Back to Water: Signature of Adaptive Evolution in Cetacean Mitochondrial tRNAs

Abstract The mitochondrion is the power plant of the eukaryotic cell, and tRNAs are the fundamental components of its translational machinery. In the present paper, the evolution of mitochondrial tRNAs was investigated in the Cetacea, a clade of Cetartiodactyla that retuned to water and thus had to adapt its metabolism to a different medium than that of its mainland ancestors. Our analysis focussed on identifying the factors that influenced the evolution of Cetacea tRNA double-helix elements, which play a pivotal role in the formation of the secondary and tertiary structures of each tRNA and consequently manipulate the whole translation machinery of the mitochondrion. Our analyses showed that the substitution pathways in the stems of different tRNAs were influenced by various factors, determining a molecular evolution that was unique to each of the 22 tRNAs. Our data suggested that the composition, AT-skew, and GC-skew of the tRNA stems were the main factors influencing the substitution process. In particular, the range of variation and the fluctuation of these parameters affected the fate of single tRNAs. Strong heterogeneity was observed among the different species of Cetacea. Finally, it appears that the evolution of mitochondrial tRNAs was also shaped by the environments in which the Cetacean taxa differentiated. This latter effect was particularly evident in toothed whales that either live in freshwater or are deep divers

An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax)

Skeletal anomalies in farmed fish are a relevant issue affecting animal welfare and health and causing significant economic losses. Here, a high-density genetic map of European seabass for QTL mapping of jaw deformity was constructed and a genome-wide association study (GWAS) was carried out on a total of 298 juveniles, 148 of which belonged to four full-sib families. Out of 298 fish, 107 were affected by mandibular prognathism (MP). Three significant QTLs and two candidate SNPs associated with MP were identified. The two GWAS candidate markers were located on ChrX and Chr17, both in close proximity with the peaks of the two most significant QTLs. Notably, the SNP marker on Chr17 was positioned within the Sobp gene coding region, which plays a pivotal role in craniofacial development. The analysis of differentially expressed genes in jaw-deformed animals highlighted the "nervous system development" as a crucial pathway in MP. In particular, Zic2, a key gene for craniofacial morphogenesis in model species, was significantly down-regulated in MP-affected animals. Gene expression data revealed also a significant down-regulation of Sobp in deformed larvae. Our analyses, integrating transcriptomic and GWA methods, provide evidence for putative mechanisms underlying seabass jaw deformity

Gone with the currents: lack of genetic differentiation at the circum-continental scale in the Antarctic krill Euphausia superba

<p>Abstract</p> <p>Background</p> <p>Southern Ocean fauna represent a significant amount of global biodiversity, whose origin may be linked to glacial cycles determining local extinction/eradication with ice advance, survival of refugee populations and post-glacial re-colonization. This pattern implies high potential for differentiation in benthic shelf species with limited dispersal, yet consequences for pelagic organisms are less clear. The present study investigates levels of genetic variation and population structure of the Antarctic krill <it>Euphausia superba </it>using mitochondrial DNA and EST-linked microsatellite markers for an unprecedentedly comprehensive sampling of its populations over a circum-Antarctic range.</p> <p>Results</p> <p>MtDNA (ND1) sequences and EST-linked microsatellite markers indicated no clear sign of genetic structure among populations over large geographic scales, despite considerable power to detect differences inferred from forward-time simulations. Based on ND1, few instances of genetic heterogeneity, not significant after correction for multiple tests, were detected between geographic or temporal samples. Neutrality tests and mismatch distribution based on mtDNA sequences revealed strong evidence of past population expansion. Significant positive values of the parameter <it>g </it>(a measure of population growth) were obtained from microsatellite markers using a coalescent-based genealogical method and suggested a recent start (60 000 - 40 000 years ago) for the expansion.</p> <p>Conclusions</p> <p>The results provide evidence of lack of genetic heterogeneity of Antarctic krill at large geographic scales and unequivocal support for recent population expansion. Lack of genetic structuring likely reflects the tight link between krill and circum-Antarctic ocean currents and is consistent with the hypothesis that differentiation processes in Antarctic species are largely influenced by dispersal potential, whereas small-scale spatial and temporal differentiation might be due to local conditions leading to genetic patchiness. The signal of recent population growth suggests differential impact of glacial cycles on pelagic Antarctic species, which experienced population expansion during glaciations with increased available habitat, <it>versus </it>sedentary benthic shelf species.</p> <p>EST-linked microsatellites provide new perspectives to complement the results based on mtDNA and suggest that data-mining of EST libraries will be a useful approach to facilitate use of microsatellites for additional species.</p

