Zebrafish stripes as a model for vertebrate colour pattern formation

GTP cyclohydrolase II (gch2) and axanthism in ball pythons: A new vertebrate model for pterin-based pigmentation

Pterin pigments are responsible for many of the bright colors observed across the animal kingdom. However, unlike melanin, the genetics of pterin-based pigmentation has received relatively little attention in animal coloration studies. Here, we investigate a lineage of axanthic ball pythons (Python regius) found in captivity as a model system to study pterin pigmentation in vertebrates. By crowdsourcing shed skin samples from commercial breeders and applying a case-control study design, we used whole-genome pool sequencing (pool-seq) and variant annotation. We identified a premature stop codon in the gene GTP cyclohydrolase II (gch2), which is associated with the axanthic phenotype. GCH2 catalyzes the first rate-limiting step in riboflavin biosynthesis. This study provides the first identification of an axanthism-associated gene in vertebrates and highlights the utility of ball pythons as a model to study pterin-based pigmentation.

Regulatory and disruptive variants in the CLCN2 gene are associated with modified skin color pattern phenotypes in the corn snake

BACKGROUND

Snakes exhibit a broad variety of adaptive colors and color patterns, generated by the spatial arrangement of chromatophores, but little is known of the mechanisms responsible for these spectacular traits. Here, we investigate a mono-locus trait with two recessive alleles, motley and stripe, that both cause pattern aberrations in the corn snake.

RESULTS

We use mapping-by-sequencing to identify the genomic interval where the causal mutations reside. With our differential gene expression analyses, we find that CLCN2 (Chloride Voltage-Gated Channel 2), a gene within the genomic interval, is significantly downregulated in Motley embryonic skin. Furthermore, we identify the stripe allele as the insertion of an LTR-retrotransposon in CLCN2, resulting in a disruptive mutation of the protein. We confirm the involvement of CLCN2 in color pattern formation by producing knock-out snakes that present a phenotype similar to Stripe. In humans and mice, disruption of CLCN2 results in leukoencephalopathy, as well as retinal and testes degeneration. Our single-cell transcriptomic analyses in snakes reveal that CLCN2 is indeed expressed in chromatophores during embryogenesis and in the adult brain, but the behavior and fertility of Motley and Stripe corn snakes are not impacted.

CONCLUSIONS

Our genomic, transcriptomic, and functional analyses identify a plasma membrane anion channel to be involved in color pattern development in snakes and show that an active LTR-retrotransposon might be a key driver of trait diversification in corn snakes.

Zebrafish identification with deep CNN and ViT architectures using a rolling training window

Zebrafish are widely used in vertebrate studies, yet minimally invasive individual tracking and identification in the lab setting remain challenging due to complex and time-variable conditions. Advancements in machine learning, particularly neural networks, offer new possibilities for developing simple and robust identification protocols that adapt to changing conditions. We demonstrate a rolling window training technique suitable for use with open-source convolutional neural networks (CNN) and vision transformers (ViT) that shows promise in robustly identifying individual maturing zebrafish in groups over several weeks. The technique provides a high-fidelity method for monitoring the temporally evolving zebrafish classes, potentially significantly reducing the need for new training images in both CNN and ViT architectures. To understand the success of the CNN classifier and inform future real-time identification of zebrafish, we analyzed the impact of shape, pattern, and color by modifying the images of the training set and compared the test results with other prevalent machine learning models.

Dynamic Chromatin Accessibility and Transcriptional Regulation in the Eyes of Red Tilapia (Oreochromis sp.) in Response to Wintering Stress

During wintering, red tilapia may develop variable black spots on their bodies, significantly reducing their market value. Understanding the mechanisms driving this phenomenon is essential for molecular improvements in body color. In this study, we investigated chromatin accessibility landscapes in the eyes of red tilapia with two distinct phenotypes (normal pure red and black spot) under wintering stress using ATAC-seq and RNA-seq analyses. We observed that approximately 32.7% of chromatin accessibility peaks were located in promoter regions, followed by intergenic regions (32.4%) and intronic regions (26.7%). One thousand two hundred twenty-nine differentially accessible regions (DARs) and 1448 differentially expressed genes (DEGs) were identified between the RS and DS groups. Notably, DEGs associated with melanin synthesis, including tyrp1, tyr, tyrp1b, pmela, slc24a5, and mlph, were significantly upregulated in the DS group, which aligns with the observed 1.85-fold increase in melanin content, compared to the RS group. 92 DEGs were associated with significant changes in chromatin accessibility between groups (R2 = 0.8059; p < 0.0001), indicating potential regulatory relationships. Interestingly, 23.92% of the DARs were located on the chromosome 3. Specifically, a 2.5-fold difference in average peak height on LG3: 11,215,273-11,217,225 were observed between DS and RS tilapia. In the region, transcription factors including HSF1 and HSF2 were identified as key regulators of chromatin structure and gene expression under wintering stress. Our findings reveal that dynamic chromatin accessibility in the eyes of red tilapia facilitates adaptation to wintering stress by regulating visual signaling, melanin production, and downstream pigmentation.

The hybrid history of zebrafish

Since the description of zebrafish (Danio rerio) in 1822, the identity of its closest living relative has been unclear. To address this problem, we sequenced the exomes of 10 species in genus Danio, using the closely related Devario aequipinnatus as outgroup, to infer relationships across the 25 chromosomes of the zebrafish genome. The majority of relationships within Danio were remarkably consistent across all chromosomes. Relationships of chromosome segments, however, depended systematically upon their genomic location within zebrafish chromosomes. Regions near chromosome centers identified Danio kyathit and/or Danio aesculapii as the closest relative of zebrafish, while segments near chromosome ends supported only D. aesculapii as the zebrafish sister species. Genome-wide comparisons of derived character states revealed that danio relationships are inconsistent with a simple bifurcating species history but support an ancient hybrid origin of the D. rerio lineage by homoploid hybrid speciation. We also found evidence of more recent gene flow limited to the high recombination ends of chromosomes and several megabases of chromosome 20 with a history distinct from the rest of the genome. Additional insights gained from incorporating genome structure into a phylogenomic study demonstrate the utility of such an approach for future studies in other taxa. The multiple genomic histories of species in the genus Danio have important implications for comparative studies in these morphologically varied and beautiful species and for our understanding of the hybrid evolutionary history of zebrafish.

Functions of thyroid hormone signaling in regulating melanophore, iridophore, erythrophore, and pigment pattern formation in spotted scat (Scatophagus argus)

BACKGROUND

Spotted scat, a marine aquaculture fish, has variable body color development stages during their ontogenesis. However, the regulatory mechanism of body color patterns formation was poorly understood. Thyroid hormones (TH) function as an important endocrine factor in regulating metamorphosis. In this study, exogenous thyroid hormones 3,5,3'-L-triiodothyronine (T3) and its inhibitor thiourea (TU) were used to treat spotted scat juveniles during the metamorphosis stage (from 60 to 90 dpf). The function and molecular mechanism of thyroid hormone signaling in regulating body color patterns formation was revealed, using the micro-observation of pigments cells distribution, colorimetric evaluation and carotenoids concentration measurement by spectrophotometry, and comparative transcriptome analysis.

RESULTS

Spotted scat body color patterns consisted of whole body black color, black bar, black and red spots, and its final pattern was formed through the metamorphosis. When spotted scat were treated with the inhibitor TU to disrupt thyroid hormone signaling, the levels of T3 and T4 were significantly decreased, the melanophores numbers were significantly increased, as well as the expression of genes involved in melanin synthesis and melanophore differentiation (tyr, tyrp1, dct, mitf, pmel, oca2, slc24a5, and erbb3) was significantly increased. Besides, the expression of genes associated with carotenoids and pteridine metabolism (apod, pnpla2, rdh12, stard10, xdh, abca1, retsat, scarb1, rgs2, and gch1) and carotenoids accumulation were stimulated, when thyroid hormone signaling was disrupted by TU. On the contrary, the levels of T3 and T4 were significantly elevated in spotted scat treated with T3, which could weaken the skin redness and reduce the number of black spots and melanophores, as well as the number and diameter of larval erythrophores. Notably, unlike melanophores and erythrophores, the differentiation of iridophore was promoted by thyroid hormones, gene related to iridophore differentiation (fhl2-l, fhl2, ltk, id2a, alx4) and guanine metabolism (gmps, hprt1, ppat, impdh1b) were up-regulated after T3 treatment, but they were down-regulated after TU treatment.

