Rodrigo Vidal

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.

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.

Phylogeny, biogeography, and rates of diversification of New World Astragalus (Leguminosae) with an emphasis on South American radiations

This study uses phylogenetic relationships of New World representatives of the species-rich genus Astragalus (Leguminosae; Papilionoideae) to follow up on recent evidence pointing to rapid and recent plant diversification patterns in the Andes. Bayesian and maximum likelihood phylogenetic analyses were done using nuclear rDNA ITS and chloroplast spacers trnD-trnT and trnfM-trnS1, either separately or in combination. The effect of using partitioned vs. nonpartitioned analyses in a Bayesian approach was evaluated. Highest resolution was obtained when the data were combined in partitioned or nonpartitioned Bayesian analyses. All phylogenies support two clades of South American species nested within the North American species, implying two separate invasions from North to South America. These two clades correspond to the original morphological classification of Johnston (1947 Journal of the Arnold Arboretum 28: 336-409). The mean ages of the South American clades were very recent but still significantly different (1.89 and 0.98 Ma). Upper and lower bounds on rates of diversification varied between 2.01 and 0.65 species/Ma for the older clade and 2.06 and 1.24 species/Ma for the younger clade. Even the lower bounds are still very high, reasserting Neo-Astragalus in the growing list of recent rapid radiations of plants, especially in areas with a high physiographic diversity, such as the Andes.

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.

Phylogeography of the genus Spongites (Corallinales, Rhodophyta) from chile

Both the records and the descriptions of the crustose species of coralline algae on the southeastern coast of South America are from the early 1900s. Unlike other algae species on the coast of Chile, the biogeography and distribution of crustose corallines have not been studied despite their abundance. Through recent studies, it has been determined that the genus Spongites is the most conspicuous genus along the rocky intertidal of the Chilean coasts. It is also common to the entire coast of the Southern Hemisphere; however, the relationship between species and the possible reasons for their distribution is unknown. We used nuclear and mitochondrial genetic markers and SEM observations of morphological characters to examine Spongites samples from the Southern Hemisphere and to establish the phylogeographic relationships of Chilean Spongites with specimens from other southern coasts. The combination of these analyses revealed the following: (i) a monophyletic clade that represents the Chilean Spongites and (ii) a paraphyletic clade for South African, New Zealand, and Argentine samples. Consequently, we postulate two nonexclusive hypotheses regarding the relationship of Spongites species in the Southern Hemisphere: (i) a complex history of extinction, speciation, and recolonization that might have erased original Gondwanan split patterns, and (ii) an Antarctic Peninsula origin for the Chilean Spongites species.

Molecular genetic identification of crustose representatives of the order Corallinales (Rhodophyta) in Chile

Knowledge on species of the order Corallinales along the coast of Chile is still scarce despite a number of studies and records of other divisions of seaweeds made since the early 20th century. This lack of information is more dramatic among crustose representatives of the order, thus depriving biogeographic studies of a thorough analysis and resulting in inadequately representative accounts of biodiversity. The currently changing taxonomy of the group makes it difficult to identify and differentiate among taxa based on morphological and developmental characters. Therefore, the use of molecular tools has been adopted in this study in order to facilitate identification and comparison of crustose corallines collected at the rocky intertidal between 27 degrees and 48 degrees S along the Pacific temperate coast of South America. A sequence 600bp (in length) from the SSU-rDNA gene was used to identify five taxa to the genus level: Lithophyllum, Spongites, Mesophyllum, Synarthrophyton, and Leptophytum. In all cases, the genus distinction based on morphological characters coincide with designations based on variation in the ribosomal DNA gene sequence. Spongites is the most frequently occurring genus and is found in all localities sampled while the others appear occasionally. Taxa recognition at species level must be examined with caution considering that morphological variability is not well understood in Chile because the SSU-rDNA region sequence does not always stand alone as an unambiguous means of identifying all coralline species. In such cases, more rapidly evolving markers are needed. For example, sequences from the ITS (rDNA) region often provide greater resolution among closely related species and genera. However, the methodology presented here remains a useful tool for species-level identification.

Microsatellites of Laminaria digitata tested in Lessonia nigrescens: Evaluation and improvement of cross amplification between kelps of two different families

The use of primers designed originally to amplify DNA for one species in a different one can save time and resources, particularly for microsatellite loci. Microsatellite amplification improvements across two kelp families are reported, where loci originally described in Laminaria digitata (Laminariaceae) were tested in Lessonia nigrescens) was observed in two localities affected by massive mortality events. Nei’s distances among five populations presented similar patterns to those of 30 multilocus dominant loci (RAPD) evaluated in the same localities. Although some success might be achieved in cross-species microsatellite amplifications, the strong mutations detected between these two Laminarian families suggests that better results of cross-amplifications should be expected at much lower taxonomic levels. Thus, although more expensive, construction of new gene libraries is strongly recommended.

Ssa miRNAs DB: Online repository of in silico predicted miRNAs in Salmo salar.

The Atlantic salmon (Salmo salar) is a very valuable commercial salmonid species. As with other aquaculture species, intensive aquaculture of Atlantic salmon often faces disease problems especially in early life stages which can limit stable production of the species. ‘Ssa miRNAs DB’, a bioinformatics and manually curated database, aims at providing a comprehensive resource of microRNA in Altantic salmon, with a user friendly interface for a convenient retrieval of each entry by microRNA ID or target gene. The current version of Ssa miRNAs DB involved the prediction of 41 and 266 homologous and novel microRNAs, respectively. Availability The database is available for free at http://www.molgenv.com/ssa_mirnas_db_home.php

Selection of reference genes for microRNA analysis associated to early stress response to handling and confinement in Salmo salar

MicroRNAs are key non-coding RNA molecules that play a relevant role in the regulation of gene expression through translational repression and/or transcript cleavage during normal development and physiological adaptation processes like stress. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) has become the approach normally used to determine the levels of microRNAs. However, this approach needs the use of endogenous reference. An improper selection of endogenous references can result in confusing interpretation of data. The aim of this study was to identify and validate appropriate endogenous reference miRNA genes for normalizing RT-qPCR survey of miRNAs expression in four different tissues of Atlantic salmon, under handling and confinement stress conditions associated to early or primary stress response. Nine candidate reference normalizers, including microRNAs and nuclear genes, normally used in vertebrate microRNA expression studies were selected from literature, validated by RT-qPCR and analyzed by the algorithms geNorm and NormFinder. The results revealed that the ssa-miR-99-5p gene was the most stable overall and that ssa-miR-99-5p and ssa-miR-23a-5p genes were the best combination. Moreover, the suitability of ssa-miR-99-5p and ssa-miR-23a-5p as endogeneuos reference genes was demostrated by the expression analysis of ssa-miR-193-5p gene.

Characterization of new microsatellite markers derived from sequence databases for the emu (Dromaius novaehollandiae)

The emu (Dromaius novaehollandiae), a member of ratite family, is native to Australia and has been introduced to other countries worldwide. In this work, 10 polymorphic microsatellite loci were isolated and characterized for emu from public sequences. Polymorphism was surveyed in 22 individuals from two different populations kept in captivity. Between two and 11 alleles were found per locus, and the observed heterozygosity ranged from 0.05 to 0.85, in accordance with expectations. These markers will be useful as tools for detecting levels of genetic variation, reconstructing pedigrees (for quantitative genetic analysis) and identifying markers associated to fitness traits in emu populations.