Restricted gene flow at the micro- and macro-geographical scale in marble trout based on mtDNA and microsatellite polymorphism

<p>Abstract</p> <p>Background</p> <p>The genetic structure of the marble trout <it>Salmo trutta marmoratus</it>, an endemic salmonid of northern Italy and the Balkan peninsula, was explored at the macro- and micro-scale level using a combination of mitochondrial DNA (mtDNA) and microsatellite data.</p> <p>Results</p> <p>Sequence variation in the mitochondrial control region showed the presence of nonindigenous haplotypes indicative of introgression from brown trout into marble trout. This was confirmed using microsatellite markers, which showed a higher introgression at nuclear level. Microsatellite loci revealed a strong genetic differentiation across the geographical range of marble trout, which suggests restricted gene flow both at the micro-geographic (within rivers) and macro-geographic (among river systems) scale. A pattern of Isolation-by-Distance was found, in which genetic samples were correlated with hydrographic distances. A general West-to-East partition of the microsatellite polymorphism was observed, which was supported by the geographic distribution of mitochondrial haplotypes.</p> <p>Conclusion</p> <p>While introgression at both mitochondrial and nuclear level is unlikely to result from natural migration and might be the consequence of current restocking practices, the pattern of genetic substructuring found at microsatellites has been likely shaped by historical colonization patterns determined by the geological evolution of the hydrographic networks.</p

Messinian salinity crisis and the origin of freshwater lifestyle in western Mediterranean gobies.

The present paper reports on a molecular study based on 12S rRNA and 16S rRNA mitochondrial genes partly sequenced in 13 species of western Mediterranean gobies, three of which are strictly freshwater-dwelling. A total of 867 bp were aligned and used for the phylogenetic reconstruction. Two major lineages were identified, one clustering the sand gobies in a monophyletic clade. Relationships among taxa based on sequence analysis only partly match those based on morphological criteria, suggesting that the latter are somehow insufficient to correctly establish phylogenetic relationships within this family. The results provide evidence for a multiple independent evolution of the freshwater lifestyle in Knipowitschia and Padogobius lineages. On the basis of the present results, it is uncertain whether the freshwater preference within the genus Padogobius originated twice independently in P. nigricans and P. martensii or only once in their common ancestor. Estimation of the ages of the two major lineages of this group of fish with a molecular clock (in combination with the construction of a linearized tree) suggests that they are much older (at least 40 Myr) than previously thought. Thus, there should be no correlation between their diversification and the Miocene-Pliocene geological events, including the so-called Messinian salinity crisis, which occurred about 10 MYA and is believed to have played a role in their evolution. Alternatively, these gobies would have an evolutionary rate at least fourfold faster than those of other vertebrates

A Microarray study of Carpet-Shell Clam (Ruditapes decussatus) shows common and organ-specific growth-related gene expression Differences in gills and digestive gland

