the fish were fed either fishmeal (FM diet) or plant protein (PP diet) as the unique protein source in their diets from 35 to 98 days postfertilization (dpf). To understand the effect of the PP diet on gene expression, individuals from three families, representative of the mean weight in both populations, were selected. To understand the effect of familiar variation on gene expression, the same families were evaluated separately. At 98 dpf, growth-related genes Igf1a, Igf2a, mTOR, Pld1a, Mrf4, Myod, Myogenin, and Myostatin1b were evaluated. In males, Myogenin, Mrf4, and Igf2a showed changes attributable to the PP diet. In females, the effect of the PP diet did not modulate the expression in any of the eight genes studied. The effect of familiar variation on gene expression was observed among families. This study shows that PP diet and family variation have effects on gene expression in fish muscle.

Comparative mapping reveals quantitative trait loci that affect spawning time in coho salmon (Oncorhynchus kisutch).

Spawning time in salmonids is a sex-limited quantitative trait that can be modified by selection. In rainbow trout (Oncorhynchus mykiss), various quantitative trait loci (QTL) that affect the expression of this trait have been discovered. In this study, we describe four microsatellite loci associated with two possible spawning time QTL regions in coho salmon (Oncorhynchus kisutch). The four loci were identified in females from two populations (early and late spawners) produced by divergent selection from the same base population. Three of the loci (OmyFGT34TUF, One2ASC and One19ASC) that were strongly associated with spawning time in coho salmon (p < 0.0002) were previously associated with QTL for the same trait in rainbow trout; a fourth loci (Oki10) with a suggestive association (p = 0.00035) mapped 10 cM from locus OmyFGT34TUF in rainbow trout. The changes in allelic frequency observed after three generations of selection were greater than expected because of genetic drift. This work shows that comparing information from closely-related species is a valid strategy for identifying QTLs for marker-assisted selection in species whose genomes are poorly characterized or lack a saturated genetic map.

SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss.

SalmonDB is a new multiorganism database containing EST sequences from Salmo salar, Oncorhynchus mykiss and the whole genome sequence of Danio rerio, Gasterosteus aculeatus, Tetraodon nigroviridis, Oryzias latipes and Takifugu rubripes, built with core components from GMOD project, GOPArc system and the BioMart project. The information provided by this resource includes Gene Ontology terms, metabolic pathways, SNP prediction, CDS prediction, orthologs prediction, several precalculated BLAST searches and domains. It also provides a BLAST server for matching user-provided sequences to any of the databases and an advanced query tool (BioMart) that allows easy browsing of EST databases with user-defined criteria. These tools make SalmonDB database a valuable resource for researchers searching for transcripts and genomic information regarding S. salar and other salmonid species. The database is expected to grow in the near feature, particularly with the S. salar genome sequencing project. Database URL: http://genomicasalmones.dim.uchile.cl/

Fluoxetine response in impulsive-aggressive behavior and serotonin transporter polymorphism in personality disorder.

BACKGROUND: Disturbances in central serotonin function have been implicated in impulsive and aggressive behavior. A deletion/insertion polymorphism within the 5-HT transporter promoter gene (5-HTTLPR) is thought to be associated with disturbed impulse control, anxiety, and depression. The serotonin transporter (5-HTT) is the primary action site for selective serotonin reuptake inhibitors (SSRIs). Several studies of major depression have shown that the l allele of 5-HTTLPR is associated with better SSRI antidepressant effects than the s allele. METHODS: This study investigates the association between response of impulsivity to treatment with fluoxetine and 5-HTTLPR polymorphism in 49 personality disordered patients. Additionally, we studied TPH1, 5HT1B and 5HT2C receptor polymorphisms as predictors of response in this population. RESULTS: Results reveal that patients with the l/l genotype of 5-HTTLPR had a significantly better response to fluoxetine when compared to s allele carriers, as evaluated on the basis of total (P<0.05) and Aggression subscale (P<0.01) Overt Aggression Scale Modified-score percentage change. There were no significant associations between fluoxetine response and TPH1 (A218C) (-6525 A>G) (-5806 G>T), HTR1B (G861C) and HTR2C (G68C) genotype groups. CONCLUSION: This is the first study assessing the association between these polymorphisms and anti-impulsive response to fluoxetine in personality disorder. As the s genotype is associated with a poorer selective serotonin reuptake inhibitors response in major depression, bulimia nervosa and borderline personality disorder, it could represent a common biological background for SSRI response.

Sequencing the genome of the Atlantic salmon (Salmo salar).