CONCLUSIONS

Above results showed that thyroid hormone signaling might play critical roles in regulation pigments synthesis and deposition, thereby affecting pigment cells (melanophores, iridophores and erythrophores) formation and body color patterns. The mechanisms of hyperthyroid and hypothyroid on different pigment cells development were different. Excess thyroid hormone might impact the rearrangement of melanophore by regulating cell cycle, resulting in the abnormalities of black spots in spotted scat. Meanwhile, the excessed thyroid hormone could reduce the number and diameter of larval erythrophores, as well as weaken the skin redness of juvenile erythrophores, but they were enhanced by the disruption of thyroid hormone. However, the formation of iridophore differentiation and guanine synthesis genes expression were stimulated by thyroid hormones. These findings provide new insights for exploring the formation of body color patterns in fish, and help to elucidate the molecular mechanism of thyroid hormone in regulating pigment cell development and body coloration, and may also contribute to selective breeding of ornamental fish.

A Ball Python Colour Morph Implicates MC1R in Melanophore-Xanthophore Distribution and Pattern Formation

Reptiles showcase an extensive array of skin colours and patterns, yet little is known about the genetics of reptile colouration. Here, we investigate the genetic basis of the Clown colour morph found in captive-bred ball pythons (Python regius) to study skin pigmentation and patterning in snakes. We obtained samples by crowdsourcing shed skin from commercial breeders and hobbyists. We applied a case-control design, whole-genome pool sequencing, variant annotation, histological analyses, and electron microscopy imaging. We identified a missense mutation in a transmembrane region of the melanocortin-1 receptor (MC1R) associated with the Clown phenotype. In classic avian and mammalian model species, MC1R is known for controlling the type and amount of melanin produced. In contrast, our results suggest that MC1R signalling might play a key role in pattern formation in ball pythons, affecting xanthophore-melanophore distribution. This work highlights the varied functions of MC1R across different vertebrate lineages and promotes a novel model system to study reptile colouration.

Dynamic colour change in zebrafish (Danio rerio) across multiple contexts

Many animals are capable of rapid dynamic colour change, which is particularly well represented in fishes. The proximate mechanisms of dynamic colour change in fishes are well understood; however, less attention has been given to understanding its ecological relevance. In this study, we investigate dynamic colour change in zebrafish (Danio rerio) across multiple contexts, using a protocol to image the colouration of live fish without anaesthesia under standardized conditions. We show that zebrafish respond to different visual environments by darkening their overall colouration in a dark environment and lightening in a light environment. This is consistent with crypsis through background matching as a function of dynamic colour change. Additionally, we find that zebrafish use dynamic colour change to increase the internal contrast of their striped patterning in the presence of conspecifics. We speculate that this may function in social signalling and/or dazzle colouration. We find no effect of a predator stimulus on dynamic colour change. Finally, we discuss the potential for zebrafish to use multiple colouration strategies simultaneously as distance-dependent effects, considering the typical viewing distances of zebrafish and their predators.

Cellular and Molecular Basis of Environment-Induced Color Change in a Tree Frog

Background color matching is essential for camouflage and thermoregulation in ectothermic vertebrates, yet several key cellular-level questions remain unresolved. For instance, it is unclear whether the number of chromatophores or the activity of individual chromatophores plays a more critical role in this process. Using single-cell RNA sequencing (scRNA-seq), we investigated the cellular and molecular mechanisms underlying color change in Rhacophorus dugritei, which adapted to its background by displaying light-green skin on white and black skin on black within two days. We identified two types of chromatophores in their skin, both responsible for the observed color differences. Our findings reveal that morphological color change (MCC) is the dominant process, with the number of chromatophores being more influential in driving color change than the transcriptional activity of melanogenesis in individual cells. Additionally, melanophores from darker individuals exhibited increased activity in energy metabolism pathways, while those from lighter individuals showed stronger immune-related gene expression, suggesting that background adaptation involves more than just morphological changes. Overall, this study successfully applied single-cell sequencing technology to investigate skin pigmentation in a non-model organism. Our results suggest that MCC driven by chromatophore proliferation is a key mechanism of background adaptation, offering new insights into amphibian color adaptation and environmental adaptation in other vertebrates.

Barramundi (Lates calcarifer) rare coloration patterns: a multiomics approach to understand the "panda" phenotype

The barramundi (Lates calcarifer), a significant aquaculture species, typically displays silver to bronze coloration. However, attention is now drawn to rare variants like the "panda" phenotype, characterized by blotch-like patterns of black (PB) and golden (PG) patches. This phenotype presents an opportunity to explore the molecular mechanisms underlying color variations in teleosts. Unlike stable color patterns in many fish, the "panda" variant demonstrates phenotypic plasticity, responding dynamically to unknown cues. We propose a complex interplay of genetic factors and epigenetic modifications, focusing on DNA methylation. Through a multiomics approach, we analyze transcriptomic and methylation patterns between PB and PG patches. Our study reveals differential gene expression related to melanosome trafficking and chromatophore differentiation. Although the specific gene responsible for the PB-PG difference remains elusive, candidate genes like asip1, asip2, mlph, and mreg have been identified. Methylation emerges as a potential contributor to the "panda" phenotype, with changes in gene promoters like hand2 and dynamin possibly influencing coloration. This research lays the groundwork for further exploration into rare barramundi color patterns, enhancing our understanding of color diversity in teleosts. Additionally, it underscores the "panda" phenotype's potential as a model for studying adult skin coloration.

Developmental plasticity and variability in the formation of egg-spots, a pigmentation ornament in the cichlid Astatotilapia calliptera

Vertebrate pigmentation patterns are highly diverse, yet we have a limited understanding of how evolutionary changes to genetic, cellular, and developmental mechanisms generate variation. To address this, we examine the formation of a sexually-selected male ornament exhibiting inter- and intraspecific variation, the egg-spot pattern, consisting of circular yellow-orange markings on the male anal fins of haplochromine cichlid fishes. We focus on Astatotilapia calliptera, the ancestor-type species of the Malawi cichlid adaptive radiation of over 850 species. We identify a key role for iridophores in initializing egg-spot aggregations composed of iridophore-xanthophore associations. Despite adult sexual dimorphism, aggregations initially form in both males and females, with development only diverging between the sexes at later stages. Unexpectedly, we found that the timing of egg-spot initialization is plastic. The earlier individuals are socially isolated, the earlier the aggregations form, with iridophores being the cell type that responds to changes to the social environment. Furthermore, we observe apparent competitive interactions between adjacent egg-spot aggregations, which strongly suggests that egg-spot patterning results mostly from cell-autonomous cellular interactions. Together, these results demonstrate that A. calliptera egg-spot development is an exciting model for investigating pigment pattern formation at the cellular level in a system with developmental plasticity, sexual dimorphism, and intraspecific variation. As A. calliptera represents the ancestral bauplan for egg-spots, these findings provide a baseline for informed comparisons across the incredibly diverse Malawi cichlid radiation.

The IgCAM BT-IgSF (IgSF11) is essential for connexin43-mediated astrocyte-astrocyte coupling in mice

The type I transmembrane protein BT-IgSF is predominantly localized in the brain and testes. It belongs to the CAR subgroup of Ig cell adhesion proteins, that are hypothesized to regulate connexin expression or localization. Here, we studied the putative link between BT-IgSF and connexins in astrocytes, ependymal cells and neurons of the mouse. Global knockout of BT-IgSF caused an increase in the clustering of connexin43 (Gja1), but not of connexin30 (Gjb6), on astrocytes and ependymal cells. Additionally, knockout animals displayed reduced expression levels of connexin43 protein in the cortex and hippocampus. Importantly, analysis of biocytin spread in hippocampal or cortical slices from mature mice of either sex revealed a decrease in astrocytic cell-cell coupling in the absence of BT-IgSF. Blocking either protein biosynthesis or proteolysis showed that the lysosomal pathway increased connexin43 degradation in astrocytes. Localization of connexin43 in subcellular compartments was not impaired in astrocytes of BT-IgSF mutants. In contrast to connexin43 the localization and expression of connexin36 (Gjd2) on neurons was not affected by the absence of BT-IgSF. Overall, our data indicate that the IgCAM BT-IgSF is essential for correct gap junction-mediated astrocyte-to-astrocyte cell communication.Significance Statement Astrocytes regulate a variety of physiological processes in the developing and adult brain that are essential for proper brain function. Astrocytes form extensive networks in the brain and communicate via gap junctions. Disruptions of gap junction coupling are found in several diseases such as neurodegeneration or epilepsy. Here, we demonstrate that the cell adhesion protein BT-IgSF is essential for gap junction mediated coupling between astrocytes in the cortex and hippocampus.

