miRTil: An extensive repository for Nile Tilapia microRNA next generation sequencing data

Nile tilapia is the third most cultivated fish worldwide and a novel model species for evolutionary studies. Aiming to improve productivity and contribute to the selection of traits of economic impact, biotechnological approaches have been intensively applied to species enhancement. In this sense, recent studies have focused on the multiple roles played by microRNAs (miRNAs) in the post-transcriptional regulation of protein-coding genes involved in the emergence of phenotypes with relevance for aquaculture. However, there is still a growing demand for a reference resource dedicated to integrating Nile Tilapia miRNA information, obtained from both experimental and in silico approaches, and facilitating the analysis and interpretation of RNA sequencing data. Here, we present an open repository dedicated to Nile Tilapia miRNAs: the "miRTil database". The database stores data on 734 mature miRNAs identified in 11 distinct tissues and five key developmental stages. The database provides detailed information about miRNA structure, genomic context, predicted targets, expression profiles, and relative 5p/3p arm usage. Additionally, miRTil also includes a comprehensive pre-computed miRNA-target interaction network containing 4936 targets and 19,580 interactions

A Streamlined DNA Tool for Global Identification of Heavily Exploited Coastal Shark Species (Genus Rhizoprionodon)

Obtaining accurate species-specific landings data is an essential step toward achieving sustainable shark fisheries. Globally distributed sharpnose sharks (genus Rhizoprionodon) exhibit life-history characteristics (rapid growth, early maturity, annual reproduction) that suggests that they could be fished in a sustainable manner assuming an investment in monitoring, assessment and careful management. However, obtaining species-specific landings data for sharpnose sharks is problematic because they are morphologically very similar to one another. Moreover, sharpnose sharks may also be confused with other small sharks (either small species or juveniles of large species) once they are processed (i.e., the head and fins are removed). Here we present a highly streamlined molecular genetics approach based on seven species-specific PCR primers in a multiplex format that can simultaneously discriminate body parts from the seven described sharpnose shark species commonly occurring in coastal fisheries worldwide. The species-specific primers are based on nucleotide sequence differences among species in the nuclear ribosomal internal transcribed spacer 2 locus (ITS2). This approach also distinguishes sharpnose sharks from a wide range of other sharks (52 species) and can therefore assist in the regulation of coastal shark fisheries around the world

The 5S rDNA family evolves through concerted and birth-and-death evolution in fish genomes: an example from freshwater stingrays

Background: Ribosomal 5S genes are well known for the critical role they play in ribosome folding and functionality. These genes are thought to evolve in a concerted fashion, with high rates of homogenization of gene copies. However, the majority of previous analyses regarding the evolutionary process of rDNA repeats were conducted in invertebrates and plants. Studies have also been conducted on vertebrates, but these analyses were usually restricted to the 18S, 5.8S and 28S rRNA genes. The recent identification of divergent 5S rRNA gene paralogs in the genomes of elasmobranches and teleost fishes indicate that the eukaryotic 5S rRNA gene family has a more complex genomic organization than previously thought. The availability of new sequence data from lower vertebrates such as teleosts and elasmobranches enables an enhanced evolutionary characterization of 5S rDNA among vertebrates.Results: We identified two variant classes of 5S rDNA sequences in the genomes of Potamotrygonidae stingrays, similar to the genomes of other vertebrates. One class of 5S rRNA genes was shared only by elasmobranches. A broad comparative survey among 100 vertebrate species suggests that the 5S rRNA gene variants in fishes originated from rounds of genome duplication. These variants were then maintained or eliminated by birth-and-death mechanisms, under intense purifying selection. Clustered multiple copies of 5S rDNA variants could have arisen due to unequal crossing over mechanisms. Simultaneously, the distinct genome clusters were independently homogenized, resulting in the maintenance of clusters of highly similar repeats through concerted evolution.Conclusions: We believe that 5S rDNA molecular evolution in fish genomes is driven by a mixed mechanism that integrates birth-and-death and concerted evolution

