The growing amount of genome information and transcriptomes data available allows for a better understanding of biological processes. However, analysis of complex transcriptomic experimental designs involving different conditions, tissues, or times is relevant. This study proposes a novel approach to analyze complex data sets combining transcriptomes and miRNAs at the chromosome-level genome. Atlantic salmon smolts were transferred to seawater under two strategies: (i) fish group exposed to gradual salinity changes (GSC) and (ii) fish group exposed to a salinity shock (SS). Gills, intestine, and head kidney samples were used for total RNA extraction, followed by mRNA and small RNA illumina sequencing. Different expression patterns among the tissues and treatments were observed through a whole-genome transcriptomic approach. Chromosome regions highly expressed between experimental conditions included a great abundance of transposable elements. In addition, differential expression analysis showed a greater number of transcripts modulated in response to SS in gills and head kidney. miRNA expression analysis suggested a small number of miRNAs involved in the smoltification process. However, target analysis of these miRNAs showed a regulatory role in growth, stress response, and immunity. This study is the first to evidence the interplaying among mRNAs and miRNAs and the structural relationship at the genome level during Atlantic salmon smoltification.

Salmon aquaculture is constantly threatened by pathogens that impact fish health, welfare, and productivity, including the sea louse Caligus rogercresseyi. This marine ectoparasite is mainly controlled through delousing drug treatments that have lost efficacy. Therein, strategies such as salmon breeding selection represent a sustainable alternative to produce fish with resistance to sea lice. This study explored the whole-transcriptome changes in Atlantic salmon families with contrasting resistance phenotypes against lice infestation. In total, 121 Atlantic salmon families were challenged with 35 copepodites per fish and ranked after 14 infestation days. Skin and head kidney tissue from the top two lowest (R) and highest (S) infested families were sequenced by the Illumina platform. Genome-scale transcriptome analysis showed different expression profiles between the phenotypes. Significant differences in chromosome modulation between the R and S families were observed in skin tissue. Notably, the upregulation of genes associated with tissue repairs, such as collagen and myosin, was found in R families. Furthermore, skin tissue of resistant families showed the highest number of genes associated with molecular functions such as ion binding, transferase, and cytokine activity, compared with the susceptible. Interestingly, lncRNAs differentially modulated in the R/S families are located near genes associated with immune response, which are upregulated in the R family. Finally, SNPs variations were identified in both salmon families, where the resistant ones showed the highest number of SNPs variations. Remarkably, among the genes with SPNs, genes associated with the tissue repair process were identified. This study reported Atlantic salmon chromosome regions exclusively expressed in R or S Atlantic salmon families’ phenotypes. Furthermore, due to the presence of SNPs and high expression of tissue repair genes in the resistant families, it is possible to suggest mucosal immune activation associated with the Atlantic salmon resistance to sea louse infestation.

The host’s physiological history and environment determine the microbiome structure. In that sense, the strategy used for the salmon transfer to seawater after parr-smolt transformation may influence the Atlantic salmon’s intestinal microbiota. Therefore, this study aimed to explore the diversity and abundance of the Atlantic salmon intestinal microbiota and metagenome functional prediction during seawater transfer under three treatments. One group was exposed to gradual salinity change (GSC), the other to salinity shock (SS), and the third was fed with a functional diet (FD) before the seawater (SW) transfer. The microbial profile was assessed through full-16S rRNA gene sequencing using the Nanopore platform. In addition, metagenome functional prediction was performed using PICRUSt2. The results showed an influence of salinity changes on Atlantic salmon gut microbiota richness, diversity, and taxonomic composition. The findings reveal that GSC and the FD increased the Atlantic salmon smolt microbiota diversity, suggesting a positive association between the intestinal microbial community and fish health during seawater transfer. The reported knowledge can be applied to surveil the microbiome in smolt fish production, improving the performance of Atlantic salmon to seawater transfer.

