Growth performance, physiological parameters, and transcript levels of lipid metabolism-related genes in hybrid yellow catfish (Tachysurus fulvidraco ♀ × Pseudobagrus vachellii ♂) fed diets containing Siberian ginseng

Transport stress induces innate immunity responses through TLR and NLR signaling pathways and increases mucus cell number in gills of hybrid yellow catfish (Tachysurus fulvidraco ♀ × Pseudobagrus vachellii ♂)

Transport stress poses a threat to most teleost fish in production, causing mass losses to the aquaculture industry. Fish gills are a mucosa-associated lymphoid tissue in direct contact with water, and they represent an ideal tissue type to study mechanisms of transport stress. In this study, hybrid yellow catfish (Tachysurus fulvidraco ♀ × Pseudobagrus vachellii ♂) were exposed to simulated transport stress for 16 h and then allowed to recover for 96 h. Gill tissues and blood samples were collected at 0 h, 2 h, 4 h, 8 h, and 16 h of transport stress and after 96 h of recovery, as well as from fish in a control group at the same sampling times. The activities of alkaline phosphatase, acid phosphatase, and superoxide dismutase and the total antioxidant capacity first increased and then decreased during the 16 h transport treatment. Exposure to 16 h of transport stress resulted in decreased serum triglyceride and total cholesterol contents, increased serum glucose content, increased activities of alanine aminotransferase and aspartate transaminase, and more mucus cells, compared with the control group. Transcriptome analysis revealed differential expression of 1525 genes (803 down-regulated and 722 up-regulated) between the control and 16 h transportation groups. Functional analyses revealed that the differentially expressed genes were enriched in immune response, signal transduction, and energy metabolism pathways. We found that tlr5, tnfɑ, hsp90ɑ, il-1ß, map2k4, il12ba were clearly up-regulated and arrdc2, syngr1a were clearly down-regulated following 8 h and/or 16 h simulated transport after qRT-PCR validation. These findings suggested that Toll- and NOD-like receptor signaling pathways potentially mediate transport stress. Transport stress altered innate immunity responses and energy use in the gill tissues of hybrid yellow catfish. After 96 h of recovery, only alanine aminotransferase and alkaline phosphatase activities and the number of mucus cells had returned to control levels. We speculate that for juvenile yellow catfish to recover to a normal state, a recovery period of more than 96 h is required after 16 h of transportation. These results provide new perspectives on the immune response of yellow catfish under transport stress and theoretical support for future optimization of their transportation.

Assembly-free rapid differential gene expression analysis in non-model organisms using DNA-protein alignment

Background

RNA-seq is being increasingly adopted for gene expression studies in a panoply of non-model organisms, with applications spanning the fields of agriculture, aquaculture, ecology, and environment. For organisms that lack a well-annotated reference genome or transcriptome, a conventional RNA-seq data analysis workflow requires constructing a de-novo transcriptome assembly and annotating it against a high-confidence protein database. The assembly serves as a reference for read mapping, and the annotation is necessary for functional analysis of genes found to be differentially expressed. However, assembly is computationally expensive. It is also prone to errors that impact expression analysis, especially since sequencing depth is typically much lower for expression studies than for transcript discovery.

Results

We propose a shortcut, in which we obtain counts for differential expression analysis by directly aligning RNA-seq reads to the high-confidence proteome that would have been otherwise used for annotation. By avoiding assembly, we drastically cut down computational costs – the running time on a typical dataset improves from the order of tens of hours to under half an hour, and the memory requirement is reduced from the order of tens of Gbytes to tens of Mbytes. We show through experiments on simulated and real data that our pipeline not only reduces computational costs, but has higher sensitivity and precision than a typical assembly-based pipeline. A Snakemake implementation of our workflow is available at: https://bitbucket.org/project_samar/samar.

Conclusions

The flip side of RNA-seq becoming accessible to even modestly resourced labs has been that the time, labor, and infrastructure cost of bioinformatics analysis has become a bottleneck. Assembly is one such resource-hungry process, and we show here that it can be avoided for quick and easy, yet more sensitive and precise, differential gene expression analysis in non-model organisms.

Supplementary Information

The online version contains supplementary material available at (10.1186/s12864-021-08278-7).

Acanthopanax senticosus Promotes Survival of Tilapia Infected With Streptococcus iniae by Regulating the PI3K/AKT and Fatty Acid Metabolism Signaling Pathway

Streptococcus has greatly restricted the development of healthy tilapia aquaculture. As a green and efficient feed addition, Acanthopanax senticosus (APS) has been increasingly used in culture, but it is unclear whether it represents a disease-resistant feed. Genetically improved farmed tilapia (GIFT, Oreochromis niloticus) was fed with a feed supplemented with 0 (control), 0.5, 1, 2, 4, and 8‰ APS for 56 days, after which fish were injected with 5.9 × 10⁶ CFU/ml Streptococcus iniae into the abdominal cavity. At 96 h after infection, the cumulative survival of GIFT in control and 0.5‰ APS treatments was significantly lower than in other treatments; at APS supplementation rates of 1 and 2‰, serum glucose, triglycerides, and cholesterol contents were all significantly lower than in control treatment fish. Hepatic glycogen and triglyceride contents of 1‰ APS treatment fish were significantly higher than those in fish in control treatment. Transcription levels of peroxisome proliferator activated receptor α (PPAR), fatty acid synthase (FAS), and lipoprotein Lipase (LPL) genes were upregulated, and their expression levels in fish in 1, 2, and 4‰ treatments were significantly higher than those in fish in control treatment at 96 h after S. iniae infection. After 96 h of infection, the red blood cells, hemoglobin, hematocrit, and white blood cells of fish in 1‰ APS treatment were significantly lower than those of fish in 4 and 8‰ treatments; hepatic catalase activity was activated at 48 h, superoxide dismutase activity was also significantly upregulated at 96 h, and the malondialdehyde content significantly decreased. It is noted that 0.5–2‰ APS treatments significantly activated the expression of PI3K and AKT in the liver, while inhibiting the expression of Caspase-9. Therefore, feed with 1‰ APS can promote hepatic glycogen and lipid metabolism in GIFT after infection with S. iniae, which is beneficial to alleviating oxidative stress damage and cell apoptosis in liver tissue.