A Systematic Study of Yiqi Qubai Standard Decoction for Treating Vitiligo Based on UPLC-Q-TOF/MS Combined with Chemometrics, Molecular Docking, and Cellular and Zebrafish Assays

The Yiqi Qubai (YQ) formula is a hospital preparation for treating vitiligo in China that has had reliable efficacy for decades. The formula consists of four herbs; however, the extraction process to produce the formula is obsolete and the active ingredients and mechanisms remain unknown. Therefore, in this paper, fingerprints were combined with the chemometrics method to screen high-quality herbs for the preparation of the YQ standard decoction (YQD). Then, the YQD preparation procedure was optimized using response surface methodology. A total of 44 chemical constituents, as well as 36 absorption components (in rat plasma) of YQD, were identified via UPLC-Q-TOF/MS. Based on the ingredients, the quality control system of YQD was optimized by establishing the SPE-UPLC-Q-TOF/MS identification method and the HPLC quantification method. Network pharmacological analysis and molecular docking showed that carasinaurone, calycosin-7-O-β-d-glucoside, methylnissolin-3-O-glucoside, genkwanin, akebia saponin D, formononetin, akebia saponin B, and apigenin may be the key active components for treating vitiligo; the core targets associated with them were AKT1, MAPK1, and mTOR, whereas the related pathways were the PI3K-Akt, MAPK, and FoxO signaling pathways. Cellular assays showed that YQD could promote melanogenesis and tyrosinase activity, as well as the transcription and expression of tyrosinase-associated proteins (i.e., TRP-1) in B16F10 cells. In addition, YQD also increased extracellular tyrosinase activity. Further efficacy validation showed that YQD significantly promotes melanin production in zebrafish. These may be the mechanisms by which YQD improves the symptoms of vitiligo. This is the first systematic study of the YQ formula that has optimized the standard decoction preparation method and investigated the active ingredients, quality control, efficacy, and mechanisms of YQD. The results of this study lay the foundations for the clinical application and further development of the YQ formula.

Pigment Identification and Gene Expression Analysis during Erythrophore Development in Spotted Scat (Scatophagus argus) Larvae

Red coloration is considered an economically important trait in some fish species, including spotted scat, a marine aquaculture fish. Erythrophores are gradually covered by melanophores from the embryonic stage. Despite studies of black spot formation and melanophore coloration in the species, little is known about erythrophore development, which is responsible for red coloration. 1-phenyl 2-thiourea (PTU) is a tyrosinase inhibitor commonly used to inhibit melanogenesis and contribute to the visualization of embryonic development. In this study, spotted scat embryos were treated with 0.003% PTU from 0 to 72 h post fertilization (hpf) to inhibit melanin. Erythrophores were clearly observed during the embryonic stage from 14 to 72 hpf, showing an initial increase (14 to 36 hpf), followed by a gradual decrease (36 to 72 hpf). The number and size of erythrophores at 36 hpf were larger than those at 24 and 72 hpf. At 36 hpf, LC-MS and absorbance spectrophotometry revealed that the carotenoid content was eight times higher than the pteridine content, and β-carotene and lutein were the main pigments related to red coloration in spotted scat larvae. Compared with their expression in the normal hatching group, rlbp1b, rbp1.1, and rpe65a related to retinol metabolism and soat2 and apoa1 related to steroid hormone biosynthesis and steroid biosynthesis were significantly up-regulated in the PTU group, and rh2 associated with phototransduction was significantly down-regulated. By qRT-PCR, the expression levels of genes involved in carotenoid metabolism (scarb1, plin6, plin2, apoda, bco1, and rep65a), pteridine synthesis (gch2), and chromatophore differentiation (slc2a15b and csf1ra) were significantly higher at 36 hpf than at 24 hpf and 72 hpf, except for bco1. These gene expression profiles were consistent with the developmental changes of erythrophores. These findings provide insights into pigment cell differentiation and gene function in the regulation of red coloration and contribute to selective breeding programs for ornamental aquatic animals.

The Unreasonable Effectiveness of Reaction Diffusion in Vertebrate Skin Color Patterning

In 1952, Alan Turing published the reaction-diffusion (RD) mathematical framework, laying the foundations of morphogenesis as a self-organized process emerging from physicochemical first principles. Regrettably, this approach has been widely doubted in the field of developmental biology. First, we summarize Turing's line of thoughts to alleviate the misconception that RD is an artificial mathematical construct. Second, we discuss why phenomenological RD models are particularly effective for understanding skin color patterning at the meso/macroscopic scales, without the need to parameterize the profusion of variables at lower scales. More specifically, we discuss how RD models (a) recapitulate the diversity of actual skin patterns, (b) capture the underlying dynamics of cellular interactions, (c) interact with tissue size and shape, (d) can lead to ordered sequential patterning, (e) generate cellular automaton dynamics in lizards and snakes, (f) predict actual patterns beyond their statistical features, and (g) are robust to model variations. Third, we discuss the utility of linear stability analysis and perform numerical simulations to demonstrate how deterministic RD emerges from the underlying chaotic microscopic agents.

kcnj13 regulates pigment cell shapes in zebrafish and has diverged by cis-regulatory evolution between Danio species

Teleost fish of the genus Danio are excellent models to study the genetic and cellular bases of pigment pattern variation in vertebrates. The two sister species Danio rerio and Danio aesculapii show divergent patterns of horizontal stripes and vertical bars that are partly caused by the divergence of the potassium channel gene kcnj13. Here, we show that kcnj13 is required only in melanophores for interactions with xanthophores and iridophores, which cause location-specific pigment cell shapes and thereby influence colour pattern and contrast in D. rerio. Cis-regulatory rather than protein coding changes underlie kcnj13 divergence between the two Danio species. Our results suggest that homotypic and heterotypic interactions between the pigment cells and their shapes diverged between species by quantitative changes in kcnj13 expression during pigment pattern diversification.

Analysis of the genetic loci of pigment pattern evolution in vertebrates

Vertebrate pigmentation patterns are amongst the best characterised model systems for studying the genetic basis of adaptive evolution. The wealth of available data on the genetic basis for pigmentation evolution allows for analysis of trends and quantitative testing of evolutionary hypotheses. We employed Gephebase, a database of genetic variants associated with natural and domesticated trait variation, to examine trends in how cis-regulatory and coding mutations contribute to vertebrate pigmentation phenotypes, as well as factors that favour one mutation type over the other. We found that studies with lower ascertainment bias identified higher proportions of cis-regulatory mutations, and that cis-regulatory mutations were more common amongst animals harbouring a higher number of pigment cell classes. We classified pigmentation traits firstly according to their physiological basis and secondly according to whether they affect colour or pattern, and identified that carotenoid-based pigmentation and variation in pattern boundaries are preferentially associated with cis-regulatory change. We also classified genes according to their developmental, cellular, and molecular functions. We found a greater proportion of cis-regulatory mutations in genes implicated in upstream developmental processes compared to those involved in downstream cellular functions, and that ligands were associated with a higher proportion of cis-regulatory mutations than their respective receptors. Based on these trends, we discuss future directions for research in vertebrate pigmentation evolution.

