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.publishedVersio

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

Phylogenetic relationships of Chilean leptodactylids: a molecular approach based on mitochondrial genes 12S and 16S Relaciones filogenéticas de los leptodactílidos chilenos: una aproximación molecular basada en los genes mitocondriales 12S y 16S

Most Chilean amphibians belong to the subfamily Telmatobiinae (Anura, Leptodactylidae). Several phylogenetic studies of Leptodactylidae and Telmatobiinae, based principally on morphological characters, have implicitly suggested closer relationships of some species of the Telmatobiinae with members of other subfamilies of leptodactylids, including the leptodactyline genus Pleurodema which is present in Chile. Furthermore, a growing number of molecular studies suggest a non monophyletic status for Telmatobiinae, although none of these studies have investigated the phylogenetic relationships of this subfamily. We compared partial sequences of the ribosomal mitochondrial genes 12S and 16S to determine the phylogenetic relationships of Chilean leptodactylids and its position within the modern anurans (Neobatrachia). We included 22 species from nine of the 10 genera of telmatobiines present in Chile (Alsodes, Atelognathus, Batrachyla, Caudiverbera, Eupsophus, Hylorina, Insuetophrynus, Telmatobufo and Telmatobius), two species of the genus Pleurodema, and one species of Rhinodermatidae, which is considered a leptodactylid derivative family by some authors. We also included 51 species representing most of the families that compose Neobatrachia. Phylogenetic reconstructions were performed using the methods of maximum parsimony, maximum likelihood and Bayesian inference. The topologies obtained in all the analyses indicate that Telmatobiinae is a polyphyletic assemblage, composed by species belonging to Hyloidea (most of the genera) and species more related to Australasian taxa (the clade Caudiverbera + Telmatobufo, defined as the tribe Calyptocephalellini). These molecular data support groups based on other kinds of evidence (Caudiverbera + Telmatobufo, Alsodes + Eupsophus and Batrachyla + Hylorina) and raise new phylogenetic hypotheses for several genera of telmatobiines (Atelognathus with Batrachyla and Hylorina, Insuetophrynus + Rhinoderma). The phylogenetic relationships recovered in this study suggest a multiple origin for Chilean temperate forest frogs and reveal an unexpected level of taxonomic diversity and evolutionary divergence among Chilean leptodactylidsLa mayoría de los anfibios chilenos pertenece a la subfamilia Telmatobiinae (Anura, Leptodactylidae). Varios estudios filogenéticos de Leptodactylidae y Telmatobiinae, basados principalmente en caracteres morfológicos, han sugerido implícitamente relaciones más estrechas de algunas especies de Telmatobiinae con miembros de otras subfamilias de leptodactílidos, incluyendo el género leptodactilino Pleurodema presente en Chile. Además, un número creciente de estudios moleculares sugieren un estatus no monofilético para Telmatobiinae, aunque ninguno de estos estudios ha investigado las relaciones filogenéticas de esta subfamilia. Secuencias parciales de los genes ribosomales mitocondriales 12S y 16S fueron comparadas para determinar las relaciones filogenéticas de los leptodactílidos chilenos y su posición dentro de los anuros modernos (Neobatrachia). Se incluyeron 22 especies de nueve de los diez géneros de telmatobinos presentes en Chile (Alsodes, Atelognathus, Batrachyla, Caudiverbera, Eupsophus, Hylorina, Insuetophrynus, Telmatobufo y Telmatobius), dos especies del género Pleurodema y una especie de Rhinodermatidae la cual es considerada una familia derivada de los leptodactílidos por algunos autores. Se incluyeron además 51 especies que representan la mayoría de las familias que componen Neobatrachia. Las reconstrucciones filogenéticas se realizaron utilizando los métodos de máxima parsimonia, máxima verosimilitud e inferencia bayesiana. Las topologías obtenidas en todos los análisis indican que Telmatobiinae es un ensamblaje polifilético, compuesto por especies que pertenecen a Hyloidea (la mayoría de los géneros) y especies más relacionadas con taxa de Australasia (el clado Caudiverbera + Telmatobufo, definido como la tribu Calyptocephalellini). Estos datos moleculares respaldan agrupaciones basadas en otro tipo de evidencia (Caudiverbera + Telmatobufo, Alsodes + Eupsophus y Batrachyla + Hylorina) y plantean nuevas hipótesis de relaciones para algunos géneros de telmatobinos (Atelognathus con Batrachyla e Hylorina, Insuetophrynus + Rhinoderma). Las relaciones filogenéticas observadas en este estudio sugieren un origen múltiple para los anuros del bosque templado de Chile y revelan un inesperado nivel de diversidad taxonómica y divergencia evolutiva entre los leptodactílidos chileno

Zebrafish as a model organism for nutrition and growth: Towards comparative studies of nutritional genomics applied to aquacultured fishes

Zebrafish (Danio rerio) is a common research model in fish studies of toxicology, developmental biology, neurobiology and molecular genetics; it has been proposed as a possible model organism for nutrition and growth studies in fish. The advantages of working with zebrafish in these areas are their small size, short generation time (12-14 weeks) and their capacity to produce numerous eggs (100-200 eggs/clutch). Since a wide variety of molecular tools and information are available for genomic analysis, zebrafish has also been proposed as a model for nutritional genomic studies in fish. The detailed study of every species employed as a model organism is important because these species are used to generalize how several biological processes occur in related organisms, and contribute considerably toward improving our understanding of the mechanisms involved in nutrition and growth. The objective of this review is to show the relevant aspects of the nutrition and growth in zebrafish that s

Utility of five SSR markers for genetic diversity and paternity exclusion analysis in the patagonian toothfish

© 2017, Escuela de Ciencias del Mar. All Right Reserved.The Patagonian toothfish or Chilean sea bass (Dissostichus eleginoides), found in the Southern Ocean surrounding Antarctica, is an important fishery species for Chile. This high-value species is regarded as overfished, making it an attractive target for aquaculture. When developing a reproduction program for any aquaculture species, it is important to implement genetic tools to evaluate diversity, inbreeding, and parentage. We calculated genetic diversity and paternity/maternity exclusion probabilities based on five commonly-used microsatellite loci in a natural population of Patagonian toothfish from southern Chile (n = 34) in order to evaluate the potential utility of these five markers in stock management. The observed number of alleles per locus (Na) and observed heterozygosities (HO) are within range as described by studies performed in other sub-Antarctic regions. All five loci were strongly polymorphic, with HO > 0.6 and N