Haplotype-resolved and near-T2T genome assembly of the African catfish (Clarias gariepinus).

Airbreathing catfish are stenohaline freshwater fish capable of withstanding various environmental conditions and farming practices, including breathing atmospheric oxygen. This unique ability has enabled them to thrive in semi-terrestrial habitats. However, the genomic mechanisms underlying their adaptation to adverse ecological environments remain largely unexplored, primarily due to the limited availability of high-quality genomic resources.

Evaluation of blood cell viability rate, gene expression, and O-GlcNAcylation profiles as indicative signatures for fungal stimulation of salmonid cell models.

Fungal diseases of fish are a significant economic problem in aquaculture. Using high-throughput expression analysis, we identified potential transcript markers in primary head kidney and secondary embryonic cells from salmonid fish after stimulation with the inactivated fungi Mucor hiemalis and Fusarium aveneacium and with purified fungal molecular patterns. The transcript levels of most of the 45 selected genes were altered in head-kidney cells after 24 h of stimulation with fungal antigens.

Comprehensive Characterization of Multitissue Expression Landscape, Co-Expression Networks and Positive Selection in Pikeperch.

Promising efforts are ongoing to extend genomics resources for pikeperch (), a species of high interest for the sustainable European aquaculture sector. Although previous work, including reference genome assembly, transcriptome sequence, and single-nucleotide polymorphism genotyping, added a great wealth of genomic tools, a comprehensive characterization of gene expression across major tissues in pikeperch still remains an unmet research need. Here, we used deep RNA-Sequencing of ten vital tissues collected in eight animals to build a high-confident and annotated trancriptome atlas, to detect the tissue-specificity of gene expression and co-expression network modules, and to investigate genome-wide selective signatures in the Percidae fish family.

Quality control in scRNA-Seq can discriminate pacemaker cells: the mtRNA bias.

Single-cell RNA-sequencing (scRNA-seq) provides high-resolution insights into complex tissues. Cardiac tissue, however, poses a major challenge due to the delicate isolation process and the large size of mature cardiomyocytes. Regardless of the experimental technique, captured cells are often impaired and some capture sites may contain multiple or no cells at all.

Effects of Chronic Hypoxia on the Immune Status of Pikeperch ( Linnaeus, 1758).

Inadequate oxygen saturation can induce stress responses in fish and further affect their immunity. Pikeperch, recently introduced in intensive aquaculture, is suggested to be reared at nearly 100% DO (dissolved oxygen), yet this recommendation can be compromised by several factors including the water temperature, stocking densities or low circulation. Herein, we aimed to investigate the effect of low oxygen saturation of 40% DO (±3.

Insights into early ontogenesis: characterization of stress and development key genes of pikeperch (Sander lucioperca) in vivo and in vitro.

There are still numerous difficulties in the successful farming of pikeperch in the anthropogenic environment of various aquaculture systems, especially during early developmental steps in the hatchery. To investigate the physiological processes involved on the molecular level, we determined the basal expression patterns of 21 genes involved in stress and immune responses and early ontogenesis of pikeperch between 0 and 175 days post hatch (dph). Their transcription patterns most likely reflect the challenges of growth and feed conversion.

Time-Dependent Effects of Acute Handling on the Brain Monoamine System of the Salmonid .

The immediate stress response involves the activation of the monoaminergic neurotransmitter systems including serotonin, dopamine and noradrenaline in particular areas of the fish brain. We chose maraena whitefish as a stress-sensitive salmonid species to investigate the influence of acute and chronic handling on the neurochemistry of monoamines in the brain. Plasma cortisol was quantified to assess the activation of the stress axis.

An ultra-high density SNP-based linkage map for enhancing the pikeperch (Sander lucioperca) genome assembly to chromosome-scale.

Pikeperch (Sander lucioperca) is a fish species with growing economic significance in the aquaculture industry. However, successful positioning of pikeperch in large-scale aquaculture requires advances in our understanding of its genome organization. In this study, an ultra-high density linkage map for pikeperch comprising 24 linkage groups and 1,023,625 single nucleotide polymorphisms markers was constructed after genotyping whole-genome sequencing data from 11 broodstock and 363 progeny, belonging to 6 full-sib families.

Comparative Analysis of the Transcriptome and Distribution of Putative SNPs in Two Rainbow Trout () Breeding Strains by Using Next-Generation Sequencing.

Selective breeding can significantly improve the establishment of sustainable and profitable aquaculture fish farming. For rainbow trout (), one of the main aquaculture coldwater species in Europe, a variety of selected hatchery strains are commercially available. In this study, we investigated the genetic variation between the local Born strain, selected for survival, and the commercially available Silver Steelhead strain, selected for growth.

Indication of Premelanosome Protein (PMEL) Expression Outside of Pigmented Bovine Skin Suggests Functions Beyond Eumelanogenesis.

The premelanosome protein (PMEL) is important for fibril formation within melanosomes during vertebrate melanogenesis. Fibrils form a matrix for pigment deposition within pigmented tissues such as skin and hair. PMEL mutations are known to modulate eumelanic pigmentation in vertebrates.

Integrative Cluster Analysis of Whole Hearts Reveals Proliferative Cardiomyocytes in Adult Mice.

