A bacterial and viral genome catalogue from Atlantic salmon highlights diverse gut microbiome compositions at pre- and post-smolt life stages.

Resolving the microbiome of the Atlantic salmon Salmo salar gut is challenged by a low microbial diversity often dominated by one or two species of bacteria, and high levels of host contamination in sequencing data. Nevertheless, existing metabarcoding and metagenomic studies consistently resolve a putative beneficial Mycoplasma species as the most abundant organism in gut samples. The remaining microbiome is heavily influenced by factors such as developmental stage and water salinity.

Inversions Dominate Evolution in the European Sardine (Sardina pilchardus) Amid Strong Gene Flow.

Inversions can play key roles in the genetic architecture of adaptation, but the scale of their effects across different species remains poorly understood. Here, we use whole-genome sequencing and demographic modelling to investigate the influence of inversions on the population genomics of the r-selected European sardine (Sardina pilchardus). Allele frequency differences from millions of SNPs across 34 populations spanning the species' range were analysed.

Identifying HEXACO personality types: what do type characteristics tell us about student misconduct?

Background: While previous research has largely focused on individual trait associations with academic misbehaviour, this study used a person-centred approach to explore personality type differences in student misconduct. The distribution of the personality types was also compared across sociodemographic groups and fields of study.

Methods: A sample of 1,398 health and non-health university students replied to a multiple-choice questionnaire covering HEXACO personality traits, eight forms of academic misconduct, and background information.

Origin of immunoglobulins and T cell receptors: A candidate gene for invasion by the RAG transposon.

Rearranging antigen receptors (AgRs) arose when a variable (V) domain exon was invaded by the recombination-activating gene (RAG) transposon ~500 million years ago. We show here that the elasmobranch immunoglobulin heavy (IgH) isotypes-IgM, IgW, and IgNAR-are linked near the αδ T cell receptor (TCRαδ) locus. This linkage presages the emergence of the osteichthyan IgH translocon arrangement and clarifies the relationship between IgH and TCRδs.

Genetic structure and historical demography of inland wetland fish using the endangered Lisbon arched-mouth nase as a case-study.

Inland wetlands are highly diverse, productive ecosystems at the transition between terrestrial and aquatic environments, providing major services to society. They are also under high human pressure and have suffered a progressive decline in total area globally. Here, we describe the genetic diversity and demography of the endangered Lisbon arched-mouth nase Iberochondrostoma olisiponense occurring in the inland wetlands of a major river in southwestern Europe, within a context of extreme habitat changes.

Validation of the academic misconduct questionnaire: exploring predictors of student misconduct.

Multiple instruments have been used to assess academic misconduct, yet robust psychometric evidence has been reported only for a few. This study aims to determine the validity and dimensionality of a novel Academic Misconduct Questionnaire (AMQ) and to explore differences between students who engage in distinct misbehaviours. A diverse sample of health and non-health students replied to the AMQ.

Genetic diversity in the American elephantfish (Chimaeriformes: Callorhinchus callorynchus) and among its congeners.

Understanding genetic population structure and connectivity is essential for effective species-specific management and conservation strategies. The American elephantfish Callorhinchus callorynchus is targeted and retained as incidental catch in commercial and recreational fisheries in Chile and Argentina. Its wide-ranging distribution across southern South America may require transnational co-operation to ensure sustainable use, but its current population structure is not known.

Improving Whole Biodiversity Monitoring and Discovery With Environmental DNA Metagenomics.

Environmental DNA (eDNA) metagenomics sequences all DNA molecules present in environmental samples and has the potential of identifying virtually any organism from which they are derived. However, due to unacceptable levels of false positives and negatives, this approach is underexplored as a tool for biodiversity monitoring across the tree of life, particularly for non-microscopic eukaryotes. We present SeqIDist, a framework that combines multilocus BLAST matches against several reference databases followed by an analysis of sequence identity distribution patterns to disentangle false positives while revealing new biodiversity and increasing the accuracy of metagenomic approaches.