Stripes and loss of color in ball pythons (Python regius) are associated with variants affecting endothelin signaling

Color patterns in nonavian reptiles are beautifully diverse, but little is known about the genetics and development of these patterns. Here, we investigated color patterning in pet ball pythons (Python regius), which have been bred to show color phenotypes that differ dramatically from the wildtype form. We report that several color phenotypes in pet animals are associated with putative loss-of-function variants in the gene encoding endothelin receptor EDNRB1: (1) frameshift variants in EDNRB1 are associated with conversion of the normal mottled color pattern to skin that is almost fully white, (2) missense variants affecting conserved sites of the EDNRB1 protein are associated with dorsal, longitudinal stripes, and (3) substitutions at EDNRB1 splice donors are associated with subtle changes in patterning compared to wildtype. We propose that these phenotypes are caused by loss of specialized color cells (chromatophores), with loss ranging from severe (fully white) to moderate (dorsal striping) to mild (subtle changes in patterning). Our study is the first to describe variants affecting endothelin signaling in a nonavian reptile and suggests that reductions in endothelin signaling in ball pythons can produce a variety of color phenotypes, depending on the degree of color cell loss.

Fish-specific N-terminal domain sequence in Connexin 39.4 plays an important role in zebrafish stripe formation by regulating the opening and closing of gap junctions and hemichannels

BACKGROUND

Connexin 39.4 (Cx39.4) is involved in zebrafish (Danio rerio) skin patterning; when mutated, zebrafish exhibit a wavy stripe/labyrinth pattern instead of stripes. Cx39.4 is unique in that it has two additional serine/arginine (SR) residues, Ser2 and Arg3, at positions 2 and 3. Here, I investigated the role of these SR residues in Cx39.4 function.

METHODS

To examine the SR residues in Cx39.4, mutants of the SR residues were generated. Voltage-clamp recordings were performed using Xenopus oocytes to characterize the channel properties of the mutants. Transgenic zebrafish expressing each mutant were generated, and the effects of each mutation on fish skin patterning were evaluated.

RESULTS

The Cx39.4R3K mutant showed essentially the same properties as the wild-type (Cx39.4WT) in both electrophysiological analyses, leading to transgenic, complete phenotype rescue. Both the Cx39.4R3A mutant and deletion mutant of SR residues (Cx39.4delSR) showed a faster decay of gap junction activity and abnormal hemichannel activity, resulting in wide stripes and interstripes that indicate instability. Although the Cx39.4R3D mutant showed no channel activity in gap junctions or hemichannels, it caused unstable phenotypes in the transgene, namely a completely rescued phenotype in some individuals and loss of melanophores in others.

CONCLUSIONS

The SR residues in the NT domain of Cx39.4 are critical for the regulation of channel function, which appears to determine skin patterning.

GENERAL SIGNIFICANCE

These results elucidate the roles of the two SR residues unique to the NT domain of Cx39.4 in its channel function, which is important for zebrafish stripe pattern formation.

Bioelectricity in Developmental Patterning and Size Control: Evidence and Genetically Encoded Tools in the Zebrafish Model

Developmental patterning is essential for regulating cellular events such as axial patterning, segmentation, tissue formation, and organ size determination during embryogenesis. Understanding the patterning mechanisms remains a central challenge and fundamental interest in developmental biology. Ion-channel-regulated bioelectric signals have emerged as a player of the patterning mechanism, which may interact with morphogens. Evidence from multiple model organisms reveals the roles of bioelectricity in embryonic development, regeneration, and cancers. The Zebrafish model is the second most used vertebrate model, next to the mouse model. The zebrafish model has great potential for elucidating the functions of bioelectricity due to many advantages such as external development, transparent early embryogenesis, and tractable genetics. Here, we review genetic evidence from zebrafish mutants with fin-size and pigment changes related to ion channels and bioelectricity. In addition, we review the cell membrane voltage reporting and chemogenetic tools that have already been used or have great potential to be implemented in zebrafish models. Finally, new perspectives and opportunities for bioelectricity research with zebrafish are discussed.

Effects of Natural and Synthetic Astaxanthin on Growth, Body Color, and Transcriptome and Metabolome Profiles in the Leopard Coral Grouper (Plectropomus leopardus)

Natural and synthetic astaxanthin can promote pigmentation in fish. In this study, the effects of dietary astaxanthin on growth and pigmentation were evaluated in leopard coral grouper (Plectropomus leopardus). Fish were assigned to three groups: 0% astaxanthin (C), 0.02% natural astaxanthin (HP), and 0.02% synthetic astaxanthin (AS). Brightness (L*) was not influenced by astaxanthin. However, redness (a*) and yellowness (b*) were significantly higher for fish fed astaxanthin-containing diets than fish fed control diets and were significantly higher in the HP group than in the AS group. In a transcriptome analysis, 466, 33, and 32 differentially expressed genes (DEGs) were identified between C and HP, C and AS, and AS and HP, including various pigmentation-related genes. DEGs were enriched for carotenoid deposition and other pathways related to skin color. A metabolome analysis revealed 377, 249, and 179 differential metabolites (DMs) between C and HP, C and AS, and AS and HP, respectively. In conclusion, natural astaxanthin has a better coloration effect on P. leopardus, which is more suitable as a red colorant in aquaculture. These results improve our understanding of the effects of natural and synthetic astaxanthin on red color formation in fish.

Generation of Albino Phenotype in Ornamental Fish by CRISPR/Cas9-Mediated Genome Editing of slc45a2 Gene

Albinism is the most common color variation described in fish and is a fascinating trait of some ornamental fish species. Albino mutants can be generated by knocking out core genes affecting melanin synthesis like slc45a2 in several fish species. However, genetic mutation remains challenging for species with unknown genome information. In this study, we generated albino mutants in two selected ornamental fish species, royal farlowella (Sturisoma panamense), and redhead cichlid (Vieja melanura). For this purpose, we carried out phylogenetic analyses of fish slc45a2 sequences and identified a highly conserved region among different fish species. A pair of degenerate primers spanning this region was designed and used to amplify a conserved slc45a2 fragment of 340 bp from the two fish species. Based on the amplified sequences, a target site in the 6^th exon was used for designing guide RNA and this targeted site was first verified by the CRISPR/Cas9 system in the zebrafish (Danio rerio) model for the effectiveness. Then, specific guide RNAs were designed for the two ornamental fish species and tested. Most of the injected larvae completely lost black pigment over the whole body and eyes. DNA sequencing confirmed a high degree of mutation at the targeted site. Overall, we described a fast and efficient method to generate albino phenotype in fish species by targeting the conserved 6^th exon of slc45a2 gene for genome editing via CRISPR/Cas9 and this approach could be a new genetic tool to generate desirable albino ornamental fish.

Skin pigmentation improvement with resveratrol microemulsion gel using polyoxyethylene hydrogenated castor oil

OBJECTIVE

To investigate the safety and efficacy of resveratrol microemulsion gel in improving pigmentation.

METHODS

Resveratrol microemulsion gel was prepared by the microemulsion solubilization method, and its quality was evaluated. The transdermal and drug retention rates of resveratrol in vivo were assessed using a transdermal test. The inhibitory effects of resveratrol suspension and microemulsion on tyrosinase activity and melanin production of A375 human melanocytes and zebrafish embryos were compared. A skin patch test was used to investigate the safety of the gel on 15 volunteers.

RESULTS

The microemulsion gel was homogeneous and stable. Compared with suspension and microemulsion, the drug penetration rate and skin retention in the microemulsion gel group were significantly increased. Compared with the suspension group, the activity of melanocyte tyrosinase in A375 human melanocyte was significantly inhibited in the microemulsion group, and the melanin production rate of A375 human melanocyte and the melanin area of zebrafish yolk was decreased. All 15 volunteers tested negative for the human skin patch.

CONCLUSIONS

The microemulsion gel could significantly enhance the ability of resveratrol to inhibit the formation of melanin without causing side effects. These data provide the experimental basis for developing and applying the preparation for improving pigmentation.

miR-330 targeting BCO2 is involved in carotenoid metabolism to regulate skin pigmentation in rainbow trout (Oncorhynchus mykiss)

BACKGROUND

MicroRNAs (miRNAs) play a critical role in regulating skin pigmentation. As a key economic trait, skin color directly affects the market value of rainbow trout (Oncorhynchus mykiss), however, the regulatory mechanism of most miRNAs in fish skin color is still unclear.