The recent development and broad application of sequencing techniques at the single-cell level is generating an unprecedented amount of data. The different techniques have their individual limits, but the datasets also offer unexpected possibilities when utilized collectively. Here, we applied snRNA-seq in whole adult murine hearts from an inbred (C57BL/6NRj) and an outbred (Fzt:DU) mouse strain to directly compare the data with the publicly available scRNA-seq data of the tabula muris project.

Identification and Annotation of Potential Function of Regulatory Antisense Long Non-Coding RNAs Related to Feed Efficiency in Bulls.

Long non-coding RNAs (lncRNAs) can influence transcriptional and translational processes in mammalian cells and are associated with various developmental, physiological and phenotypic conditions. However, they remain poorly understood and annotated in livestock species. We combined phenotypic, metabolomics and liver transcriptomic data of bulls divergent for residual feed intake (RFI) and fat accretion.

Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity.

Analyses on the cellular level are indispensable to expand our understanding of complex tissues like the mammalian heart. Single-nucleus sequencing (snRNA-seq) allows for the exploration of cellular composition and cell features without major hurdles of single-cell sequencing. We used snRNA-seq to investigate for the first time an entire adult mammalian heart.

Gene Profiling in the Adipose Fin of Salmonid Fishes Supports its Function as a Flow Sensor.

In stock enhancement and sea-ranching procedures, the adipose fin of hundreds of millions of salmonids is removed for marking purposes annually. However, recent studies proved the significance of the adipose fin as a flow sensor and attraction feature. In the present study, we profiled the specific expression of 20 neuron- and glial cell-marker genes in the adipose fin and seven other tissues (including dorsal and pectoral fin, brain, skin, muscle, head kidney, and liver) of the salmonid species rainbow trout and maraena whitefish Moreover, we measured the transcript abundance of genes coding for 15 mechanoreceptive channel proteins from a variety of mechanoreceptors known in vertebrates.

Biological Network Approach for the Identification of Regulatory Long Non-Coding RNAs Associated With Metabolic Efficiency in Cattle.

Genomic regions associated with divergent livestock feed efficiency have been found predominantly outside protein coding sequences. Long non-coding RNAs (lncRNA) can modulate chromatin accessibility, gene expression and act as important metabolic regulators in mammals. By integrating phenotypic, transcriptomic, and metabolomic data with quantitative trait locus data in prioritizing co-expression network analyses, we aimed to identify and functionally characterize lncRNAs with a potential key regulatory role in metabolic efficiency in cattle.

Early response of salmonid head-kidney cells to stress hormones and toll-like receptor ligands.

The functional spectrum of the teleostean head kidney covers haematopoietic, immune and endocrine signalling pathways with physiological effects that are likely to conflict if activated at the same time. An in vivo experiment on the salmonid fish maraena whitefish (Coregonus maraena) revealed that the head kidney shows a remarkably strong response after injection of Aeromonas salmonicida within 48 h. In order to investigate the potential influence of endocrine signalling on the initiation of immune responses, we established a primary culture of head-kidney cells of maraena whitefish.

The First Highly Contiguous Genome Assembly of Pikeperch (), an Emerging Aquaculture Species in Europe.

The pikeperch () is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and domestication process.

Differentiating Staphylococcus aureus from Escherichia coli mastitis: S. aureus triggers unbalanced immune-dampening and host cell invasion immediately after udder infection.

The etiology determines quality and extent of the immune response after udder infection (mastitis). Infections with Gram negative bacteria (e.g.

Establishment and Characterization of an SV40 Large T Antigen-Transduced Porcine Colonic Epithelial Cell Line.

Continuous cell lines have become indispensable tools that have enabled investigations into cellular mechanisms by increasing experimental reproducibility and sample availability, and decreasing the use of experimental animals. To facilitate studies of epithelial barrier function of the porcine colon, we aimed to establish an epithelial cell line with an extended replicative capacity. Cells were isolated from the proximal colon of a 3-week-old piglet and transduced using a recombinant retroviral vector construct containing the simian virus 40 large T antigen (SV40 TAg).

Transcriptome sequencing of maraena whitefish (Coregonus maraena).

Maraena whitefish (Coregonus maraena, Bloch, 1779) is a high-quality food fish belonging to the family Salmonidae with considerable economic relevance in the Baltic area. Aquaculture of this species is fundamental for its successful conservation and thus sustainable fisheries. Robust fishes obtained from breeding lines build the basis for effective aquaculture.

Cloning and characterization of the proximal promoter region of rainbow trout (Oncorhynchus mykiss) interleukin-6 gene.

Interleukin-6 (IL6) is a pleiotropic cytokine with important immunoregulatory functions. Its expression is inducible in immune cells and tissues of several fish species. We also found that IL6 mRNA abundance was significantly increased in spleen, liver, and gill of rainbow trout after experimental infection with Aeromonas salmonicida.

Genome-Wide Association Identifies TBX5 as Candidate Gene for Osteochondrosis Providing a Functional Link to Cartilage Perfusion as Initial Factor.

Osteochondrosis (OC) is an orthopedic syndrome of the joints that occurs in children and adolescents and domestic animals, particularly pigs, horses, and dogs. OC is the most frequent cause of leg weakness in rapidly growing pigs causing animal welfare issues and economic losses. In this study, a genome-wide association study (GWAS) was performed using the Porcine 60k SNPChip in animals of the breed Large White (n = 298) to identify chromosome regions and candidate genes associated with OC lesion scores.