Transcriptomic insights on the ABC transporter gene family in the salmon louse Caligus rogercresseyi

Background  ATP-binding cassette (ABC) protein family encode for membrane proteins involved in the transport of various biomolecules through the cellular membrane. These proteins have been identified in all taxa and present important physiological functions, including the process of insecticide detoxification in arthropods. For that reason the ectoparasiteCaligus rogercresseyirepresents a model species for understanding the molecular underpinnings involved in insecticide drug resistance.  Methods  llumina sequencing was performed using sea lice exposed to 2 and 3 ppb of deltamethrin and azamethiphos. Contigs obtained fromde novoassembly were annotated by Blastx. RNA-Seq analysis was performed and validated by qPCR analysis.  Results  From the transcriptome database ofC. rogercresseyi, 57 putative members of ABC protein sequences were identified and phylogenetically classified into the eight subfamilies described for ABC transporters in arthropods. Transcriptomic profiles for ABC proteins subfamilies were evaluated throughoutC. rogercresseyidevelopment. Moreover, RNA-Seq analysis was performed for adult male and female salmon lice exposed to the delousing drugs azamethiphos and deltamethrin. High transcript levels of the ABCB and ABCC subfamilies were evidenced. Furthermore, SNPs mining was carried out for the ABC proteins sequences, revealing pivotal genomic information.  Conclusions  The present study gives a comprehensive transcriptome analysis of ABC proteins fromC. rogercresseyi,providing relevant information about transporter roles during ontogeny and in relation to delousing drug responses in salmon lice. This genomic information represents a valuable tool for pest management in the Chilean salmon aquaculture industry

Long noncoding RNAs (lncRNAs) dynamics evidence immunomodulation during ISAV-Infected Atlantic salmon (Salmo salar)

Despite evidence for participation in the host response to infection, the roles of many long non-coding RNAs (lncRNAs) remain unknown. Therefore, the aims of this study were to identify lncRNAs in Atlantic salmon (Salmo salar) and evaluate their transcriptomic regulation during ISA virus (ISAV) infection, an Orthomyxoviridae virus associated with high mortalities in salmonid aquaculture. Using next-generation sequencing, whole-transcriptome analysis of theSalmo salarresponse to ISAV infection was performed, identifying 5,636 putative lncRNAs with a mean length of 695 base pairs. The transcriptional modulation evidenced a similar number of differentially expressed lncRNAs in the gills (3,294), head-kidney (3,275), and liver (3,325) over the course of the infection. Moreover, analysis of a subset of these lncRNAs showed the following: (i) Most were similarly regulated in response to ISA virus infection; (ii) The transcript subsets were uniquely modulated in each tissue (gills, liver, and head-kidney); and (iii) A subset of lncRNAs were upregulated for each tissue and time analysed, indicating potential markers for ISAV infection. These findings represent the first discovery of widespread differential expression of lncRNAs in response to virus infection in non-model species, suggesting that lncRNAs could be involved in regulating the host response during ISAV infection

Proximity ligation strategy for the genomic reconstruction of microbial communities associated with the ectoparasite Caligus rogercresseyi

The sea louse Caligus rogercresseyi has become one of the main constraints for the sustainable development of salmon aquaculture in Chile. Although this parasite's negative impacts are well recognized by the industry, some novel potential threats remain unnoticed. The recent sequencing of the C. rogercresseyi genome revealed a large bacterial community associated with the sea louse, however, it is unknown if these microorganisms should become a new focus of sanitary concern. Herein, chromosome proximity ligation (Hi-C) coupled with long-read sequencing were used for the genomic reconstruction of the C. rogercresseyi microbiota. Through deconvolution analysis, we were able to assemble and characterize 413 bacterial genome clusters, including six bacterial genomes with more than 80% of completeness. The most represented bacterial genome belonged to the fish pathogen Tenacibacullum ovolyticum (97.87% completeness), followed by Dokdonia sp. (96.71% completeness). This completeness allowed identifying 21 virulence factors (VF) within the T. ovolyticum genome and four antibiotic resistance genes (ARG). Notably, genomic pathway reconstruction analysis suggests putative metabolic complementation mechanisms between C. rogercresseyi and its associated microbiota. Taken together, our data highlight the relevance of Hi-C techniques to discover pathogenic bacteria, VF, and ARGs and also suggest novel host-microbiota mutualism in sea lice biology.info:eu-repo/semantics/publishedVersio