RESULTS

In this study, the full-length cDNA sequence of β-carotene oxygenase 2 (BCO2, a key regulator of carotenoid metabolism) from the rainbow trout was obtained using rapid-amplification of cDNA ends (RACE) technology, and qRT-PCR was used to investigate the differential expression of miR-330 and BCO2 in 14 developmental stages and 13 tissues between wild-type rainbow trout (WTrt) and yellow mutant rainbow trout (YMrt). Additionally, the function of miR-330 was verified by overexpression and silencing in vitro and in vivo. The results showed that the complete cDNA sequence of BCO2 was 2057 bp with a 1707 bp ORF, encoding a 568 amino acid protein having a molecular weight of 64.07 kD. Sequence alignment revealed that higher conservation of BCO2 protein amongst fishes than amongst other vertebrates, which was further confirmed by phylogenetic analysis. The analysis of spatial and temporal expression patterns suggested that BCO2 and miR-330 were abundantly expressed from fertilized-stage to multi-cell as well as in the dorsal and ventral skin of WTrt and YMrt, and their expression patterns were opposite in most of the same periods and tissues. In vitro, luciferase reporter assay confirmed that BCO2 was a direct target of miR-330, and transfection of miR-330 mimics into rainbow trout liver cells resulted in a decrease in the expression of BCO2; conversely, miR-330 inhibitor had the opposite effect to the miR-330 mimics. In vivo, miR-330 agomir significantly decreased BCO2 expression in dorsal skin, tail fin, and liver. Furthermore, overexpression of miR-330 could suppress cell proliferation and induce apoptosis.

CONCLUSION

Our results showed that miR-330 is involved in the regulation of skin pigmentation in rainbow trout by targeting BCO2 and shows its promise as a potential molecular target to assist the selection of rainbow trout with better skin color patterns.

Generation of a transparent killifish line through multiplex CRISPR/Cas9mediated gene inactivation

Body pigmentation is a limitation for in vivo imaging and thus for the performance of longitudinal studies in biomedicine. A possibility to circumvent this obstacle is the employment of pigmentation mutants, which are used in fish species like zebrafish and medaka. To address the basis of aging, the short-lived African killifish Nothobranchius furzeri has recently been established as a model organism. Despite its short lifespan, N. furzeri shows typical signs of mammalian aging including telomere shortening, accumulation of senescent cells, and loss of regenerative capacity. Here, we report the generation of a transparent N. furzeri line by the simultaneous inactivation of three key loci responsible for pigmentation. We demonstrate that this stable line, named klara, can serve as a tool for different applications including behavioral experiments and the establishment of a senescence reporter by integration of a fluorophore into the cdkn1a (p21) locus and in vivo microscopy of the resulting line.

Lack of the Ig cell adhesion molecule BT-IgSF (IgSF11) induced behavioral changes in the open maze, water maze and resident intruder test

The brain- and testis-specific Ig superfamily protein (BT-IgSF, also termed IgSF11) is a homotypic cell adhesion protein. In the nervous system, BT-IgSF regulates the stability of AMPA receptors in the membrane of cultured hippocampal neurons, modulates the connectivity of chandelier cells and controls gap junction-mediated astrocyte-astrocyte communication. Here, we performed behavioral tests in BT-IgSF-deficient mice. BT-IgSF-deficient mice were similar to control littermates with respect to their reflexes, motor coordination and gating, and associative learning. However, BT-IgSF-deficient mice displayed an increased tendency to stay in the central illuminated areas in the open field and O-Maze paradigms suggesting reduced anxiety or increased scotophobia (fear of darkness). Although BT-IgSF-deficient mice initially found the platform in the water maze their behavior was compromised when the platform was moved, indicating reduced behavioral flexibility. This deficit was overcome by longer training to improve their spatial memory. Furthermore, male BT-IgSF-deficient mice displayed increased aggression towards an intruder. Our results show that specific behaviors are modified by the lack of BT-IgSF and demonstrate a contribution of BT-IgSF to network functions.

Characterization and functional analysis of pax3 in body color transition of polychromatic Midas cichlids (Amphilophus citrinellus)

As the representative genetic and economic trait of ornamental fish, skin color has a strong impact on speciation and adaptation. However, the genetic basis of skin color pigmentation, differentiation and change is still not understood. The Midas cichlid fish with three typical body color transition stages of "black-gray‑gold" is an ideal model system for investigating the formation and change of fish body color. In this study, to investigate the regulatory role of the pair box 3 (pax3) gene in the early body color fading process of Midas cichlids, the complete cDNA sequence (3513 bp) of pax3 was successfully isolated from Midas cichlids (Amphilophus Citrinellus), and found to encode polypeptides of 491 amino acids. Expression patterns of the pax3 gene in tissues of Midas cichlids during different periods, including embryonic development and body color fading stages were detected by quantitative real-time PCR. The qRT-PCR analysis showed that pax3 was expressed in all tissues of adult fish, with a higher expression level in muscle and skin. The highest expression level in muscle tissue was significantly higher than that in other tissues (P < 0.05). During embryonic development, the expression tendency of pax3 was first increased and then decreased. In the three typical stages of early skin color fading from black to gold, pax3 expression in skin, caudal fin and scales all showed a downward trend. The expression level in the black stage was significantly higher than that in other stages (P < 0.05). Positive signal of pax3 protein was detected in the three typical skin color conversion stages, and the highest positive signal intensity was detected in the black stage, which was consistent with qRT-PCR results. After pax3 RNA interference, pax3 and the downstream genes mitf and tyr all decreased, while dct mRNA expression increased in the skin of fish. Western blotting also showed a decrease in pax3 protein concentration. Those results suggest that pax3 plays an important role in skin color formation, distribution and change in Midas cichlids through the melanogenesis pathway.

A community-science approach identifies genetic variants associated with three color morphs in ball pythons (Python regius)

Color morphs in ball pythons (Python regius) provide a unique and largely untapped resource for understanding the genetics of coloration in reptiles. Here we use a community-science approach to investigate the genetics of three color morphs affecting production of the pigment melanin. These morphs-Albino, Lavender Albino, and Ultramel-show a loss of melanin in the skin and eyes, ranging from severe (Albino) to moderate (Lavender Albino) to mild (Ultramel). To identify genetic variants causing each morph, we recruited shed skins of pet ball pythons via social media, extracted DNA from the skins, and searched for putative loss-of-function variants in homologs of genes controlling melanin production in other vertebrates. We report that the Albino morph is associated with missense and non-coding variants in the gene TYR. The Lavender Albino morph is associated with a deletion in the gene OCA2. The Ultramel morph is associated with a missense variant and a putative deletion in the gene TYRP1. Our study is one of the first to identify genetic variants associated with color morphs in ball pythons and shows that pet samples recruited from the community can provide a resource for genetic studies in this species.

Molecular and functional analysis of the microphthalmia-associated transcription factor (mitf) gene duplicates in red tilapia

In vertebrates, the microphthalmia-associated transcription factor (mitf) is at the hub of the melanin synthesis regulation network. However, little information is known about its molecular characterization, expression, location, or function in skin color differentiation and variation of red tilapia. The full-length cDNA sequences (1977 bp and 1999 bp) of mitfa and mitfb, encoding polypeptides of 491 and 514 amino acids, were effectively identified from red tilapia in this study. The Mitfa and Mitfb sequences of red tilapia clustered first with O. aureus, then with other teleost fish, according to phylogenetic analysis. Mitfa and mitfb mRNA were highly expressed in the brain, dorsal skin and eye tissues using quantitative real-time PCR. The mRNA expressions of mitfa and mitfb were the highest in the cleavage stage during the early development of red tilapia. Among three different colors of red tilapia, the expression levels of mitfa and mitfb were highest in the PB (pink with scattered black spots) dorsal skin. After overwintering, the mitfa and mitfb mRNA expressions were high in the dorsal skin of PB (color changed from pink to black). Mitfa and mitfb were mostly found in the epidermal layer of the dorsal skin, according to in situ hybridization (ISH) analysis. After injecting mitf-dsRNA duplicates along the tail vein of red tilapia, the activity of tyrosinase and the level of melanin in the dorsal skin both decreased significantly. The mRNA expressions of mitfa and its downstream genes (tyrb, tyrp1a and dct) decreased, whereas the mRNA expression of mitfb increased after mitfa-dsRNA injection. The mRNA expressions of mitfb, tyrb, tyrp1a and dct decreased, whereas the mRNA expression of mitfa increased after injecting mitfb-dsRNA. These findings suggest that mitf gene duplicates may play an important role in red tilapia skin color differentiation and variation via the melanogenesis pathway.

