Comparative metabolomics analysis of pigmentary and structural coloration in discus fish (Symphysodon haraldi)

Gut Microbiome-Driven metabolites influence skin pigmentation in TYRP1 mutant Oujiang Color Common Carp

The gut microbiome plays a key role in regulating the gut-skin axis, and host genetics partially influence this regulation. The study investigated the role of gut microbiota and host genetics in the gut-skin axis, focusing on the unusual "coffee-like" color phenotype observed in TYRP1 mutant Oujiang Color Common Carp. We employed comparative high-throughput omics data from wild-type and mutant fish to quantify the influence of both genetics and gut microbes on skin transcriptomic expression and blood metabolites. We found 525 differential metabolites (DMs) and 45 distinct gut microbial genera in TYRP1 mutant fish compared to wild type. Interaction and causal mediation analyses revealed a complex interplay. The TYRP1 mutation likely triggers an inflammatory pathway involving Acinetobacter bacteria, Leukotrience-C4 and Spermine. This inflammatory response appears to be counterbalanced by an anti-inflammatory cardiovascular genetic network. The net effect is the upregulation of COMT, PLG, C2, C3, F10, TDO2, MHC1, and SERPINF2, leading to unusual coffee-like coloration. This study highlights the intricate interplay between gut microbiota, host genetics, and metabolic pathways in shaping complex phenotypes.

Comparative Transcriptome Analysis Reveals Differential Cutaneous Gene Expression in the Color Variation of Two Ornamental Discus, Red Melon and Red Cover

Red Melon (RM) and Red Cover (RC) discus (Symphysodon spp.) are ornamental fish varieties that were selectively bred from the wild parental lineages of the brown discus S. aquafaciatus over many generations, resulting in distinct cutaneous patterns from juveniles to adults. To better understand the underlying mechanisms, skin samples were collected from juveniles aged 60 days and adults aged 1 year from RM and RC for investigations. Microscopic observation detected xanthophores and erythrophores in all samples, except RC juveniles with no erythrophores. Melanophores were presented only in RC. The comparative analysis revealed that genes involved in pteridine synthesis (gch1 and zgc:153031), one-carbon metabolism (aldh1l2 and zgc153031), and lipid metabolism (apoda and klf1) were differentially expressed in RM juveniles, which may be associated with the development of erythrophores and xanthophores. The temporal inhibition of melanophore differentiation and development was observed in RM juveniles, coupled with elevated expression of notum2 and sost, two antagonist genes in Wnt-signaling, suggesting their roles in melanophore development. Distinct pigment pattern between RM and RC since the juvenile stage may be driven by the differential expression of multiple axial developmental genes, including GATA, ankyrin, and mitotic spindle orientation proteins. This is the first report to describe the differential growth of cutaneous pigments and the molecular processes involved in red discus. The results provided valuable insights into pigment pattern differences in an interesting ornamental fish model.

Bioinspired Low-Angle-Dependent Photonic Crystal Elastomer for Highly Sensitive Visual Strain Sensor

Photonic crystals (PCs) possess unique photonic band gap properties that can be used in the field of sensors and smart displays if modulated on the micronano structure. Both nonclose-packed (NCP) structure and high refractive index (RI) contrast of PC play important roles in response sensitivity during stretching. Herein, we constructed an NCP-structured PC strain sensor with high RI by a novel coating-etching strategy. Stretch-induced changes in structural color correspond to the strength of the force, enabling the detection of the strength of the acting force by the naked eye. The flexible 3D cross-linked network constructed by poly(ethylene glycol) phenyl ether acrylate and pentaerythritol tetrakis(3-mercaptopropionate) endows the sensor with excellent elasticity and robustness. The designed PC strain sensor achieves high mechanochromic sensitivity (∼8.3 nm/%, 0.02 to 4.21 MPa) and a substantial reflection peak shift (Δλ = 249 nm). More importantly, the high RI contrast (Δn = 0.43) between CdS and polymers imparts isotropic optical properties, ensuring a broad viewing angle while avoiding misleading signals. The research provides a novel fabrication strategy to construct sensitive PC strain sensors, expanding the prospective applicability to human movement monitoring and secure message encryption.

