About
103
Publications
11,835
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
1,448
Citations
Citations since 2017
Publications
Publications (103)
The molecular factors and gene regulation involved in sex determination and gonad differentiation in bivalve molluscs are unknown. It has been suggested that doubly uniparental inheritance (DUI) of mitochondria may be involved in these processes in species such as the ubiquitous and commercially relevant Manila clam, Ruditapes philippinarum. We pre...
The presence of Listeria monocytogenes (Lm) in the food processing environment (facilities and products) is a challenging problem in food safety management. Lm is one of the main causes of mortality in foodborne infections, and the trend is continuously increasing. In this study, a collection of 323 Lm strain isolates recovered from food matrices a...
Amyl salicylate (AS) is a fragrance massively used as a personal care product (PCP) and following the discharged in wastewaters may end up in the aquatic environment representing a potential threat for the ecosystem and living organisms. AS was recently detected in water of the Venice Lagoon, a vulnerable area continuously subjected to the income o...
The mitogenome of the species belonging to the Papilionodea (Lepidoptera) is a double stranded circular molecule containing the 37 genes shared by Metazoa. Eight mitochondrial gene orders are known in the Papilionoidea. MIQGO is the plesiomorphic gene order for this superfamily, while other mitochondrial arrangements have a very limited distributio...
Background
Susceptibility of European sea bass ( Dicentrarchus labrax L.) to viral nervous necrosis (VNN) is well-known. Interest towards selective breeding as a tool to enhance genetic resistance in this species has increased sharply due to the major threat represented by VNN for farmed sea bass and limitations concerning specific therapeutical me...
Chronic exposure to pollutants affects natural populations, creating specific molecular and biochemical signatures. In the present study, we tested the hypothesis that chronic exposure to pollutants might have substantial effects on the Manila clam hologenome long after removal from contaminated sites. To reach this goal, a highly integrative appro...
The giant Antarctic toothfish Dissostichus mawsoni is one of the most economically valued fishery resources from the Southern Ocean. However, the distinctive biological characteristics and life history of this species, including large body size, long life span, late sexual maturity, and specialization to freezing polar waters, make it particularly...
Disease resistance represents a key trait for breeding programs in aquaculture species. Here we re-analysed 2bRAD sequence data from two experimental challenges of gilthead sea bream with Photobacterium damsealae piscicida. Using a high quality reference genome, we carried out variant calling and data imputation with Beagle to obtain a large set of...
Vibrios represent a natural contaminant of seafood products. V. alginolyticus, V. cholerae, V. parahaemolyticus and V. vulnificus are the most hazardous species to human health. Given the worldwide consumption of mollusc products, reliable detection of Vibrio species is recommended to prevent human vibriosis. In this study, culture-dependent and -i...
The gilthead sea bream (Sparus aurata) is a marine fish of great importance for Mediterranean aquaculture. This species has long been considered resistant to Nervous Necrosis Virus (NNV), an RNA virus that causes massive mortalities in several farmed fish animals. However, the recent appearance of RGNNV/SJNNV reassortant strains started to pose a s...
The vertebrate mitochondrial genomes generally present a typical gene order. Exceptions are uncommon and important to study the genetic mechanisms of gene order rearrangements and their consequences on phylogenetic output and mitochondrial function. Antarctic notothenioid fish carry some peculiar rearrangements of the mitochondrial gene order. In t...
Whole-genome sequencing data were produced from a single flathead grey mullet female and assembled into a draft genome sequence, whereas publicly available sequence data were used to obtain a male draft sequence. Two pools, each consisting of 60 unrelated individuals, respectively, of male and female fish were analyzed using Pool-Sequencing. Mappin...
• Sharks are a priority for conservation because numerous species, including small‐sized coastal species, are being heavily exploited by commercial and recreational fisheries. Understanding the genetic population structure of sharks is key to effective management, maximizing their evolutionary potential in a rapidly changing environment and prevent...
As filter‐feeders, bivalve molluscs accumulate Vibrio into edible tissues. Consequently, an accurate assessment of depuration procedures and the characterization of the persistent Vibrio community in depurated shellfish represent a key issue to guarantee food safety in shellfish products. The present study investigated changes in the natural Vibrio...