Growth rate is one of the most important traits from the point of view of individual fitness and commercial production in mollusks, but its molecular and physiological basis is poorly known. We have studied differential gene expression related to differences in growth rate in adult individuals of the commercial marine clam Ruditapes decussatus. Gene expression in the gills and the digestive gland was analyzed in 5 fast-growing and five slow-growing animals by means of an oligonucleotide microarray containing 14,003 probes. A total of 356 differentially expressed genes (DEG) were found. We tested the hypothesis that differential expression might be concentrated at the growth control gene core (GCGC), i. e., the set of genes that underlie the molecular mechanisms of genetic control of tissue and organ growth and body size, as demonstrated in model organisms. The GCGC includes the genes coding for enzymes of the insulin/ insulin-like growth factor signaling pathway (IIS), enzymes of four additional signaling pathways (Raf/ Ras/ Mapk, Jnk, TOR, and Hippo), and transcription factors acting at the end of those pathways. Only two out of 97 GCGC genes present in themicroarray showed differential expression, indicating a very little contribution of GCGC genes to growth-related differential gene expression. Forty eight DEGs were shared by both organs, with gene ontology (GO) annotations corresponding to transcription regulation, RNA splicing, sugar metabolism, protein catabolism, immunity, defense against pathogens, and fatty acid biosynthesis. GO termenrichment tests indicated that genes related to growth regulation, development and morphogenesis, extracellular matrix proteins, and proteolysis were overrepresented in the gills. In the digestive gland overrepresented GO terms referred to gene expression control through chromatin rearrangement, RAS-related small GTPases, glucolysis, and energy metabolism. These analyses suggest a relevant role of, among others, some genes related to the IIS, such as the ParaHox gene Xlox, CCAR and the CCN family of secreted proteins, in the regulation of growth in bivalves.Direccion General de Investigacion Cientifica y Tecnica of the Spanish Government [AGL2010-16743, AGL2013-49144-C3-3-R]; COMPETE Program; Portuguese National Funds [PEst-255 C/MAR/LA0015/2011]; Portuguese FCT [UID/Multi/04326/2013]; Generalitat Valenciana; Ministry of Education, Culture, and Sports of the Spanish Government; Association of European Marine Biology Laboratoriesinfo:eu-repo/semantics/publishedVersio

Transcriptional profiling of populations in the clam Ruditapes decussatus suggests genetically determined differentiation in gene expression along parallel temperature gradients and between races of the Atlantic ocean and west Mediterranean sea

Ongoing ocean warming due to climate change poses new challenges for marine life and its exploitation. We have used transcriptomics to find genetically based responses to increased temperature in natural populations of the marine clam Ruditapes decussatus, which lives along parallel thermal gradients in southern Europe. Clams of the Atlantic and West Mediterranean races were collected in northern (cool) and a southern (warm) localities. The animals were kept in running seawater in the warm, southern Atlantic locality for a 15-week period. During this period, water temperature was raised to typical southern European summer values. After this period, an expression profile was obtained for a total of 34 clams and 11,025 probes by means of an oligonucleotide microarray. We found distinct transcriptional patterns for each population based on a total of 552 differentially expressed genes (DEGs), indicating innate differences which probably have a genetic basis. Race and latitude contributed significantly to gene expression differences, with very different sets of DEGs. A gene ontology analysis showed that races differed mainly in the genes involved in ribosomal function and protein biosynthesis, while genes related to glutathione metabolism and ATP synthesis in the mitochondria were the most outstanding with respect to north/south transcriptional differences.Grant AGL2010-16743;info:eu-repo/semantics/publishedVersio

Development of an oligo DNA microarray for the European sea bass and its application to expression profiling of jaw deformity

<p>Abstract</p> <p>Background</p> <p>The European sea bass (<it>Dicentrarchus labrax</it>) is a marine fish of great importance for fisheries and aquaculture. Functional genomics offers the possibility to discover the molecular mechanisms underlying productive traits in farmed fish, and a step towards the application of marker assisted selection methods in this species. To this end, we report here on the development of an oligo DNA microarray for <it>D. labrax</it>.</p> <p>Results</p> <p>A database consisting of 19,048 unique transcripts was constructed, of which 12,008 (63%) could be annotated by similarity and 4,692 received a GO functional annotation. Two non-overlapping 60mer probes were designed for each unique transcript and <it>in-situ </it>synthesized on glass slides using Agilent SurePrint™ technology. Probe design was positively completed for 19,035 target clusters; the oligo microarray was then applied to profile gene expression in mandibles and whole-heads of fish affected by prognathism, a skeletal malformation that strongly affects sea bass production. Statistical analysis identified 242 transcripts that are significantly down-regulated in deformed individuals compared to normal fish, with a significant enrichment in genes related to nervous system development and functioning. A set of genes spanning a wide dynamic range in gene expression level were selected for quantitative RT-PCR validation. Fold change correlation between microarray and qPCR data was always significant.</p> <p>Conclusions</p> <p>The microarray platform developed for the European sea bass has a high level of flexibility, reliability, and reproducibility. Despite the well known limitations in achieving a proper functional annotation in non-model species, sufficient information was obtained to identify biological processes that are significantly enriched among differentially expressed genes. New insights were obtained on putative mechanisms involved on mandibular prognathism, suggesting that bone/nervous system development might play a role in this phenomenon.</p