Aplicação da genética molecular no manejo e conservação de tubarões

Muitas espécies marinhas estão em risco de extinção devido à exploração excessiva e carência de manejo de nossos oceanos. Reduzir a intensidade do impacto das atividades antrópicas sobre o ambiente marinho é uma tarefa complexa, uma vez que grande parte da população mundial reside próximo às áreas costeiras, e por isso, freqüentemente depende dos recursos marinhos para sua subsistência e lazer. Essa dependência dos seres humanos em relação aos oceanos torna crucial o conhecimento dos ecossistemas marinhos para adequado manejo de seus recursos. Hoje em dia, a pesquisa nessa área é ainda bastante limitada, principalmente, devido às dificuldades de se trabalhar nos oceanos. Entretanto as análises de DNA estão contribuindo significativamente para o nosso conhecimento acerca da distribuição e saúde das populações de espécies marinhas criticamente ameaçadas. Dentre as espécies ameaçadas destaca-se o tubarão-martelo Sphyrna lewini cujas populações naturais estão atualmente em acelerada depleção devido à excessiva exploração pela pesca, principalmente para a comercialização de suas valorizadas nadadeiras nos mercados asiáticos. Esta espécie apresenta características relacionadas à sua disribuição e ao seu ciclo de vida que podem conduzir à estruturação em finaescala de suas populações. No presente trabalho foi verificada a existência de estruturação genética de S. lewini no Atlantico entre as populações do Brasil, Golfo do México e Mar do Caribe. Também foi detectada estruturação em fina escala ao longo da costa do Brasil, possivelmente em função do comportamento filopátrico de fêmeas dessa espécie e à existência de áreas de berçários costeiras. Os dados obtidos no presente trabalho evidenciam que as populações de tubarões-martelo do Atlantico Ocidental são geneticamente distintas, mesmo considerando-se curtas...The scalloped hammerhead shark Sphyrna lewini is a cosmopolitan species heavily exploited for fisheries and fin trade. Here we used mitochondrial DNA control region sequences to trace market-derived Sphyrna lewini fins back to their geographical region of origin. We showed that twenty-one percent of these fins were derived from the Western Atlantic, where this species is endangered. We also evaluated the population genetic structure and differentiation of S. lewini along Western Atlantic employing mtDNA and microsatellites. Our mtDNA results indicate strong population subdivision and four distinct genetic stocks along the studied area due to philopatric females with high fidelity to natal region. Contrarily, males facilitate gene flow dispersal and connection among areas as supported by low genetic differentiation verified in the 10 microsatellite loci analysis. We also report the occurrence of a rare cryptic scalloped hammerhead shark species lineage in the Southeastern Atlantic based on the analysis of nuclear (ITS2) and mitochondrial control region (CR) markers. Finally, we also developed a suite of species-specific primers sharks for global identification of sharpnose sharks (genus Rhizoprionodon). These species are morphologically very similar to one another and exhibit life-history characteristics (rapid growth, early maturity, annual reproduction) that suggests that they could be fished in a sustainable manner assuming an investment in monitoring, assessment and careful management. Here we successfully validated an approach that accurately distinguishes sharpnose sharks from a wide range of other sharks (52 species) and can therefore assist in the regulation of coastal shark fisheries around the worldFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