Glyphosate, the most widely used herbicide worldwide, targets the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) enzyme in the shikimate pathway found in plants and some microorganisms. While the potential for glyphosate to induce a broad range of biological effects in exposed organisms has been demonstrated, the global molecular mechanisms of...
The tight connection between immunity and reproduction has been studied for decades. However, basic knowledge at the molecular level of the effect of mating on immune function is still lacking in many taxa. Determining whether and how the immune system is engaged after mating is a crucial step in understanding post‐mating mechanisms of reproduction...
Antarctic fish belonging to Notothenioidei represent an extraordinary example of radiation in the cold. In addition to the absence of hemoglobin, icefish show a number of other striking peculiarities including large-diameter blood vessels, high vascular densities, mitochondria-rich muscle cells, and unusual mitochondrial architecture. In order to i...
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
The aim of this study was to estimate the heritability for mortality after a VNN challenge test in a sea bass experimental population derived from a commercial stock, as well as for cortisol concentration after stress exposure and body weight at a fixed age. Genetic and phenotypic correlations among traits were also estimated, with the aim of ident...
Information on the population dynamics of a reservoir species have been increasingly adopted to understand and eventually predict the dispersal patterns of infectious diseases throughout an area. Although potentially relevant, to date there are no studies which have investigated the genetic structure of the red fox population in relation to infecti...
Sample table.
Table showing in sequence year of collection, country of origin, specific location, disease status, sample ID, list of alleles for each microsatellite locus.
(XLSX)
Correlogram of the autocorrelation coefficient (r) as a function of distance classes.
Correlogram of the whole dataset with distance classes of 10 km. Correlation coefficient (r) is shown in the vertical axis. Error bars bound the 95% confidence interval determined by bootstrap resampling (999 iterations). Upper (U) and lower (L) confidence limits...
Distribution of the genetic groups (A-B-C) in the study area. Considering structure result K = 3 for the complete dataset, individuals assigned to groups A, B and C are identified with violet, light green and orange dots, respectively. Samples with an assignment probability greater than or equal to 0.7 (Q ≥ 0.7) are shown with dots; admixed individ...
Structure program results.
Structure analysis performed on the Italian subset estimated K = 4 as the most likely number of clusters.
(TIF)
Mantel test.
Geographic Distance in km (GGD) on the x-axes and Linear Genetic Distance (LinGD) on the y-axes.
(TIF)
Material and methods supplemental information.
(DOCX)
Sexual dimorphism is a fascinating subject in evolutionary biology and mostly results from sex-biased expression of genes, which have been shown to evolve faster in gonochoristic species. We report here genome and sex-specific transcriptome sequencing of Sparus aurata, a sequential hermaphrodite fish. Evolutionary comparative analysis reveals that...
Yellowfin tuna, Thunnus albacares, is one of the most important seafood commodities in the world. Despite its great biological and economic importance, conflicting evidence arises from classical genetic and tagging studies concerning the yellowfin tuna population structure at local and global oceanic scales. Access to more powerful and cost effecti...
We sequenced the mitochondrial genomes of the spider crabs Maja crispata and Maja squinado (Majidae, Brachyura). Both genomes contain the whole set of 37 genes characteristic of Bilaterian genomes, encoded on both α- and β-strands. Both species exhibit the same gene order, which is unique among known animal genomes. In particular, all the genes loc...
Human pharmaceuticals such as Acetaminophen, Atenolol and Carbamazepine are pseudo persistent aquatic pollutants with yet unknown sub-lethal effects at environmentally relevant concentrations. Gilthead seabream (Sparus aurata) were exposed to Acetaminophen: 31.90 ± 11.07 μg L⁻¹; Atenolol: 0.95 ± 0.38 μg L⁻¹ and Carbamazepine: 6.95 ± 0.13 μg L⁻¹ in...
A study was conducted on the habitat distribution of four sympatric species of Periophthalmus (the silver-lined mudskipper Periophthalmus argentilineatus, the slender mudskipper Periophthalmus gracilis, the kalolo mudskipper Periophthalmus kalolo and the Malacca mudskipper Periophthalmus malaccensis) from northern Sulawesi. Molecular phylogenetic r...