„DNA barkodiranje“ za pouzdano utvrđivanje izvornosti morskih rakova, mekušaca i riba dostupnih na tržištu

Animal DNA barcoding allows researchers to identify different species by analyzing a short nucleotide sequence, typically the mitochondrial gene cox1. In this paper, we use DNA barcoding to genetically identify seafood samples that were purchased from various locations throughout Italy. We adopted a multi-locus approach to analyze the cob, 16S-rDNA and cox1 genes, and compared our sequences to reference sequences in the BOLD and GenBank online databases. Our method is a rapid and robust technique that can be used to genetically identify crustaceans, mollusks and fishes. This approach could be applied in the future for conservation, particularly for monitoring illegal trade of protected and endangered species. Additionally, this method could be used for authentication in order to detect mislabeling of commercially processed seafood.DNA barkodiranje“ omogućuje istraživačima identifikaciju različitih životinjskih vrsta analizom kratke sekvencije nukleotida, i to obično mitohondrijskog gena cox1. U ovom je radu „DNA barkodiranje“ primjenjeno za identifikaciju uzoraka morskih rakova, mekušaca i riba kupljenih na različitim lokacijama diljem Italije. Sekvencionirani su geni cob, cox1 i 16S-rDNA, a dobivene su sekvencije uspoređene s odgovarajućim sekvencijama u online bazama podataka BOLD i GenBank. Ova metoda omogućuje brzo i točno utvrđivanje genetičkog porijekla rakova, mekušaca i riba, što se može ubuduće primijeniti u svrhu zaštite ugroženih vrsta, te sprečavanje njihove ilegalne prodaje. Također se ovom metodom može utvrditi istinitost podataka na deklaracijama prehrambenih proizvoda od riba, rakova i mekušaca

„DNA barkodiranje“ za pouzdano utvrđivanje izvornosti morskih rakova, mekušaca i riba dostupnih na tržištu

Animal DNA barcoding allows researchers to identify different species by analyzing a short nucleotide sequence, typically the mitochondrial gene cox1. In this paper, we use DNA barcoding to genetically identify seafood samples that were purchased from various locations throughout Italy. We adopted a multi-locus approach to analyze the cob, 16S-rDNA and cox1 genes, and compared our sequences to reference sequences in the BOLD and GenBank online databases. Our method is a rapid and robust technique that can be used to genetically identify crustaceans, mollusks and fishes. This approach could be applied in the future for conservation, particularly for monitoring illegal trade of protected and endangered species. Additionally, this method could be used for authentication in order to detect mislabeling of commercially processed seafood.DNA barkodiranje“ omogućuje istraživačima identifikaciju različitih životinjskih vrsta analizom kratke sekvencije nukleotida, i to obično mitohondrijskog gena cox1. U ovom je radu „DNA barkodiranje“ primjenjeno za identifikaciju uzoraka morskih rakova, mekušaca i riba kupljenih na različitim lokacijama diljem Italije. Sekvencionirani su geni cob, cox1 i 16S-rDNA, a dobivene su sekvencije uspoređene s odgovarajućim sekvencijama u online bazama podataka BOLD i GenBank. Ova metoda omogućuje brzo i točno utvrđivanje genetičkog porijekla rakova, mekušaca i riba, što se može ubuduće primijeniti u svrhu zaštite ugroženih vrsta, te sprečavanje njihove ilegalne prodaje. Također se ovom metodom može utvrditi istinitost podataka na deklaracijama prehrambenih proizvoda od riba, rakova i mekušaca