Patterning, From Conifers to Consciousness: Turing's Theory and Order From Fluctuations

This is a brief account of Turing's ideas on biological pattern and the events that led to their wider acceptance by biologists as a valid way to investigate developmental pattern, and of the value of theory more generally in biology. Periodic patterns have played a key role in this process, especially 2D arrays of oriented stripes, which proved a disappointment in theoretical terms in the case of Drosophila segmentation, but a boost to theory as applied to skin patterns in fish and model chemical reactions. The concept of "order from fluctuations" is a key component of Turing's theory, wherein pattern arises by selective amplification of spatial components concealed in the random disorder of molecular and/or cellular processes. For biological examples, a crucial point from an analytical standpoint is knowing the nature of the fluctuations, where the amplifier resides, and the timescale over which selective amplification occurs. The answer clarifies the difference between "inelegant" examples such as Drosophila segmentation, which is perhaps better understood as a programmatic assembly process, and "elegant" ones expressible in equations like Turing's: that the fluctuations and selection process occur predominantly in evolutionary time for the former, but in real time for the latter, and likewise for error suppression, which for Drosophila is historical, in being lodged firmly in past evolutionary events. The prospects for a further extension of Turing's ideas to the complexities of brain development and consciousness is discussed, where a case can be made that it could well be in neuroscience that his ideas find their most important application.

Oca2 targeting using CRISPR/Cas9 in the Malawi cichlid Astatotilapia calliptera

Identifying genetic loci underlying trait variation provides insights into the mechanisms of diversification, but demonstrating causality and characterizing the role of genetic loci requires testing candidate gene function, often in non-model species. Here we establish CRISPR/Cas9 editing in Astatotilapia calliptera, a generalist cichlid of the remarkably diverse Lake Malawi radiation. By targeting the gene oca2 required for melanin synthesis in other vertebrate species, we show efficient editing and germline transmission. Gene edits include indels in the coding region, probably a result of non-homologous end joining, and a large deletion in the 3' untranslated region due to homology-directed repair. We find that oca2 knock-out A. calliptera lack melanin, which may be useful for developmental imaging in embryos and studying colour pattern formation in adults. As A. calliptera resembles the presumed generalist ancestor of the Lake Malawi cichlids radiation, establishing genome editing in this species will facilitate investigating speciation, adaptation and trait diversification in this textbook radiation.

Ultrastructure and regulation of color change in blue spots of leopard coral trout Plectropomus leopardus

The leopard coral trout generally exhibited numerous round, minute blue spots covering its head (about the size of nostril) and body (except ventral side). This is a characteristic that distinguishes them from similar species. Recently, however, we found the leopard coral trout with black spots. Here, the distribution and ultrastructure of chromatophores in the blue and black spots were investigated with light and transmission electron microscopies. The results showed that in the blue spots, two types of chromatophores are present in the dermis, with the light-reflecting iridophores located in the upper layer and the aggregated light-absorbing melanophores in the lower layer. Black spots have a similar chromatophore composition, except that the melanosomes within the melanophores disperse their dendritic processes to encircle the iridophores. Interestingly, after the treatment of forskolin, a potent adenylate cyclase activator, the blue spots on the body surface turned black. On the other hand, using the skin preparations in vitro, the electrical stimulation and norepinephrine treatment returned the spots to blue color again, indicating the sympathetic nerves were involved in regulating the coloration of blue spots. Taken together, our results revealed that the blue spots of the leopard coral trout can change color to black and vice versa, resulting from the differences in the distribution of melanosomes, which enriches our understanding of the body color and color changes of fishes.

Studies of Turing pattern formation in zebrafish skin

Skin patterns are the first example of the existence of Turing patterns in living organisms. Extensive research on zebrafish, a model organism with stripes on its skin, has revealed the principles of pattern formation at the molecular and cellular levels. Surprisingly, although the networks of cell-cell interactions have been observed to satisfy the 'short-range activation and long-range inhibition' prerequisites for Turing pattern formation, numerous individual reactions were not envisioned based on the classical reaction-diffusion model. For example, in real skin, it is not an alteration in concentrations of chemicals, but autonomous migration and proliferation of pigment cells that establish patterns, and cell-cell interactions are mediated via direct contact through cell protrusions. Therefore, the classical reaction-diffusion mechanism cannot be used as it is for modelling skin pattern formation. Various studies are underway to adapt mathematical models to the experimental findings on research into skin patterns, and the purpose of this review is to organize and present them. These novel theoretical methods could be applied to autonomous pattern formation phenomena other than skin patterns. This article is part of the theme issue 'Recent progress and open frontiers in Turing's theory of morphogenesis'.

An Orthotopic Model of Uveal Melanoma in Zebrafish Embryo: A Novel Platform for Drug Evaluation

Uveal melanoma is a highly metastatic tumor, representing the most common primary intraocular malignancy in adults. Tumor cell xenografts in zebrafish embryos may provide the opportunity to study in vivo different aspects of the neoplastic disease and its response to therapy. Here, we established an orthotopic model of uveal melanoma in zebrafish by injecting highly metastatic murine B16-BL6 and B16-LS9 melanoma cells, human A375M melanoma cells, and human 92.1 uveal melanoma cells into the eye of zebrafish embryos in the proximity of the developing choroidal vasculature. Immunohistochemical and immunofluorescence analyses showed that melanoma cells proliferate during the first four days after injection and move towards the eye surface. Moreover, bioluminescence analysis of luciferase-expressing human 92.1 uveal melanoma cells allowed the quantitative assessment of the antitumor activity exerted by the canonical chemotherapeutic drugs paclitaxel, panobinostat, and everolimus after their injection into the grafted eye. Altogether, our data demonstrate that the zebrafish embryo eye is a permissive environment for the growth of invasive cutaneous and uveal melanoma cells. In addition, we have established a new luciferase-based in vivo orthotopic model that allows the quantification of human uveal melanoma cells engrafted in the zebrafish embryo eye, and which may represent a suitable tool for the screening of novel drug candidates for uveal melanoma therapy.

Genetic basis of orange spot formation in the guppy (Poecilia reticulata)

Background

To understand the evolutionary significance of female mate choice for colorful male ornamentation, the underlying regulatory mechanisms of such ornamentation must be understood for examining how the ornaments are associated with “male qualities” that increase the fitness or sexual attractiveness of offspring. In the guppy (Poecilia reticulata), an established model system for research on sexual selection, females prefer males possessing larger and more highly saturated orange spots as potential mates. Although previous studies have identified some chromosome regions and genes associated with orange spot formation, the regulation and involvement of these genetic elements in orange spot formation have not been elucidated. In this study, the expression patterns of genes specific to orange spots and certain color developmental stages were investigated using RNA-seq to reveal the genetic basis of orange spot formation.

Results

Comparing the gene expression levels of male guppy skin with orange spots (orange skin) with those without any color spots (dull skin) from the same individuals identified 1102 differentially expressed genes (DEGs), including 630 upregulated genes and 472 downregulated genes in the orange skin. Additionally, the gene expression levels of the whole trunk skin were compared among the three developmental stages and 2247 genes were identified as DEGs according to color development. These analyses indicated that secondary differentiation of xanthophores may affect orange spot formation.

Conclusions

The results suggested that orange spots might be formed by secondary differentiation, rather than de novo generation, of xanthophores, which is induced by Csf1 and thyroid hormone signaling pathways. Furthermore, we suggested candidate genes associated with the areas and saturation levels of orange spots, which are both believed to be important for female mate choice and independently regulated. This study provides insights into the genetic and cellular regulatory mechanisms underlying orange spot formation, which would help to elucidate how these processes are evolutionarily maintained as ornamental traits relevant to sexual selection.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01942-2.

