Comparative transcriptome analysis of trout skin pigment cells

Insights into the mechanism of color formation of the freshwater prawn (Macrobrachium rosenbergii) revealed by de novo assembly transcriptome analysis

Body color is an important visual indicator of crustacean quality and plays a major role in consumer acceptability, perceived quality, and the market price of crustaceans. The freshwater prawn (Macrobrachium rosenbergii) has two distinct phenotypic variations, characterized by dark blue and light yellow body colors. However, the underlying mechanisms regulating the body color of M. rosenbergii remain unclear. In this study, the composition of shell color parameters and pigment cells of raw and cooked dark blue and light yellow M. rosenbergii was investigated and the mechanisms associated with body color were elucidated by transcriptome analysis. The results showed significant differences in the raw shells of the dark blue and light yellow M. rosenbergii (L: 26.20 ± 0.53 vs. 29.25 ± 0.45; a: -0.88 ± 0.19 vs. 0.35 ± 0.18; b: 1.73 ± 0.20 vs. 3.46 ± 0.37; dE: 70.33 ± 0.53 vs. 67.34 ± 0.45, respectively, p = 0.000) as well as the cooked shells (L: 58.14 ± 0.81 vs. 55.78 ± 0.55; a: 19.30 ± 0.56 vs. 16.42 ± 0.40; b: 23.60 ± 0.66 vs. 20.30 ± 0.40, respectively, p < 0.05). Transcriptome differential gene analysis obtained 39.02 Gb of raw data and 158,026 unigenes. Comprehensive searches of the SwissProt, Nr, KEGG, Pfam, and KOG databases resulted in successful annotations of 23,902 (33 %), 40,436 (25.59 %), 32,015 (20.26 %), 26,139 (16.54 %), and 22,155 (14.02 %) proteins, respectively. By KEGG pathway analysis, numerous differentially expressed genes were related to pigmentation-related pathways (MAPK signaling pathway, Wnt signaling pathway, melanin production, tyrosine metabolism, and cell-cell communication process). Candidate DEGs that may be involved in body color included apolipoprotein D, crustacyanin, cytochrome P450, and tyrosinase, as verified by quantitative real-time PCR. The results of this study provide useful references to further elucidate the molecular mechanisms of color formation of M. rosenbergii and other crustaceans.

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.

Comparative transcriptome analysis reveals sex bias in expression patterns of genes related to sex steroids and immunity in the skin of spinyhead croaker Collichthys lucidus

Fish skin is the first barrier against external invasion, and also an important interface for communication between males and females during reproduction. Nonetheless, sexual dimorphism in the physiology of fish skins is still poorly understood. Herein, transcriptomes of skin were comparatively analysed between males and females in spinyhead croaker, Collichthys lucidus. Totally, 170 differentially expressed genes (DEG) were detected, including 79 female-biased genes and 91 male-biased genes. Gene ontology (GO) annotation items of the DEGs were mainly enriched in biological process items (86.2%), including regulation of biological processes, responses to chemical and biological stimuli, transport and secretion, movement, immune response, tissue development, etc. In KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis, the male-biased genes were enriched in pathways including those related to immunity such as the TNF signalling pathway and IL-17 signalling pathway, whereas the female-biased genes were enriched in pathways including those related to female steroids such as ovarian steroidogenesis and oestrogen signalling pathway. In addition, odf3 was found to be a male-specific expression gene, being a candidate marker for phenotypic sex. Thus, the sexual difference in gene expression in fish skin in spawning season was uncovered by transcriptome analysis for the first time, providing new insights into sexual dimorphism in the physiology and functions of fish skin.

The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into the melanic pigmentation of anemonefish

Anemonefish are an emerging group of model organisms for studying genetic, ecological, evolutionary, and developmental traits of coral reef fish. The yellowtail clownfish Amphiprion clarkii possesses species-specific characteristics such as inter-species co-habitation, high intra-species color variation, no anemone specificity, and a broad geographic distribution, that can increase our understanding of anemonefish evolutionary history, behavioral strategies, fish-anemone symbiosis, and color pattern evolution. Despite its position as an emerging model species, the genome of A. clarkii is yet to be published. Using PacBio long-read sequencing and Hi-C chromatin capture technology, we generated a high-quality chromosome-scale genome assembly initially comprised of 1,840 contigs with an N50 of 1,203,211 bp. These contigs were successfully anchored into 24 chromosomes of 843,582,782 bp and annotated with 25,050 protein-coding genes encompassing 97.0% of conserved actinopterygian genes, making the quality and completeness of this genome the highest among all published anemonefish genomes to date. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further analyses revealed higher copy numbers of erbb3b (a gene involved in melanocyte development) in A. clarkii compared with other anemonefish, thus suggesting a possible link between erbb3b and the natural melanism polymorphism observed in A. clarkii. The publication of this high-quality genome, along with A. clarkii's many unique traits, position this species as an ideal model organism for addressing scientific questions across a range of disciplines.