Allele co-segregation and haplotype diversity of MHC IIβ genes in the small-spotted catshark Scyliorhinus canicula.

The major histocompatibility complex (MHC) constitutes a functionally relevant multigene family playing an essential role in the adaptive immune responses of jawed vertebrates, being directly involved in pathogen recognition. MHC diversity, driven by pathogen-mediated selection, is vital for species survival and is characterized by high genetic diversity in many taxa, namely at the sequence, allelic and haplotype levels. Chondrichthyans, the most basal jawed vertebrates with an adaptive immune system, exhibit a high diversity of MHC gene lineages conservatively organized in a compact region of the genome.

Freshwater fish community assessment using eDNA metabarcoding vs. capture-based methods: Differences in efficiency and resolution coupled to habitat and ecology.

Environmental DNA (eDNA) metabarcoding has revolutionized ecological and environmental research by describing communities without relying on direct observations, making it a powerful, non-invasive, and cost-effective tool in biodiversity monitoring. However, the adoption of eDNA as a standard protocol in long-term monitoring programs, which have traditionally relied on capture-based methods, presents challenges in terms of data comparability. Here, we compared freshwater fish communities assessed through eDNA metabarcoding and electrofishing, across 35 sampling sites in the lower Tagus River basin, Portugal.

The mitochondrial genomes of Iberian freshwater and diadromous fishes.

The Iberian Peninsula, in southwestern Europe, is home to a distinctive freshwater fish fauna, predominantly composed of endemic species. This is a consequence of the prolonged isolation from western Europe caused by the Pyrenees, the diverse geological and climatic gradients, and the isolation of river basins. Freshwater and diadromous fishes have diversified in the Iberian Peninsula and include 72 currently recognized native species, 50 of which are endemic to the region.

Core Competences of School Nurses for the Development of Anti-Bullying Strategies: Protocol for a Scoping Review.

Background/objectives: School nurses are capable of fostering safe and healthy school environments that are favorable to quality learning and social interactions. To this end, it is essential that they acquire a set of skills needed to implement bullying intervention programs. This article describes the protocol for a scoping review to identify and map the core competences for school nurses to develop anti-bullying strategies.

The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production.

Microbiome-directed dietary interventions such as microbiota-directed fibers (MDFs) have a proven track record in eliciting responses in beneficial gut microbes and are increasingly being promoted as an effective strategy to improve animal production systems. Here we used initial metataxonomic data on fish gut microbiomes as well as a wealth of a priori mammalian microbiome knowledge on α-mannooligosaccharides (MOS) and β-mannan-derived MDFs to study effects of such feed supplements in Atlantic salmon (Salmo salar) and their impact on its gut microbiome composition and functionalities. Our multi-omic analysis revealed that the investigated MDFs (two α-mannans and an acetylated β-galactoglucomannan), at a dose of 0.

Engineering the Rhizosphere Microbiome with Plant Growth Promoting Bacteria for Modulation of the Plant Metabolome.

Plant-growth-promoting bacteria (PGPB) have beneficial effects on plants. They can promote growth and enhance plant defense against abiotic stress and disease, and these effects are associated with changes in the plant metabolite profile. The research problem addressed in this study was the impact of inoculation with PGPB on the metabolite profile of L.

The complete mitogenome of the Atlantic longnose chimaera (Holt & Byrne, 1909).

Holocephali is a subclass of chondrichthyans with ample geographic distribution in marine ecosystems. Holocephalan species are organized into three families: Callorhinchidae, Chimaeridae, and Rhinochimaeridae. Despite the critical ecological and evolutionary importance, genomic information from holocephalans is still scarce, particularly from rhinochimaerids.

Fatty Acid Profiling as a Tool for Fostering the Traceability of the Halophyte Plant and Contributing to Its Nutritional Valorization.