Capturing and analyzing pattern diversity: an example using the melanistic spotted patterns of leopard geckos

Animal color patterns are widely studied in ecology, evolution, and through mathematical modeling. Patterns may vary among distinct body parts such as the head, trunk or tail. As large amounts of photographic data is becoming more easily available, there is a growing need for general quantitative methods for capturing and analyzing the full complexity and details of pattern variation. Detailed information on variation in color pattern elements is necessary to understand how patterns are produced and established during development, and which evolutionary forces may constrain such a variation. Here, we develop an approach to capture and analyze variation in melanistic color pattern elements in leopard geckos. We use this data to study the variation among different body parts of leopard geckos and to draw inferences about their development. We compare patterns using 14 different indices such as the ratio of melanistic versus total area, the ellipticity of spots, and the size of spots and use these to define a composite distance between two patterns. Pattern presence/absence among the different body parts indicates a clear pathway of pattern establishment from the head to the back legs. Together with weak within-individual correlation between leg patterns and main body patterns, this suggests that pattern establishment in the head and tail may be independent from the rest of the body. We found that patterns vary greatest in size and density of the spots among body parts and individuals, but little in their average shapes. We also found a correlation between the melanistic patterns of the two front legs, as well as the two back legs, and also between the head, tail and trunk, especially for the density and size of the spots, but not their shape or inter-spot distance. Our data collection and analysis approach can be applied to other organisms to study variation in color patterns between body parts and to address questions on pattern formation and establishment in animals.

Carotenoid coloration and coloration-linked gene expression in red tilapia (Oreochromis sp.) tissues

Background

Production, marketability and consumer preference of red tilapia often depends upon the intensity of coloration. Hence, new approaches to develop coloration are now geared to improve market acceptability and profit. This study evaluated the effects of carotenoid-rich diets on the phenotypic coloration, carotenoid level, weight gain and expression of coloration-linked genes in skin, fin and muscle tissues. Carotenoids were extracted from dried Daucus carota peel, Ipomoea aquatica leaves, and Moringa oleifera leaves. Eighty (80) size-14 fish were fed with carotenoid-rich treatments twice a day for 120 days. The phenotypic effect of the carotenoid extracts was measured through a color chart. Skin carotenoid level was measured through UV-vis spectrophotometer. csf1ra, Bcdo2 and StAR expression analysis was done using qRT-PCR.

Results

Treatments with carotenoid extracts yielded higher overall scores on phenotypic coloration and tissue carotenoid levels. Differential expression of carotenoid-linked genes such as the elevated expression in csf1ra and lower expression in Bcdo2b following supplementation of the enhanced diet supports the phenotypic redness and increased carotenoid values in red tilapia fed with D. carota peel and I. aquatica leaves.

Conclusions

Overall improvement in the redness of the tilapia was achieved through the supplementation of carotenoid-rich diet derived from readily available plants. Differential expression of coloration-linked genes supports the increase in the intensity of phenotypic coloration and level of carotenoids in the tissues. The study emphasizes the importance of carotenoids in the commercial tilapia industry and highlights the potential of the plant extracts for integration and development of feeds for color enhancement in red tilapia.

Whole-organism 3D quantitative characterization of zebrafish melanin by silver deposition micro-CT

We previously described X-ray histotomography, a high-resolution, non-destructive form of X-ray microtomography (micro-CT) imaging customized for three-dimensional (3D), digital histology, allowing quantitative, volumetric tissue and organismal phenotyping (Ding et al., 2019). Here, we have combined micro-CT with a novel application of ionic silver staining to characterize melanin distribution in whole zebrafish larvae. The resulting images enabled whole-body, computational analyses of regional melanin content and morphology. Normalized micro-CT reconstructions of silver-stained fish consistently reproduced pigment patterns seen by light microscopy, and further allowed direct quantitative comparisons of melanin content across wild-type and mutant samples, including subtle phenotypes not previously noticed. Silver staining of melanin for micro-CT provides proof-of-principle for whole-body, 3D computational phenomic analysis of a specific cell type at cellular resolution, with potential applications in other model organisms and melanocytic neoplasms. Advances such as this in whole-organism, high-resolution phenotyping provide superior context for studying the phenotypic effects of genetic, disease, and environmental variables.

Developmental genetics of color pattern establishment in cats

Intricate color patterns are a defining aspect of morphological diversity in the Felidae. We applied morphological and single-cell gene expression analysis to fetal skin of domestic cats to identify when, where, and how, during fetal development, felid color patterns are established. Early in development, we identify stripe-like alterations in epidermal thickness preceded by a gene expression pre-pattern. The secreted Wnt inhibitor encoded by Dickkopf 4 plays a central role in this process, and is mutated in cats with the Ticked pattern type. Our results bring molecular understanding to how the leopard got its spots, suggest that similar mechanisms underlie periodic color pattern and periodic hair follicle spacing, and identify targets for diverse pattern variation in other mammals.

Phylogenetic Analysis of Core Melanin Synthesis Genes Provides Novel Insights Into the Molecular Basis of Albinism in Fish

Melanin is the most prevalent pigment in animals. Its synthesis involves a series of functional genes. Particularly, teleosts have more copies of these genes related to the melanin synthesis than tetrapods. Despite the increasing number of available vertebrate genomes, a few systematically genomic studies were reported to identify and compare these core genes for the melanin synthesis. Here, we performed a comparative genomic analysis on several core genes, including tyrosinase genes (tyr, tyrp1, and tyrp2), premelanosome protein (pmel), microphthalmia-associated transcription factor (mitf), and solute carrier family 24 member 5 (slc24a5), based on 90 representative vertebrate genomes. Gene number and mutation identification suggest that loss-of-function mutations in these core genes may interact to generate an albinism phenotype. We found nonsense mutations in tyrp1a and pmelb of an albino golden-line barbel fish, in pmelb of an albino deep-sea snailfish (Pseudoliparis swirei), in slc24a5 of cave-restricted Mexican tetra (Astyanax mexicanus, cavefish population), and in mitf of a transparent icefish (Protosalanx hyalocranius). Convergent evolution may explain this phenomenon since nonsense mutations in these core genes for melanin synthesis have been identified across diverse albino fishes. These newly identified nonsense mutations and gene loss will provide molecular guidance for ornamental fish breeding, further enhancing our in-depth understanding of human skin coloration.

The genetics and evolution of eye color in domestic pigeons (Columba livia)

The eye color of birds, generally referring to the color of the iris, results from both pigmentation and structural coloration. Avian iris colors exhibit striking interspecific and intraspecific variations that correspond to unique evolutionary and ecological histories. Here, we identified the genetic basis of pearl (white) iris color in domestic pigeons (Columba livia) to explore the largely unknown genetic mechanism underlying the evolution of avian iris coloration. Using a genome-wide association study (GWAS) approach in 92 pigeons, we mapped the pearl iris trait to a 9 kb region containing the facilitative glucose transporter gene SLC2A11B. A nonsense mutation (W49X) leading to a premature stop codon in SLC2A11B was identified as the causal variant. Transcriptome analysis suggested that SLC2A11B loss of function may downregulate the xanthophore-differentiation gene CSF1R and the key pteridine biosynthesis gene GCH1, thus resulting in the pearl iris phenotype. Coalescence and phylogenetic analyses indicated that the mutation originated approximately 5,400 years ago, coinciding with the onset of pigeon domestication, while positive selection was likely associated with artificial breeding. Within Aves, potentially impaired SLC2A11B was found in six species from six distinct lineages, four of which associated with their signature brown or blue eyes and lack of pteridine. Analysis of vertebrate SLC2A11B orthologs revealed relaxed selection in the avian clade, consistent with the scenario that during and after avian divergence from the reptilian ancestor, the SLC2A11B-involved development of dermal chromatophores likely degenerated in the presence of feather coverage. Our findings provide new insight into the mechanism of avian iris color variations and the evolution of pigmentation in vertebrates.