Size-age population structure of an endangered and anthropogenically introgressed northern Adriatic population of marble trout (Salmo marmoratus Cuv.): insights for its conservation and sustainable exploitation

Salmonid species are main actors in the Italian socio-ecological landscape of inland fisheries. We present novel data on the size-age structure of one of the remnant Italian populations of the critically endangered marble trout Salmo marmoratus, which co-occurs with other stocked non-native salmonids in a large glacial river of the Lake Maggiore basin (Northern Italy-Southern Switzerland). Like other Italian native trout populations, the Toce River marble trout population is affected by anthropogenic introgression with the non-native brown trout S. trutta. Our sample includes 579 individuals, mainly collected in the Toce River main channel. We estimated the length-weight relationship, described the population size-age structure, estimated the age-specific growth trajectories, and fit an exponential mortality model. A subset of the sample was also used to measure numerical and biomass density. The estimated asymptotic maximum length is ~105 cm total length (TL). Mean length at first maturity is ~55 cm TL, and mean length at maximum yield per recruit is ~68 cm TL. Approximately 45-70% of the population are estimated to die annually, along with a fishing annual mortality of ~37%, with an exploitation ratio of ~0.5. The frequency distribution of length classes in a sample collected by angling shows that ~80% of the individuals that could be retained according to the current recreational fishing regulations likely never reproduced, and large fish disproportionally contributing to recruitment are fished and retained. We identify possible overfishing risks posed by present regulations, and propose updated harvest-slot length limits to mitigate such risks. More detailed and long-term datasets on this system are needed to more specifically inform the fishery management and monitor the effects of any change in the management strategy on the size-age structure of the marble trout population of the Toce River.

Redundancy analysis, genome-wide association studies and the pigmentation of brown trout (Salmo trutta L.)

The association of molecular variants with phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited, use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single- and multitrait GWAS to explore the molecular basis of pigmentation variation in brown trout (Salmo trutta) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single- and multitrait GWAS allowed the extraction of 337 independent colour patterning loci (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (i) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (ii) were found to be associated with 218 candidate genes, including 197 genes formerly mentioned in the literature associated to skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (Onchorhynchus mykiss), and (iii) related to functions relevant to pigmentation variation (e.g., calcium- and ion-binding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown to be useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression.

Cell Junction and Vesicle Trafficking-Mediated Melanosome/Melanin Transfer Are Involved in the Dynamic Transformation of Goldfish Carassius auratus Skin Color

Goldfish are one of the most popular models for studying the genetic diversity of skin color. Transcriptome sequencing (RNA-seq) and whole genome bisulfate sequencing (WGBS) of skin tissues from the third filial (F3) cyan (CN), black (BK), and white (WH) goldfish were conducted to analyze the molecular mechanism of color transformation in fish. The RNA-seq yielded 56 Gb of clean data and 56,627 transcripts from nine skin samples. The DEGs (differentially expressed genes) were enriched in cell junction cellular components and the tight junction pathway. Ninety-five homologs of the claudin family were predicted and 16 claudins were identified in correlation with skin color transformation. WGBS yielded 1079 Gb of clean data from 15 samples. Both the DEGs and the DMRs (differentially methylated regions) in the BK_CN group were found to be enriched in cytoskeleton reorganization and vesicle trafficking. Masson staining and TEM (transmission electron microscopy) confirmed the varied distribution and processes of melanosome/melanin in skin tissues. Our results suggested that cytoskeleton reorganization, cell junction, and the vesicle trafficking system played key roles in the transfer of the melanosome/melanin, and it was the extracellular translocation rather than the biosynthesis or metabolism of the melanin process that resulted in the color transformation of cyan goldfish. The data will facilitate the understanding of the molecular mechanisms underlying dynamic skin color transformation in goldfish.