Selection signatures of wool color in Gangba sheep revealed by genome-wide SNP discovery

BACKGROUND

Gangba sheep as a famous breed of Tibetan sheep, its wool color is mainly white and black. Gangba wool is economically important as a high-quality raw material for Tibetan blankets and Tibetan serge. However, relatively few studies have been conducted on the wool color of Tibetan sheep.

RESULTS

To fill this research gap, this study conducted an in-depth analysis of two populations of Gangba sheep (black and white wool color) using whole genome resequencing to identify genetic variation associated with wool color. Utilizing PCA, Genetic Admixture, and N-J Tree analyses, the present study revealed a consistent genetic relationship and structure between black and white wool colored Gangba sheep populations, which is consistent with their breed history. Analysis of selection signatures using multiple methods (FST, π ratio, Tajima's D), 370 candidate genes were screened in the black wool group (GBB vs GBW); among them, MC1R, MLPH, SPIRE2, RAB17, SMARCA4, IRF4, CAV1, USP7, TP53, MYO6, MITF, MC2R, TET2, NF1, JAK1, GABRR1 genes are mainly associated with melanin synthesis, melanin delivery, and distribution. The enrichment results of the candidate genes identified 35 GO entries and 19 KEGG pathways associated with the formation of the black phenotype. 311 candidate genes were screened in the white wool group (GBW vs GBB); among them, REST, POU2F1, ADCY10, CCNB1, EP300, BRD4, GLI3, and SDHA genes were mainly associated with interfering with the differentiation of neural crest cells into melanocytes, affecting the proliferation of melanocytes, and inhibiting melanin synthesis. 31 GO entries and 22 KEGG pathways were associated with the formation of the white phenotype.

CONCLUSIONS

This study provides important information for understanding the genetic mechanism of wool color in Gangba, and provides genetic knowledge for improving and optimizing the wool color of Tibetan sheep. Genetic improvement and selective breeding to produce wool of specific colors can meet the demand for a diversity of wool products in the Tibetan wool textile market.

Captivating Colors, Crucial Roles: Astaxanthin's Antioxidant Impact on Fish Oxidative Stress and Reproductive Performance

Fish, constantly exposed to environmental stressors due to their aquatic habitat and high metabolic rates, are susceptible to oxidative stress. This review examines the interplay between oxidative stress and fish reproduction, emphasizing the potent antioxidant properties of astaxanthin. Our primary objective is to highlight astaxanthin's role in mitigating oxidative stress during critical reproductive stages, leading to improved gamete quality, ovary development, and hormone levels. We also explore its practical applications in aquaculture, including enhanced pigmentation and overall fish health. We conducted a comprehensive literature review, analyzing studies on astaxanthin's antioxidant properties and its impact on fish reproduction. Astaxanthin, a carotenoid pigment, effectively combats reactive oxygen species, inhibiting lipid peroxidation and maintaining membrane integrity. It significantly enhances reproductive success in fish and improves overall fish health in aquaculture settings. This review reveals astaxanthin's multifaceted benefits in fish health and reproduction, offering economic advantages in aquaculture. Future research should delve into species-specific responses, optimal dosages, and the long-term effects of astaxanthin supplementation to inform sustainable aquaculture strategies.