The International Collaboration to Sequence the Atlantic Salmon Genome (ICSASG) will produce a genome sequence that identifies and physically maps all genes in the Atlantic salmon genome and acts as a reference sequence for other salmonids.

Planning in borderline personality disorder: evidence for distinct subpopulations.

OBJECTIVE: Borderline personality disorder is a severe mental disorder, whereas previous studies suggest executive functions may be impaired. The aim of this study was to evaluate executive planning in a sample of 85 individuals. METHODS: Planning was assessed by means of the Tower of London (Drexel University version) task. Latent class cluster analysis models were adjusted to the data. RESULTS: We identified two different subpopulations of borderline personality disorder patients, one of them with significantly reduced performance. CONCLUSION;. Neuropsychological mechanisms may be involved in borderline personality disorder, at least in a subgroup of patients.

Relaciones entre el trastorno límite de personalidad y el espectro bipolar: [revisión] / Relationship between borderline personality disorder and bipolar spectrum: [review]

Existe una controversia respecto a la independencia nosológica del trastorno límite de personalidad. Algunos autores sostienen que es parte del trastorno bipolar, mientras otros afirman que es una entidad independiente. En este trabajo se analiza la evolución histórica de los conceptos de trastorno límite y trastorno bipolar. Se discuten los argumentos a favor y en contra de incluir el trastorno límite dentro del trastorno bipolar. Por último se proponen nuevas estrategias para abordar este problema.

The independent nosological status of borderline personality disorder is a controversial issue. Some authors consider borderline as part of bipolar spectrum, but other sustain that is a independent entity. The historical evolution of borderline personality disorder and bipolar disorder is analyzed in this work. The arguments for include, or not include, borderline personality disorder in bipolar disorder is discussed. Finally, new strategies for study this problem are proposed.

Estudio farmacogenómico en trastorno límite de personalidad / Borderline personality disorder: a pharmacogenomic study

Antecedentes: Las conductas agresivas e impulsivas han sido asociadas con disfunciones del sistema serotoninérgico central. Polimorfismos del transportador de serotonina, de la triptófano hidroxilasa (TPH1) y de los receptores serotoninérgicos 5HT1B y 5HT2C han sido vinculados a agresión e impulsividad. Varios estudios en depresión mayor han demostrado que el alelo corto (S) del promotor del gen transportador de serotonina se asocia a una peor respuesta a los inhibidores selectivos de la recapacitación de serotonina (ISNS). Material y métodos: En este estudio se investigó la asociación entre la respuesta de la impulsividad al tratamiento con fluoxetina y polimorfismos del transportador de serotonina, TPH1 y de los receptores 5HT1B y 5HT2C, en 49 pacientes con trastorno límite de personalidad. Resultados: Los pacientes con el genotipo L/L del promotor del gen transportador de serotonina, evaluados mediante la Overt Aggression Scale-Modified (OAS-M), tuvieron una respuesta a fluoxetina significativamente mejor que los portadores del alelo S. No se encontró asociación entre la respuesta a fluoxetina y los genotipos de TPH1 y de los receptores 5HT1B y 5HT2C. Conclusiones: Este es el primer estudio en el que se evalúa la asociación entre estos polimorfismos y la respuesta anti-impulsiva a la fluoxetina en pacientes con trastorno límite de personalidad. El alelo S puede representar un factor común de peor respuesta a los ISRS en enfermedades asociadas a una disfunción serotoninérgica.

Background: Disturbances in central serotonin function have been implicated in impulsive and aggressive behavior. Serotonin transporter tryptophan hydroxylase (TPH1) and serotoninergic receptor (5HT1B, 5HT2C) polymorphisms have been linked to aggression and impulsivity. Several studies of major depression have shown that the short allele (S) of the serotonin transporter promoter gene is associated with a worse response to selective serotonin reuptake inhibitors (SSRIs). Material and methods: This study investigates the association between the response of impulsivity to fluoxetine treatment and serotonin transporter, TPH1 and 5HT1B and 5HT2C receptor polymorphisms in 49 patients with borderline personality disorder. Results: Patients with the Long/Long (L/L) genotype of the serotonin transporter promoter had a significantly better response to fluoxetine when compared to the S allele carriers, as evaluated by the Overt Aggression Scale-Modified (OAS-M). There were no significant associations between these polymorphisms and anti-impulsive response to fluoxetine in patients with borderline personality disorder. The S allele may represent a common factor of worse response to SSRIs in diseases associated to serotonin dysfunction.