MiR-382 Functions on the Regulation of Melanogenesis via Targeting dct in Rainbow Trout (Oncorhynchus mykiss)

MicroRNAs (miRNAs) are a class of endogenous small noncoding RNAs that are involved in a diverse collection of biological processes as important post-transcriptional regulators. However, little is known about the molecular regulatory mechanism of miRNAs in fish skin pigmentation. In this study, we first confirmed that dopachrome tautomerase (dct), a key gene of melanogenesis, is a target of miR-382 in rainbow trout (Oncorhynchus mykiss) using luciferase reporter assay. The analysis of different developmental stages and tissue expression patterns between wild-type and yellow mutant rainbow trout suggested that miR-382 is a potential regulator during the process of skin pigmentation. In vitro, miR-382 mimics in rainbow trout primary liver cells significantly downregulated dct expression and resulted in decreased expression of key melanogenic genes including tyrosine-related protein 1 (tyrp1) and premelanosome protein (pmel), whereas the expression level of dct was markedly increased after transfected with miR-382 inhibitor. In vivo, overexpression of miR-382 by injection of miR-382 agomir significantly depressed the expression of dct in dorsal skin, tail fin, and liver and then reduced the expression levels of tyrp1 and pmel. Furthermore, transfection of miR-382 mimics inhibited cell proliferation and induced apoptosis. Taken together, our results identified a functional role of miR-382 in rainbow trout skin pigmentation through targeting dct, which facilitate understanding the regulatory mechanism of rainbow trout skin color at the post-transcriptional level and provide a theoretical basis for molecular breeding with skin color as the target trait.

Isolation of Chromatophores from Brown Trout (Salmo trutta) Skin

As new techniques for single-cell analysis are evolving, there is a growing need for streamlined and flexible protocols for single-cell suspension preparation and single-cell isolation. Based on previous research on the model species zebrafish (Danio rerio), a novel protocol for the isolation of chromatophores from brown trout (Salmo trutta) skin was developed and specific gene expression in chromatophore types evaluated with qPCR. This is the first report on a protocol for the isolation of chromatophores from the skin of salmonids. The method is simple and fast (taking about 90 min), requires no special equipment and is in line with the high ethical standards required in animal research, as no animals need to be sacrificed. In addition, skin biopsies can be taken from the same fish at multiple time points, allowing monitoring of chromatophore differentiation and their involvement in the formation of pigmentation patterns. The protocol should be effective for the vast majority of salmonid species due to similarities in skin morphology.

Genetic and correlative light and electron microscopy evidence for the unique differentiation pathway of erythrophores in brown trout skin

Based on their cell ultrastructure, two types of erythrophores in the spotted skin regions of brown trout (Salmo trutta) were previously described. To test the hypothesis regarding the origin of a new cell type following genome duplication, we analysed the gene and paralogue gene expression patterns of erythrophores in brown trout skin. In addition, the ultrastructure of both erythrophore types was precisely examined using transmission electron microscopy (TEM) and correlative light microscopy and electron microscopy (CLEM). Ultrastructural differences between the sizes of erythrophore inclusions were confirmed; however, the overlapping inclusion sizes blur the distinction between erythrophore types, which we have instead defined as cell subtypes. Nevertheless, the red spots of brown trout skin with subtype 2 erythrophores, exhibited unique gene expression patterns. Many of the upregulated genes are involved in melanogenesis or xanthophore differentiation. In addition, sox10, related to progenitor cells, was also upregulated in the red spots. The expressions of paralogues derived from two genome duplication events were also analysed. Multiple paralogues were overexpressed in the red spots compared with other skin regions, suggesting that the duplicated gene copies adopted new functions and contributed to the origin of a new cell subtype that is characteristic for red spot. Possible mechanisms regarding erythrophore origin are proposed and discussed. To the best of our knowledge, this is the first study to evaluate pigment cell types in the black and red spots of brown trout skin using the advanced CLEM approach together with gene expression profiling.

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'.

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.

Connexins in melanoma: Potential role of Cx46 in its aggressiveness

Melanoma is the most aggressive skin cancer, and in metastatic advanced states, it is completely refractory to chemotherapy. Therefore, it is relevant to understand the molecular bases that rule their aggressiveness. Connexins (Cxs) are proteins that under normal physiological conditions participate in intercellular communication, via the exchange of signaling molecules between the cytoplasm and extracellular milieu and the exchange of ions/second messengers between the cytoplasm of contacting cells. These proteins have shown important roles in cancer progression, chemo- and radiotherapy resistance, and metastasis. Accordingly, Cx26 and Cx43 seem to play important roles in melanoma progression and metastasis. On the other hand, Cx46 is typically expressed in the eye lens, where it seems to be associated with oxidative stress protection in fiber lens cells. However, in the last decade, Cx46 expression has been associated with breast and brain cancers, due to its role in potentiation of both extracellular vesicle release and cancer stem cell-like properties. In this review, we analyzed a potential role of Cx46 as a new biomarker and therapeutic target in melanoma.