Transcriptomic Analysis of Skin Color in Anole Lizards

Color and color pattern are critical for animal camouflage, reproduction, and defense. Few studies, however, have attempted to identify candidate genes for color and color pattern in squamate reptiles, a colorful group with over 10,000 species. We used comparative transcriptomic analyses between white, orange, and yellow skin in a color-polymorphic species of anole lizard to 1) identify candidate color and color-pattern genes in squamates and 2) assess if squamates share an underlying genetic basis for color and color pattern variation with other vertebrates. Squamates have three types of chromatophores that determine color pattern: guanine-filled iridophores, carotenoid- or pteridine-filled xanthophores/erythrophores, and melanin-filled melanophores. We identified 13 best candidate squamate color and color-pattern genes shared with other vertebrates: six genes linked to pigment synthesis pathways, and seven genes linked to chromatophore development and maintenance. In comparisons of expression profiles between pigment-rich and white skin, pigment-rich skin upregulated the pteridine pathway as well as xanthophore/erythrophore development and maintenance genes; in comparisons between orange and yellow skin, orange skin upregulated the pteridine and carotenoid pathways as well as melanophore maintenance genes. Our results corroborate the predictions that squamates can produce similar colors using distinct color-reflecting molecules, and that both color and color-pattern genes are likely conserved across vertebrates. Furthermore, this study provides a concise list of candidate genes for future functional verification, representing a first step in determining the genetic basis of color and color pattern in anoles.

Genetics of white color and iridophoroma in "Lemon Frost" leopard geckos

The squamates (lizards and snakes) are close relatives of birds and mammals, with more than 10,000 described species that display extensive variation in a number of important biological traits, including coloration, venom production, and regeneration. Due to a lack of genomic tools, few genetic studies in squamates have been carried out. The leopard gecko, Eublepharis macularius, is a popular companion animal, and displays a variety of coloration patterns. We took advantage of a large breeding colony and used linkage analysis, synteny, and homozygosity mapping to investigate a spontaneous semi-dominant mutation, “Lemon Frost”, that produces white coloration and causes skin tumors (iridophoroma). We localized the mutation to a single locus which contains a strong candidate gene, SPINT1, a tumor suppressor implicated in human skin cutaneous melanoma (SKCM) and over-proliferation of epithelial cells in mice and zebrafish. Our work establishes the leopard gecko as a tractable genetic system and suggests that a tumor suppressor in melanocytes in humans can also suppress tumor development in iridophores in lizards.

The squamates (lizards and snakes) comprise a diverse group of reptiles, with more than 10,000 described species that display extensive variation in a number of important biological traits, including coloration. In this manuscript, we used quantitative genetics and genomics to map the mutation underlying white coloration in the Lemon Frost morph of the common leopard gecko, Eublepharis macularius. Lemon Frost geckos have increased white body coloration with brightened yellow and orange areas. This morph also displays a high incidence of iridophoroma, a tumor of white-colored cells. We obtained phenotype information and DNA samples from geckos in a large breeding colony and used genome sequencing and genetic linkage analysis to localize the Lemon Frost mutation to a single locus. This locus contains a strong candidate gene, SPINT1, a tumor suppressor implicated in human skin cutaneous melanoma. Together with other recent advances, our work brings reptiles into the modern genetics era.

In Silico Prediction of Transcription Factor Collaborations Underlying Phenotypic Sexual Dimorphism in Zebrafish (Danio rerio)

The transcriptional regulation of gene expression in higher organisms is essential for different cellular and biological processes. These processes are controlled by transcription factors and their combinatorial interplay, which are crucial for complex genetic programs and transcriptional machinery. The regulation of sex-biased gene expression plays a major role in phenotypic sexual dimorphism in many species, causing dimorphic gene expression patterns between two different sexes. The role of transcription factor (TF) in gene regulatory mechanisms so far has not been studied for sex determination and sex-associated colour patterning in zebrafish with respect to phenotypic sexual dimorphism. To address this open biological issue, we applied bioinformatics approaches for identifying the predicted TF pairs based on their binding sites for sex and colour genes in zebrafish. In this study, we identified 25 (e.g., STAT6-GATA4; JUN-GATA4; SOX9-JUN) and 14 (e.g., IRF-STAT6; SOX9-JUN; STAT6-GATA4) potentially cooperating TFs based on their binding patterns in promoter regions for sex determination and colour pattern genes in zebrafish, respectively. The comparison between identified TFs for sex and colour genes revealed several predicted TF pairs (e.g., STAT6-GATA4; JUN-SOX9) are common for both phenotypes, which may play a pivotal role in phenotypic sexual dimorphism in zebrafish.

Nile Tilapia: A Model for Studying Teleost Color Patterns

The diverse color patterns of cichlid fishes play an important role in mate choice and speciation. Here we develop the Nile tilapia (Oreochromis niloticus) as a model system for studying the developmental genetics of cichlid color patterns. We identified 4 types of pigment cells: melanophores, xanthophores, iridophores and erythrophores, and characterized their first appearance in wild-type fish. We mutated 25 genes involved in melanogenesis, pteridine metabolism, and the carotenoid absorption and cleavage pathways. Among the 25 mutated genes, 13 genes had a phenotype in both the F0 and F2 generations. None of F1 heterozygotes had phenotype. By comparing the color pattern of our mutants with that of red tilapia (Oreochromis spp), a natural mutant produced during hybridization of tilapia species, we found that the pigmentation of the body and eye is controlled by different genes. Previously studied genes like mitf, kita/kitlga, pmel, tyrb, hps4, gch2, csf1ra, pax7b, and bco2b were proved to be of great significance for color patterning in tilapia. Our results suggested that tilapia, a fish with 4 types of pigment cells and a vertically barred wild-type color pattern, together with various natural and artificially induced color gene mutants, can serve as an excellent model system for study color patterning in vertebrates.

Reaction-diffusion in a growing 3D domain of skin scales generates a discrete cellular automaton

We previously showed that the adult ocellated lizard skin colour pattern is effectively generated by a stochastic cellular automaton (CA) of skin scales. We additionally suggested that the canonical continuous 2D reaction-diffusion (RD) process of colour pattern development is transformed into this discrete CA by reduced diffusion coefficients at the borders of scales (justified by the corresponding thinning of the skin). Here, we use RD numerical simulations in 3D on realistic lizard skin geometries and demonstrate that skin thickness variation on its own is sufficient to cause scale-by-scale coloration and CA dynamics during RD patterning. In addition, we show that this phenomenon is robust to RD model variation. Finally, using dimensionality-reduction approaches on large networks of skin scales, we show that animal growth affects the scale-colour flipping dynamics by causing a substantial decrease of the relative length scale of the labyrinthine colour pattern of the lizard skin.

Color as an important biological variable in zebrafish models: Implications for translational neurobehavioral research

Color is an important environmental factor that in multiple ways affects human and animal behavior and physiology. Widely used in neuroscience research, various experimental (animal) models may help improve our understanding of how different colors impact brain and behavioral processes. Complementing laboratory rodents, the zebrafish (Danio rerio) is rapidly emerging as an important novel model species to explore complex neurobehavioral processes. The growing utility of zebrafish in biomedicine makes it timely to consider the role of colors in their behavioral and physiological responses. Here, we summarize mounting evidence implicating colors as a critical variable in zebrafish models and neurobehavioral traits, with a particular relevance to CNS disease modeling, genetic and pharmacological modulation, as well as environmental enrichment and animal welfare. We also discuss the growing value of zebrafish models to study color neurobiology and color-related neurobehavioral phenomics, and outline future directions of research in this field.

In situ differentiation of iridophore crystallotypes underlies zebrafish stripe patterning

Skin color patterns are ubiquitous in nature, impact social behavior, predator avoidance, and protection from ultraviolet irradiation. A leading model system for vertebrate skin patterning is the zebrafish; its alternating blue stripes and yellow interstripes depend on light-reflecting cells called iridophores. It was suggested that the zebrafish’s color pattern arises from a single type of iridophore migrating differentially to stripes and interstripes. However, here we find that iridophores do not migrate between stripes and interstripes but instead differentiate and proliferate in-place, based on their micro-environment. RNA-sequencing analysis further reveals that stripe and interstripe iridophores have different transcriptomic states, while cryogenic-scanning-electron-microscopy and micro-X-ray diffraction identify different crystal-arrays architectures, indicating that stripe and interstripe iridophores are different cell types. Based on these results, we present an alternative model of skin patterning in zebrafish in which distinct iridophore crystallotypes containing specialized, physiologically responsive, organelles arise in stripe and interstripe by in-situ differentiation.

The skin of zebrafish is patterned by alternating blue stripes and yellow interstripes which arises from guanine crystal-containing cells called iridophores that reflect light. Here the authors track iridophores and see that they do not migrate between stripes and interstripes, but instead differentiate and proliferate in place based on their micro-environment.