Effects of dietary soybean protein levels on energy budget of the southern catfish, Silurus meridionalis

Chromosome-level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles

The Southern catfish (Silurus meridionalis) is a nocturnal and benthic freshwater fish endemic to the Yangtze River and its tributaries. In this study, we constructed a chromosome-level draft genome of S. meridionalis using 69.7-Gb Nanopore long reads and 49.5-Gb Illumina short reads. The genome assembly was 741.2 Mb in size with a contig N50 of 13.19 Mb. An additional 116.4 Gb of Bionano and 77.4 Gb of Hi-C data were applied to assemble contigs into scaffolds and further into 29 chromosomes, resulting in a 738.9-Mb genome with a scaffold N50 of 28.04 Mb. A total of 22,965 protein-coding genes were predicted from the genome with 22,519 (98.06%) genes functionally annotated. Comparative genomic and transcriptomic analyses revealed a rod-dominated visual system which was responsible for scotopic vision. The absence of cone opsins SWS1 and SWS2 resulted in the lack of ultraviolet and blue violet sensitivity. Mutations at key amino acid sites of RH1.1, RH1.2 and RH2 resulted in spectral tuning good for dim light vision and narrow colour vision. A higher expression level of rod phototransduction genes than that of cone genes and higher rod-to-cone ratio led to higher optical sensitivity under dim light conditions. In addition, analysis of the genes involved in eye morphogenesis and development revealed the loss of some conserved noncoding elements, which might be associated with the small eyes in catfish. Together, our study provides important clues for the adaptation of the catfish visual system to the nocturnal and benthic lifestyles. The draft genome of S. meridionalis represents a valuable resource for studies of the molecular mechanisms of ecological adaptation.

Metabolic compensations in mitochondria isolated from the heart, liver, kidney, brain and white muscle in the southern catfish (Silurus meridionalis) by seasonal acclimation

In order to examine the effects of seasonal acclimation on mitochondrial metabolic functions and test tissue-specific pattern of the metabolic compensation within individuals of the southern catfish (Silurus meridionalis Chen), rates of mitochondrial respiration and activities of cytochrome c oxidase (COX) in the heart, liver, kidney, brain and white muscle of this fish in the summer-acclimatized group (153.20±1.66 g) and winter-acclimatized group (177.71±3.04 g) were measured at seven assay temperatures (7.5, 12.5, 17.5, 22.5, 27.5, 32.5 and 37.5°C), respectively. The results show that compensatory adjustments in state III respiratory rate and COX activity occur significantly in the heart, kidney and liver, but do not in the brain and white muscle, which suggest that the metabolic compensation of this fish in response to seasonal acclimation exhibits a tissue-specific pattern. The cold acclimation increases mitochondrial oxidative capacities in the heart, kidney and liver concomitantly with reducing their upper thermal limits of mitochondrial functions at acute warming and the thermal tolerance shifts in the same tissue-specific pattern as the metabolic compensation. When combining the effects of seasonal acclimation on mitochondrial oxidative capacity and organ mass, the metabolic compensation demonstrates an organ-specific pattern with four categories: over-compensation in the heart, complete compensation in the kidney, partial compensation in the liver and no compensation in the brain. The organ-specific pattern of metabolic compensation might be a trade-off strategy of the performance adjustments in the seasonal acclimation for this fish to maximize its fitness.

Dietary protein source influence on body size and composition in growing zebrafish

The importance of nutritional components on growth and body composition outcomes has been demonstrated in multiple model organisms. Although zebrafish (Danio rerio) have an established role in research laboratories for its utility in understanding developmental biology and genetics, the influence of diet composition on basic growth outcomes is less well demonstrated. In the current study, four protein sources were tested in isolation using isonitrogenous diets or combined using a defined lab diet. Fish (n≈60/group) were group housed (n≤10 fish/1.8 L tank) and fed ad libitum three times daily for 12 weeks. Fish were assessed for effects on length, body weight, and body composition (lean and fat mass). Individuals fed wheat gluten protein were significantly shorter in length, with significantly lower body weight and lean mass in both male and female fish, although percent body fat was high compared with other diets. Casein-fed fish similarly had significantly reduced body length, body weight, and lean and fat mass in both male and female fish, with a low percent body fat compared with other diets (leanest). Fish protein hydrolysate-fed fish had significantly lower lean mass and a high percent body fat, whereas soy protein isolate diet performed similarly to a mixed-protein control diet for all measured outcomes. These results suggest that the protein source, with accompanying amino acid ratios or additional protein source differences, has a significant impact on growth and body composition outcomes in zebrafish when fed in a semipurified, defined diet background.