Brightened body coloration in female guppies (Poecilia reticulata) serves as an in vivo biomarker for environmental androgens: The example of 17β-trenbolone

In vivo testing systems for environmental androgens are scarce. The aim of this study was to evaluate the potential of male-specific brightened body coloration in female guppies (Poecilia reticulata) to serve as an in vivo biomarker of environmental androgens using 17β-trenbolone as an example. The high bioaccumulation of 17β-trenbolone in the skin of female guppies suggests that it is a potential target tissue of environmental androgens. The coloration index, pigment cell ultrastructure, pigment levels, sexual attractiveness, and reproductive capability of female guppies were analyzed following 28 days of exposure to 20 ng/L, 200 ng/L, and 2000 ng/L 17β-trenbolone. Increases in the coloration index caused by 17β-trenbolone exposure were attributable to increased pteridine and melanin levels. Decreases in the sexual attractiveness, number of offspring, and survival rate of offspring suggested that the changes in body coloration translated into adverse outcomes. Finally, mRNA sequencing indicated that 17β-trenbolone increased pteridine levels by activating genomic effects of androgen receptor on xanthine dehydrogenase and increased melanin levels by exerting non-genomic effects targeting microphthalmia-associated transcription factor, tyrosinase, and tyrosinase-related protein 1 that were mediated by mitogen-activated protein kinase and calcium signaling pathways. We have derived a robust adverse outcome pathway of environmental androgens, and our findings suggest that indicators at different biological levels related to brightened body coloration in female guppies can serve as less-invasive or noninvasive in vivo biomarkers of short-term exposure to environmental androgens.

Malpigmentation of Common Sole (Solea solea) during Metamorphosis Is Associated with Differential Synaptic-Related Gene Expression

Simple Summary

Common sole (Solea solea) is an important species for the aquaculture industry. Defects in pigmentation of the species are very common in farmed conditions. Differences in gene expression between normally pigmented juveniles and those that present both sides full pigmented, ocular and blind, were investigated. Differentially expressed transcripts were functionally annotated, and gene ontology was carried out. The results indicated that ambicolorated juveniles showed a significant upregulation of genes involved in the signal transmission at the synaptic level and regulation of ion channels, affecting the plasticity and the development of the synapses, as well as the transmission of signals or ions through channels.

Abstract

In farmed flatfish, such as common sole, color disturbances are common. Dyschromia is a general term that includes the color defects on the blind and ocular sides of the fish. The purpose was to examine the difference in gene expression between normal pigmented and juveniles who present ambicoloration. The analysis was carried out with next-generation sequencing techniques and de novo assembly of the transcriptome. Transcripts that showed significant differences (FDR < 0.05) in the expression between the two groups, were related to those of zebrafish (Danio rerio), functionally identified, and classified into categories of the gene ontology. The results revealed that ambicolorated juveniles exhibit a divergent function, mainly of the central nervous system at the synaptic level, as well as the ionic channels. The close association of chromophore cells with the growth of nerve cells and the nervous system was recorded. The pathway, glutamate binding–activation of AMPA and NMDA receptors–long-term stimulation of postsynaptic potential–LTP (long term potentiation)–plasticity of synapses, appears to be affected. In addition, the development of synapses also seems to be affected by the interaction of the LGI (leucine-rich glioma inactivated) protein family with the ADAM (a disintegrin and metalloprotease) ones.

Insights Into the Albinism Mechanism for Two Distinct Color Morphs of Northern Snakehead, Channa argus Through Histological and Transcriptome Analyses