Seawater carbonate chemistry and immune response of the edible mussel Mytilus chilensis

Ocean acidification (OA) is one of the main consequences of increasing atmospheric carbon dioxide (CO2), impacting key biological processes of marine organisms such as development, growth and immune response. However, there are scarce studies on the influence of OA on marine invertebrates' ability to cope with pathogens. This study evaluated the single and combined effects of OA and bacterial infection on the transcription expression of genes related to antioxidant system, antimicrobial peptides and pattern recognition receptors in the edible mussel Mytilus chilensis. Individuals of M. chilensis were exposed during 60 days at two concentrations of pCO2 (550 and 1200 μatm) representing respectively current and future scenario of OA and were then injected with the pathogenic bacterium Vibrio anguillarum. Results evidenced an immunomodulation following the OA exposure with an up-regulation of C-type Lectin and Mytilin B and a down-regulation of Myticin A and PGRP. This immunomodulation pattern is partially counteracted after challenge with V. anguillarum with a down-regulation of the C-type lectin and Mytilin B and the up-regulation of Myticin A. In turn, these results evidence that pCO2-driven OA scenarios might triggers specific immune-related genes at early stages of infection, promoting the transcription of antimicrobial peptides and patterns recognition receptors. This study provides new evidence of how the immune response of bivalves is modulated by higher CO2 conditions in the ocean, as well one factor for the resili

High-Temperature Stress Induces Autophagy in Rainbow Trout Skeletal Muscle

Ectothermic animals, such as teleosts, have increasingly been exposed to stressful high-temperature events due to global warming. Currently, the effects of thermal stress on skeletal muscle, a key tissue for fish growth, are unknown. This study examined the impact of high-temperature stress on the skeletal muscle transcriptome of rainbow trout (Oncorhynchus mykiss) in control (15 °C) and high-temperature (20 °C) conditions. Additionally, we examined the plasmatic levels of cortisol, glucose, and creatine kinase activity, and examined oxidative damage and autophagy activation in skeletal muscle. High-temperature stress induced significant increases in cortisol and glucose plasmatic levels. Nevertheless, no changes were observed in creatine kinase activity in plasma and skeletal muscle oxidation. Skeletal muscle RNA was isolated and sequenced using the HiSeq Illumina platform. A total of 383,796,290 reads were mapped onto the reference rainbow trout genome. The transcriptomic analysis showed that 293 genes were upregulated in the high-temperature group, mainly associated with autophagosome assembly, amino acid transport, and the glutamine metabolic process. On the other hand, 119 genes were downregulated in the high-temperature group, mainly associated with digestion, proteolysis, and the muscle contraction process. In addition, RT-qPCR of differentially expressed representative genes and Western blot analysis of LC3-II/LC3-I levels confirmed skeletal muscle autophagy induced by high temperature. This study sheds light on intriguing facets of the adaptive response of rainbow trout skeletal muscle to high-temperature stress and provides significant insights into the physiology of autophagy in teleosts

Additional file 1: Table S1. of mRNA-seq reveals skeletal muscle atrophy in response to handling stress in a marine teleost, the red cusk-eel (Genypterus chilensis)

Complete list of up-regulated and down-regulated transcripts in response to handling stress. (XLSX 66 kb

Additional file 2: Table S2. of mRNA-seq reveals skeletal muscle atrophy in response to handling stress in a marine teleost, the red cusk-eel (Genypterus chilensis)

Enriched Molecular functions of up-regulated and down-regulated transcripts in response to handling stress. (XLSX 10 kb