Whole Genome Resequencing Reveals Selection Signals Related to Wool Color in Sheep

Wool color is controlled by a variety of genes. Although the gene regulation of some wool colors has been studied in relative depth, there may still be unknown genetic variants and control genes for some colors or different breeds of wool that need to be identified and recognized by whole genome resequencing. Therefore, we used whole genome resequencing data to compare and analyze sheep populations of different breeds by population differentiation index and nucleotide diversity ratios (Fst and θπ ratio) as well as extended haplotype purity between populations (XP-EHH) to reveal selection signals related to wool coloration in sheep. Screening in the non-white wool color group (G1 vs. G2) yielded 365 candidate genes, among which PDE4B, GMDS, GATA1, RCOR1, MAPK4, SLC36A1, and PPP3CA were associated with the formation of non-white wool; an enrichment analysis of the candidate genes yielded 21 significant GO terms and 49 significant KEGG pathways (p < 0.05), among which 17 GO terms and 21 KEGG pathways were associated with the formation of non-white wool. Screening in the white wool color group (G2 vs. G1) yielded 214 candidate genes, including ABCD4, VSX2, ITCH, NNT, POLA1, IGF1R, HOXA10, and DAO, which were associated with the formation of white wool; an enrichment analysis of the candidate genes revealed 9 significant GO-enriched pathways and 19 significant KEGG pathways (p < 0.05), including 5 GO terms and 12 KEGG pathways associated with the formation of white wool. In addition to furthering our understanding of wool color genetics, this research is important for breeding purposes.

Effects of monochromatic lights on the melanophores arrangement in the spotted snakehead fish Channa punctata (Bloch, 1793)

Some freshwater teleost fish have pigment cells whose arrangement and shape are affected by the environment. Natural light has a wide range of light intensity. Fish are sensitive to the background and exposed light colour. Fish body colour is a significant criterion in fixing its market value, whether it is ornamental or edible. By favourable light exposure, a culturist may get a good market value of fish on most ethical grounds. In this study, we recorded the changes in melanophore response with the changes in light colour on Channa punctata. Adult fish were treated with monochromatic lights (darkness, white, blue and red light) for 5 and 28 days. After treatment, their body colour and melanophore size, number, length and the number of dendrites were studied. The results showed a significant influence of monochromatic light on melanophore arrangement in fish skin. The data showed that blue light is appropriate for the overall species colour of photic C. punctata. Continuous black or white light caused severe damage to the fish's appearance.

Astaxanthin mitigates oxidative stress caused by microplastics at the expense of reduced skin pigmentation in discus fish

Microplastics (MPs) exposure generally triggers oxidative stress in fish species and vertebrate pigmentation is commonly influenced by oxidative stress, but MPs-induced oxidative stress on fish pigmentation and body color phenotype has not been reported. The aim of this study is to determine whether astaxanthin could mitigate the oxidative stress caused by MPs but at the expense of reduced skin pigmentation in fish. Here, we induced oxidative stress in discus fish (red skin color) by 40 or 400 items/L MPs under both astaxanthin (ASX) deprivation and supplementation. We found that lightness (L*) and redness (a*) values of fish skin were significantly inhibited by MPs under ASX deprivation. Moreover, MPs exposure significantly reduced ASX deposition in fish skin. The total antioxidant capacity (T-AOC) and superoxide dismutase (SOD) activity in fish liver and skin were both significantly increased with the increase of MPs concentration, but content of glutathione (GSH) in fish skin showed a significant decrease. For ASX supplementation, the L*, a* values and ASX deposition were significantly improved by ASX, including the skin of MPs-exposed fish. The T-AOC and SOD levels changed non-significantly in fish liver and skin under the interaction of MPs and ASX, but ASX significantly reduced GSH content in fish liver. Biomarker response index indicated that ASX could improve the moderately altered antioxidant defense status of MPs-exposed fish. This study suggests that the oxidative stress caused by MPs was mitigated by ASX but at expense of reduced fish skin pigmentation.