Aplicação da genética molecular no manejo e conservação de tubarões

Muitas espécies marinhas estão em risco de extinção devido à exploração excessiva e carência de manejo de nossos oceanos. Reduzir a intensidade do impacto das atividades antrópicas sobre o ambiente marinho é uma tarefa complexa, uma vez que grande parte da população mundial reside próximo às áreas costeiras, e por isso, freqüentemente depende dos recursos marinhos para sua subsistência e lazer. Essa dependência dos seres humanos em relação aos oceanos torna crucial o conhecimento dos ecossistemas marinhos para adequado manejo de seus recursos. Hoje em dia, a pesquisa nessa área é ainda bastante limitada, principalmente, devido às dificuldades de se trabalhar nos oceanos. Entretanto as análises de DNA estão contribuindo significativamente para o nosso conhecimento acerca da distribuição e saúde das populações de espécies marinhas criticamente ameaçadas. Dentre as espécies ameaçadas destaca-se o tubarão-martelo Sphyrna lewini cujas populações naturais estão atualmente em acelerada depleção devido à excessiva exploração pela pesca, principalmente para a comercialização de suas valorizadas nadadeiras nos mercados asiáticos. Esta espécie apresenta características relacionadas à sua disribuição e ao seu ciclo de vida que podem conduzir à estruturação em finaescala de suas populações. No presente trabalho foi verificada a existência de estruturação genética de S. lewini no Atlantico entre as populações do Brasil, Golfo do México e Mar do Caribe. Também foi detectada estruturação em fina escala ao longo da costa do Brasil, possivelmente em função do comportamento filopátrico de fêmeas dessa espécie e à existência de áreas de berçários costeiras. Os dados obtidos no presente trabalho evidenciam que as populações de tubarões-martelo do Atlantico Ocidental são geneticamente distintas, mesmo considerando-se curtas...The scalloped hammerhead shark Sphyrna lewini is a cosmopolitan species heavily exploited for fisheries and fin trade. Here we used mitochondrial DNA control region sequences to trace market-derived Sphyrna lewini fins back to their geographical region of origin. We showed that twenty-one percent of these fins were derived from the Western Atlantic, where this species is endangered. We also evaluated the population genetic structure and differentiation of S. lewini along Western Atlantic employing mtDNA and microsatellites. Our mtDNA results indicate strong population subdivision and four distinct genetic stocks along the studied area due to philopatric females with high fidelity to natal region. Contrarily, males facilitate gene flow dispersal and connection among areas as supported by low genetic differentiation verified in the 10 microsatellite loci analysis. We also report the occurrence of a rare cryptic scalloped hammerhead shark species lineage in the Southeastern Atlantic based on the analysis of nuclear (ITS2) and mitochondrial control region (CR) markers. Finally, we also developed a suite of species-specific primers sharks for global identification of sharpnose sharks (genus Rhizoprionodon). These species are morphologically very similar to one another and exhibit life-history characteristics (rapid growth, early maturity, annual reproduction) that suggests that they could be fished in a sustainable manner assuming an investment in monitoring, assessment and careful management. Here we successfully validated an approach that accurately distinguishes sharpnose sharks from a wide range of other sharks (52 species) and can therefore assist in the regulation of coastal shark fisheries around the worldFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

Tracking the Fin Trade: Genetic Stock Identification in Western Atlantic Scalloped Hammerhead Sharks Sphyrna lewini

Location or stock-specific landing data are necessary to improve management of shark stocks, especially those imperiled by overexploitation as a result of the international shark fin trade. In the current absence of catch monitoring directly at extraction sites, genetic stock identification of fins collected from major market supply chain endpoints offers an overlooked but potentially useful approach for tracing the fins back to their geographical, or stock of, origin. To demonstrate the feasibility of this approach, we used mitochondrial control region (mtCR) sequences to trace the broad geographical origin of 62 Hong Kong market-derived Sphyrna lewini fins. Of these fins 21% were derived from the western Atlantic, where this species is listed as ‘Endangered’ by the International Union for the Conservation of Nature (IUCN). We also show that S. lewini mtCR sequences are geographically segregated in the western Atlantic (overall ΦST = 0.74, n = 177 sharks), indicating that breeding females either remain close to, or home back to, their natal region for parturition. Mixed stock analysis simulations showed that it is possible to estimate the relative contributions of these mitochondrial stocks to fin mixtures in globally sourced trade hubs. These findings underscore the feasibility of using genetic stock identification to source market-derived shark fins to obtain essential and otherwise unavailable data on exploitation levels, and thus to productively inform stock assessment and management of S. lewini and potentially also of other fished shark species