The great northern snakehead (Channa argus) is one of the most important economic and conservational fish in China. In this study, the melanocytes in the skin of two distinct color morphs C. argus were investigated and compared through employment of the microscopic analysis, hematoxylin and eosin (H&E) and Masson Fontana staining. Our results demonstrated the uneven distribution of melanocytes with extremely low density and most of them were in the state of aging or death. Meanwhile, there was no obvious pigment layer and melanocytes distribution pattern found in the albino-type (AT), while the melanocytes were evenly distributed with abundance in the bicolor-type (BT). The transcriptome analysis through Illumina HiSeq sequencing showed that a total of 34.93 Gb Clean Data was obtained, and Q30 base percentage reached 92.66%. The BT and AT northern snakeheads transcriptome data included a total of 56,039,701 and 60,410,063 clean reads (n = 3), respectively. In gene expression analyses, the sample correlation coefficients (r) were ranged between 0.92 and 1.00; the contribution of PC1 and PC2 were 50.25 and 13.73% by using PCA cluster analysis, the total number of DEGs were 1024 (559 up-regulated and 465 down-regulated), and the number of annotated DEGs was 767 (COG 172, KEGG 262, GO 288, SwissProt 548, Pfam 579 and NR 765). Additionally, 46,363 ± 873 and 44,947 ± 392 single nucleotide polymorphisms (SNPs) were compiled via genetic structure analysis, respectively. Ten key pigment-related genes were screened using qRT-PCR. And all of them revealed extremely higher expression levels in the skin of BT than those of AT. This is the first study to analyze the mechanism of albino characteristics of Channa via histology and transcriptomics, and also provide the oretical and practical support for the protection and development of germplasm resources for C. argus.

Linking genotype, cell behavior, and phenotype: multidisciplinary perspectives with a basis in zebrafish patterns

Zebrafish are characterized by dark and light stripes, but mutants display a rich variety of altered patterns. These patterns arise from the interactions of brightly colored pigment cells, making zebrafish a self-organization problem. The diversity of patterns present in zebrafish and other emerging fish models provides an excellent system for elucidating how genes, cell behavior, and visible animal characteristics are related. With the goal of highlighting how experimental and mathematical approaches can be used to link these scales, I overview current descriptions of zebrafish patterning, describe advances in the understanding of the mechanisms underlying cell communication, and discuss new work that moves beyond zebrafish to explore patterning in evolutionary relatives.

Dark-rearing uncovers novel gene expression patterns in an obligate cave-dwelling fish

Extreme environments often result in the evolution of dramatic adaptive features. The Mexican tetra, Astyanax mexicanus, includes 30 different populations of cave-dwelling forms that live in perpetual darkness. As a consequence, many populations have evolved eye loss, reduced pigmentation, and amplification of nonvisual sensory systems. Closely-related surface-dwelling morphs demonstrate typical vision, pigmentation, and sensation. Transcriptomic assessments in this system have revealed important developmental changes associated with the cave morph, however, they have not accounted for photic rearing conditions. Prior studies reared individuals under a 12:12 hr light/dark (LD) cycle. Here, we reared cavefish under constant darkness (DD) for 5+ years. From these experimental individuals, we performed mRNA sequencing and compared gene expression of surface fish reared under LD conditions to cavefish reared under DD conditions to identify photic-dependent gene expression differences. Gene Ontology enrichment analyses revealed a number of previously underappreciated cave-associated changes impacting blood physiology and olfaction. We further evaluated the position of differentially expressed genes relative to QTL positions from prior studies and found several candidate genes associated with these ecologically relevant lighting conditions. In sum, this work highlights photic conditions as a key environmental factor impacting gene expression patterns in blind cave-dwelling fish.

Topological data analysis of zebrafish patterns

Self-organized pattern behavior is ubiquitous throughout nature, from fish schooling to collective cell dynamics during organism development. Qualitatively these patterns display impressive consistency, yet variability inevitably exists within pattern-forming systems on both microscopic and macroscopic scales. Quantifying variability and measuring pattern features can inform the underlying agent interactions and allow for predictive analyses. Nevertheless, current methods for analyzing patterns that arise from collective behavior capture only macroscopic features or rely on either manual inspection or smoothing algorithms that lose the underlying agent-based nature of the data. Here we introduce methods based on topological data analysis and interpretable machine learning for quantifying both agent-level features and global pattern attributes on a large scale. Because the zebrafish is a model organism for skin pattern formation, we focus specifically on analyzing its skin patterns as a means of illustrating our approach. Using a recent agent-based model, we simulate thousands of wild-type and mutant zebrafish patterns and apply our methodology to better understand pattern variability in zebrafish. Our methodology is able to quantify the differential impact of stochasticity in cell interactions on wild-type and mutant patterns, and we use our methods to predict stripe and spot statistics as a function of varying cellular communication. Our work provides an approach to automatically quantifying biological patterns and analyzing agent-based dynamics so that we can now answer critical questions in pattern formation at a much larger scale.