Transcriptomic and proteomic analyses reveal the common and unique pathway(s) underlying different skin colors of leopard coral grouper (Plectropomus leopardus)

To gain a comprehensive and unbiased molecular understanding of the different skin colors of P. leopardus, we used Illumina HiSeq 2500 and TMT (Tandem Mass Tag) to compare transcription and protein levels between red and black skin of P. leopardus. We identified 797 upregulated and 314 downregulated genes (differentially expressed genes; DEGs) in red (RG) compared with black (BG) skin of P. leopardus. We also identified 377 differentially abundant proteins (DAPs), including 314 upregulated and 63 downregulated proteins. These DEGs and DAPs were significantly enriched in melanin synthesis (e.g., pyrimidine metabolism, Phenylalanine, tyrosine, and tryptophan biosynthesis, melanogenesis, phenylalanine metabolism, and tyrosine metabolism), oxidative phosphorylation (e.g., phosphonate and phosphinate metabolism, and oxidative phosphorylation), energy metabolism (e.g., HIF-1, glycolysis/gluconeogenesis, fatty acid biosynthesis, and fatty acid degradation), and signal transduction (e.g., Wnt, calcium, MAPK, and cGMP-PKG signaling pathways), etc. Further analysis of MAPKs showed that the activation levels of its main members JNK1 and ERK1/2 differed significantly between red and black skin colors. After RNAi was used to interfere with ERK1/2, it was found that the local skin of the tail of P. leopardus would turn black. Combined transcriptome and proteome analysis showed that most DEGs-DAPs in red skin were higher than in black skin (58 were upregulated, 1 was downregulated, and 4 were opposite). These DEGs-DAPs showed that the differences between red and black skin tissues of P. leopardus were related primarily to energy metabolism, signal transduction and cytoskeleton. These findings are not only conducive to understand the skin color regulation mechanism of P. leopardus and other coral reef fish, but also provide an important descriptive to the breeding of color strains. SIGNIFICANCE OF THE STUDY: The skin color of P. leopardus gradually darkens or blackens due to environmental factors such as changes in light intensity and human activities, and this directly affects its ornamental and economic value. In this study, RNAseq and TMT were used to conduct comparative quantitative transcriptomics and proteomics and analyze differences between red and black P. leopardus skin. The results showed that energy metabolism, signal transduction and cytoskeleton were the main metabolic pathways causing their skin color differences. These findings contribute to existing data describing fish skin color, and provide information about protein levels, which are of great significance to a deeper understanding of the skin color regulation mechanism in P. leopardus and other coral reef fishes.

Integrative mRNA-miRNA interaction analysis reveals the molecular mechanism of skin color variation between wild-type and yellow mutant rainbow trout (Oncorhynchus mykiss)

Rainbow trout (Oncorhynchus mykiss) is an important economic fish in China. Skin color affects the economic value of trout. However, the molecular mechanism of the skin color variation between wild-type (WR) and yellow mutant rainbow trout (YR) is unclear. We sequenced mRNAs and miRNAs of dorsal skin to identify key color variation-associated mRNAs and miRNAs between WR and YR. Overall, 2060 out of 3625 differentially expressed genes were upregulated in YR, and 196 out of 275 differentially expressed miRNAs were downregulated in WR. We identified three key YR-upregulated genes related to the formation of xanthophores (GCH1, SLC2A11, and SOX10). Interestingly, several genes related to melanogenesis (TYR, TYRP1, TYRP2, MC1R, MITF, PMEL, SLC45A2, and OCA2) were downregulated in WR. Integrated analysis identified five miRNAs that target at least two skin color-related genes (miR-495-y, miR-543-y, miR-665-z, miR-433-y, and miR-382-x). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses of target genes identified noncoding RNA metabolic process as the most significantly enriched GO term, and several metabolic pathways associated with skin color were enriched significantly, such as tyrosine metabolism, histidine metabolism, and vitamin B6 metabolism. Quantitative real-time PCR of selected mRNAs and miRNAs validated the reliability of the integrated analysis. This study provides in-depth insights into the molecular mechanism of skin color variation between WR and YR, which will accelerate the genetic selection and breeding of rainbow trout with consumer-favored traits.