Infection processes displayed by pathogens require the acquisition of essential inorganic nutrients and trace elements from the host to survive and proliferate. Without a doubt, iron is a crucial trace metal for all living organisms and also a pivotal component in the host–parasite interactions. In particular, the host reduces the iron available to face the infectious disease, increasing iron transport proteins’ expression and activating the heme synthesis and degradation pathways. Moreover, recent findings have suggested that iron metabolism modulation in fish promotes the immune response by reducing cellular iron toxicity. We hypothesized that recombinant proteins related to iron metabolism could modulate the fish’s immune system through iron metabolism and iron-responsive genes. Here a chimeric iron transport protein (IPath^®) was bioinformatically designed and then expressed in a recombinant bacterial system. The IPath^® protein showed a significant chelating activity under in vitro conditions and biological activity. Taking this evidence, a vaccine candidate based on IPath^® was evaluated in Atlantic salmon challenged with three different fish pathogens. Experimental trials were conducted using two fish groups: one immunized with IPath^® and another injected with adjutant as the control group. After 400 accumulated thermal units (ATUs), two different infection trials were performed. In the first one, fish were infected with the bacterium Aeromonas salmonicida, and in a second trial, fish were exposed to the ectoparasite Caligus rogercresseyi and subsequently infected with the intracellular bacterium Piscirickettsia salmonis. Fish immunized with IPath^® showed a significant delay in the mortality curve in response to A. salmonicida and P. salmonis infections. However, no significant differences between infected and control fish groups were observed at the end of the experiment. Notably, sea lice burden reduction was observed in vaccinated Atlantic salmon. Transcriptional analysis evidenced a high modulation of iron-homeostasis-related genes in fish vaccinated with IPath^® compared to the control group during the infection. Moreover, increasing expression of Atlantic salmon IgT was associated with IPath^® immunization. This study provides evidence that the IPath^® protein could be used as an antigen or booster in commercial fish vaccines, improving the immune response against relevant pathogens for salmon aquaculture.

The sea louse Caligus rogercresseyi genome has opened the opportunity to apply the reverse vaccinology strategy for identifying antigens with potential effects on lice development and its application in sea lice control. This study aimed to explore the efficacy of three sea lice vaccines against the early stage of infestation, assessing the transcriptome modulation of immunized Atlantic salmon. Therein, three experimental groups of Salmo salar (Atlantic salmon) were vaccinated with the recombinant proteins: Peritrophin (prototype A), Cathepsin (prototype B), and the mix of them (prototype C), respectively. Sea lice infestation was evaluated during chalimus I-II, the early-infective stages attached at 7-days post infestation. In parallel, head kidney and skin tissue samples were taken for mRNA Illumina sequencing. Relative expression analyses of genes were conducted to identify immune responses, iron transport, and stress responses associated with the tested vaccines during the early stages of sea lice infection. The vaccine prototypes A, B, and C reduced the parasite burden by 24, 44, and 52% compared with the control group. In addition, the RNA-Seq analysis exhibited a prototype-dependent transcriptome modulation. The high expression differences were observed in genes associated with metal ion binding, molecular processes, and energy production. The findings suggest a balance between the host’s inflammatory response and metabolic process in vaccinated fish, increasing their transcriptional activity, which can alter the early host–parasite interactions. This study uncovers molecular responses produced by three vaccine prototypes at the early stages of infestation, providing new knowledge for sea lice control in the salmon aquaculture.

The role of trypsin genes in pharmacological sensitivity has been described in numerous arthropod species, including the sea louse Caligus rogercresseyi. This ectoparasite species is mainly controlled by xenobiotic drugs in Atlantic salmon farming. However, the post-transcriptional regulation of trypsin genes and the molecular components involved in drug response remain unclear. In particular, the miRNA bantam family has previously been associated with drug response in arthropods and is also found in C. rogercresseyi, showing a high diversity of isomiRs. This study aimed to uncover molecular interactions among trypsin genes and bantam miRNAs in the sea louse C. rogercresseyi in response to delousing drugs. Herein, putative mRNA/miRNA sequences were identified and localized in the C. rogercresseyi genome through genome mapping and blast analyses. Expression analyses were obtained from the mRNA transcriptome and small-RNA libraries from groups with differential sensitivity to three drugs used as anti-sea lice agents: azamethiphos, deltamethrin, and cypermethrin. The validation was conducted by qPCR analyses and luciferase assay of selected bantam and trypsin genes identified from in silico transcript prediction. A total of 60 trypsin genes were identified in the C. rogercresseyi genome, and 39 bantam miRNAs were differentially expressed in response to drug exposure. Notably, expression analyses and correlation among values obtained from trypsin and bantam revealed an opposite trend and potential binding sites with significant ΔG values. The luciferase assay showed a reduction of around 50% in the expression levels of the trypsin 2-like gene, which could imply that this gene is a potential target for bantam. The role of trypsin genes and bantam miRNAs in the pharmacological sensitivity of sea lice and the use of miRNAs as potential markers in these parasites are discussed in this study.