RNA-Seq Transcriptome Analysis of Pronounced Biconcave Vertebrae: A Common Abnormality in Rainbow Trout (Oncorhynchus mykiss, Walbaum) Fed a Low-Phosphorus Diet

Abstract

International audienceThe prevalence of bone deformities, particularly linked with mineral deficiency, is an important issue for fish production. Juvenile triploid rainbow trout (Oncorhynchus mykiss) were fed a low-phosphorus (P) diet for 27 weeks (60 to 630 g body mass). At study termination, 24.9% of the fish fed the low-P diet displayed homogeneous biconcave vertebrae (deformed vertebrae phenotype), while 5.5% displayed normal vertebral phenotypes for the entire experiment. The aim of our study was to characterize the deformed phenotype and identify the putative genes involved in the appearance of P deficiency-induced deformities. Both P status and biomechanical measurements showed that deformed vertebrae were significantly less mineralized (55.0 ± 0.4 and 59.4 ± 0.5,% ash DM, for deformed and normal vertebrae, respectively) resulting in a lower stiffness (80.3 ± 9.0 and 140.2 ± 6.3 N/mm, for deformed and normal phenotypes, respectively). The bone profiles based on μCT observations showed no difference in the osteoclastic resorption while no difference in matrix production was observed between deformed (total bone area 5442.0 ± 110.1 μm2) and normal vertebrae (total bone area 5931.2 ± 249.8 μm2) in this study. Consequently, the lower P content rather results from a reduced degree of mineralization in the deformed phenotype. Finally, we quantified differential gene expression between deformed vertebrae (pronounced biconcave) and normal phenotype by employing deep RNA-sequencing and mapping against a reference bone transcriptome for rainbow trout. In total, 1289 genes were differentially expressed. Among them, in deformed fish we observed that BGLAP, MGP and NOG, an inhibitor of BMP signalling pathway, were up-regulated while COL11a1 was down-regulated. These genes are central actors involved in the reduced degree of mineralization triggering vertebral deformities. These results will further the understanding of P deficiency-induced deformities; hence providing new tools for improved P management in production setting

RNA-Seq-Based Analysis of Cortisol-Induced Differential Gene Expression Associated with Piscirickettsia salmonis Infection in Rainbow Trout (Oncorhynchus mykiss) Myotubes

“…The quality obtained from RNA-seq data was as expected, and the mapping results against the rainbow trout reference genome were in line with studies using this strategy [25,38]. According to these results, other recent reports in trout presented similar results using comparable parameters of RNA-seq analysis [39,40].…”

Dual RNAseq highlights the kinetics of skin microbiome and fish host responsiveness to bacterial infection

“…Nearly all the genes found up-regulated in infected24h clustered in moduleblue-host (n = 2,352; 98.5%). Not surprisingly, main drivers genes ('hub-genes') encompass several transcriptional activators such as for the moduleturquoise-host several Zinc finger proteins, Transcription factor GATA-3 (gata-3), Forkhead box protein O3 (foxpo3), activators of the autophagy pathways and main drivers of naïve specific T-cells differentiation and activation [56], Runt-related transcription factor 2 (runt2) coding genes, involved in osteoblast differentiation, a mineral depositing cells and enhancer of T-cells receptor and sialoproteins [57]. In the moduleblue-host, 'hub-genes' mainly report actors of the innate immune system, inflammatory response, wound healing, oxidative and adhesion activity ( Figure 3B).…”

“…Moreover, commercial clay (Clay Bacter ®) was added daily at a rate of 1g/d/m 3 per percent of hourly water renewal from day 1 to day 19, the beginning of living prey weaning period. In addition, an input of probiotic Pseudoalteromonas piscicida B1 (local strain), produced in CIP facilities (see supplementary methods), was realised daily in fish fed (0.5mL/day/tank) and in the water (0.5 ml/day/tank) at a concentration of 10 9 cfu/ml of bacterial suspension from day 1 to day 57. At the end of the larval phase, day 20, 700 fingerlings/tank were randomly kept.…”

Dual RNAseq Highlights the Kinetics of Skin Microbiome and Fish Host Responsiveness to Bacterial Infection

“…Nearly all the genes found to be upregulated in infected 24h clustered in module blue−host (n = 2,352; 98.5%). Not surprisingly, the main driver genes ('hub-genes') include several transcriptional activators, such as, for module turquoise−host , several Zinc nger proteins, Transcription factor GATA-3 (gata-3), Forkhead box protein O3 (foxpo3), activators of the autophagy pathways and the main drivers of naïve speci c T-cell differentiation and activation [56], Runt-related transcription factor 2-(runt2) coding genes, involved in osteoblast differentiation, mineraldepositing cells and sialoproteins [57,58]. In module blue−host , 'hub-genes' mainly reported actors of the innate immune system, in ammatory response, wound healing, oxidative and adhesion activity (Fig.…”