, commonly known as glasswort or sea asparagus, is a halophyte plant cultivated for human consumption that is often referred to as a sea vegetable rich in health-promoting -3 fatty acids (FAs). Yet, the effect of abiotic conditions, such as salinity and temperature, on the FA profile of remains largely unknown. These factors can potentially shape its nutritional composition and yield unique fatty acid signatures that can reveal its geographical origin.

CD4 and LAG-3 from sharks to humans: related molecules with motifs for opposing functions.

CD4 and LAG-3 are related molecules that are receptors for MHC class II molecules. Their major functional differences are situated in their cytoplasmic tails, in which CD4 has an activation motif and LAG-3 an inhibitory motif. Here, we identify shark and show that a previously identified shark gene has a genomic location, expression pattern, and motifs similar to in other vertebrates.

An Ancestral Major Histocompatibility Complex Organization in Cartilaginous Fish: Reconstructing MHC Origin and Evolution.

Cartilaginous fish (sharks, rays, and chimeras) comprise the oldest living jawed vertebrates with a mammalian-like adaptive immune system based on immunoglobulins (Ig), T-cell receptors (TCRs), and the major histocompatibility complex (MHC). Here, we show that the cartilaginous fish "adaptive MHC" is highly regimented and compact, containing (i) a classical MHC class Ia (MHC-Ia) region containing antigen processing (antigen peptide transporters and immunoproteasome) and presenting (MHC-Ia) genes, (ii) an MHC class II (MHC-II) region (with alpha and beta genes) with linkage to beta-2-microglobulin (β2m) and bromodomain-containing 2, (iii) nonclassical MHC class Ib (MHC-Ib) regions with 450 million-year-old lineages, and (iv) a complement C4 associated with the MHC-Ia region. No MHC-Ib genes were found outside of the elasmobranch MHC.

Dataset of the complete mitogenome of the deep-sea sailfin roughshark, Frade, 1929.

Chondrichthyans comprise a diverse group of vertebrate species with extraordinary ecological relevance. Yet, multiple members of this evolutionary lineage are associated with significant extinction risk. The sailfin roughshark is a deep-water benthic shark currently listed as vulnerable due to population declines in parts of its range.

Identification and characterization of a polyomavirus in the thornback skate (Raja clavata).

Members of the family Polyomaviridae have a circular double-stranded DNA genome that have been identified in various hosts ranging from mammals to arachnids. Here we report the identification and analysis of a complete genome sequence of a novel polyomavirus, Raja clavata polyomavirus (RcPyV1), from a cartilaginous fish, the thornback skate (Raja clavata). The genome sequence was determined using a metagenomics approach with an aim to provide baseline viral data in cartilaginous fish in different ecosystems.

Warming during embryogenesis induces a lasting transcriptomic signature in fishes.

Exposure to elevated temperatures during embryogenesis can influence the plasticity of tissues in later life. Despite these long-term changes in plasticity, few differentially expressed genes are ever identified, suggesting that the developmental programming of later life plasticity may occur through the modulation of other aspects of transcriptomic architecture, such as gene network organisation. Here, we use network modelling approaches to demonstrate that warm temperatures during embryonic development (developmental warming) have consistent effects in later life on the organisation of transcriptomic networks across four diverse species of fishes: Scyliorhinus canicula, Danio rerio, Dicentrarchus labrax, and Gasterosteus aculeatus.

Corrigendum: Uncovering a 500 million year old history and evidence of pseudogenization for TLR15.

[This corrects the article DOI: 10.3389/fimmu.2022.

Extensive MHC class IIβ diversity across multiple loci in the small-spotted catshark (Scyliorhinus canicula).

The major histocompatibility complex (MHC) is a multigene family responsible for pathogen detection, and initiation of adaptive immune responses. Duplication, natural selection, recombination, and their resulting high functional genetic diversity spread across several duplicated loci are the main hallmarks of the MHC. Although these features were described in several jawed vertebrate lineages, a detailed MHC IIβ characterization at the population level is still lacking for chondrichthyans (chimaeras, rays and sharks), i.