The aim of the present study was to identify transcriptional modifications and regulatory networks accounting for physiological and metabolic responses to specific nutrients in the liver of young Belgian Blue × Holstein bulls using RNA-sequencing. A larger trial has been carried out in which animals were fed with different diets: 1] a conventional...
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 fou...
Boxplot of the natural log transformed estimated gene counts per animal after trimmed mean of M-values (TMM) normalization.
Boxplots were created with the ggplot2 package in the R statistical environment.
(TIFF)
Mapping summary statistics of RNA sequencing data.
Comparative results obtained by CLC Genomics Workbench and HTSeq-count tools.
(XLS)
Differentially expressed genes (FDR < 0.05) for comparison among experimental diets.
LowI: low-impact; Conv: conventional diet; Nutr: nutraceutical diet.
(XLSX)
Correlation matrix of Pearson product-moment correlations between liver mineral profiles and differentially expressed genes.
Pearson product-moment correlation coefficients and P values are reported for all correlations.
(TXT)
Differential alternative splicing events for all comparisons using rMATS.
Significant differences (FDR < 0.05) in the inclusion of splicing events across the experimental diets. Conv: conventional diet; LowI: low-impact diet.
(XLSX)
Canonical pathways enriched in the experimental diets using IPA.
The ratio values (number of molecules in a given pathway that meets cut criteria, divided by total number of molecules that make up that pathway) are also presented.
(XLSX)
Upstream regulators analysis results for comparison among experimental diets using IPA.
IPA prediction of upstream regulators that are activated or inhibited to explain the upregulated and downregulated genes observed in the experimental diets.
(XLSX)
Interclass principal component analysis (PCA) of normalized gene count data.
The plot was created using principal component analysis function implemented in the ade4 R package with samples as variables and differential expression comparison groups as class levels.
(TIFF)
Corresponding author at: Environmental and Life Sciences, Universiti Brunei Darussalam, Bandar Seri Begawan, Gadong, Negara Brunei Darussalam.
Global population genetic structure of yellowfin tuna (Thunnus albacares) is still poorly understood despite its relevance for the tuna fishery industry. Low levels of genetic differentiation among oceans speak in favour of the existence of a single panmictic population worldwide of this highly migratory fish. However, recent studies indicated gene...
The advent of Next-Generation Sequencing (NGS) has dramatically changed bacterial typing technologies, increasing our ability to differentiate bacterial isolates. Despite it is now possible to sequence a bacterial genome in a few days and at reasonable costs, most genetic analyses do not require whole-genome sequencing, which also remains impractic...
The euryhaline European sea bass Dicentrarchus labrax L., inhabiting the coasts of the eastern Atlantic Ocean and Mediterranean Sea, has had many opportunities for differentiation throughout its large natural range. However, evidence for this has been incompletely documented geographically and with an insufficient number of markers. Therefore, its...
Insect mitochondrial genomes (mtDNA) are usually double helical and circular molecules containing 37 genes that are encoded on both strands. The arrangement of the genes is not constant for all species, and produces distinct gene orders (GOs) that have proven to be diagnostic in defining clades at different taxonomic levels. In general, it is belie...
The Manila clam (Ruditapes philippinarum) is a cultured bivalve with worldwide commercial importance, and diseases cause high economic losses. For this reason, interest in the immune genes in this species has recently increased. The present work describes the construction of the first R. philippinarum microarray containing immune-related hemocyte s...
This study provides a first description of the phylogeographic patterns and evolutionary history of two species of the mudskipper genus Periophthalmus. These amphibious gobies are distributed throughout the whole Indo-Pacific region and Atlantic coast of Africa, in peritidal habitats of soft-bottom coastal ecosystems. Three sequence datasets of two...
Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome-wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneit...
The introduction of Next Generation Sequencing (NGS) has revolutionised population genetics, providing studies of non-model species with unprecedented genomic coverage, allowing evolutionary biologists to address questions previously far beyond the reach of available resources. Furthermore, the simple mutation model of Single Nucleotide Polymorphis...
