Insertion of a novel transposable element in the tyrosinase gene is responsible for an albino mutation in the medaka fish, Oryzias latipes

Molecular characterization, spatiotemporal expression, and background adaptation regulation of tyrosinase in loach (Misgurnus anguillicaudatus)

The Poyang Lake region is home to large-blackspot loaches (LBL), small-blackspot loaches (SBL), and non-blackspot loaches (NBL), Misgurnus anguillicaudatus. To investigate the impact of tyrosinase on spot development, the complementary DNAs (cDNA) of tyrosinase in M. anguillicaudatus (designated as Matyr) were cloned using the rapid amplification of cDNA ends (RACE)-PCR method. The full-length cDNA for Matyr was 2020 bp, and the open-reading frame comprised 1617 bp, encoding a predicted protein with 538 amino acids. Phylogenetic studies revealed that MaTyr was first grouped with Tyr of Triplophysa tibetana and Leptobotia taeniops, and then Tyr of other cyprinid fish. The quantitative reverse-transcription-PCR results show that Matyr was highly expressed in the muscle, caudal fin, and dorsal skin. The Matyr gene's messenger RNA expression pattern steadily increased from the fertilized ovum period to the somitogenesis period, and from the muscle effect stage to 6 days after fertilization, it considerably increased (p < 0.01). The Matyr hybridization signals with similar location could be found in all developmental stages of three kinds of loaches using whole-mount in situ hybridization (WISH) technology and were the strongest during the organ development period and melanin formation period. Dot hybridization signals in LBLs rapidly spread to the back of the body beginning at the period when the eyes first formed melanin, and their dimensions were larger than those of NBLs during the same time period. The body color of loaches could change reversibly with black/white background adaptation. The α-msh, mitfa, and tyr are mainly expressed in loaches adapted with a black background. Tyr gene could be involved in the development of blackspots and body color polymorphism, and contribute to organ development in the loach.

Differential expression and alternative splicing analyses of multiple tissues reveal albinism-associated genes in the Wels catfish (Silurus glanis)

Albinism is a widespread departure from a typical body colouration due to altered melanin production. The Wels catfish (Silurus glanis) is among the largest freshwater fish species in the world, and albino individuals occur both in the wild and in aquaculture. Here, we performed transcriptome-wide analysis of albino and normally pigmented S. glanis using four tissues (skin, dorsal fin, whole eye and liver) to identify genes associated with albinism by exploring patterns of differential expression (DE) and differential alternative splicing (DAS). Multi-tissue analyses revealed a large number of genes in skin (n = 1355) and fin (n = 614) tissue associated with the albino phenotype in S. glanis, while the number of DE genes in eye and liver tissues was lower (n = 188, n = 189, respectively). Several DE genes across multiple tissues were detected as the most promising candidates (e.g., hsp4, hsp90b1, raph1, uqcrfs1, adcy-family and wnt-family) potentially causally linked to the albino phenotype in Wels catfish. Moreover, our findings supported earlier observations of physiological differences between albino and normally pigmented individuals, particularly in energy metabolism and immune response. In contrast, there were only a few pigmentation-related genes observed among DAS genes (4 in skin, 2 in fin), the overlap between DAS and DE genes was low (n = 25) and did not include known pigmentation-related genes. This suggests that DAS and DE in Wels catfish are, to a large extent, independent processes, and the observed alternative splicing cases are probably not causally linked with albinism in S. glanis. This work provides the first transcriptome-wide multi-tissue insights into the albinism of Wels catfish and serves as a valuable resource for further understanding the genetic mechanisms of pigmentation in fish.

Identification of Candidate Genes for Red-Eyed (Albinism) Domestic Guppies Using Genomic and Transcriptomic Analyses

Guppies are small tropical fish with brightly colored bodies and variable tail shapes. There are two phenotypes of domestic guppy eye color: red and black. The wild type is black-eyed. The main object of this study was to identify candidate genes for the red-eyed phenotype in domestic guppies. We hope to provide molecular genetic information for the development of new domestic guppy strains. Additionally, the results also contribute to basic research concerning guppies. In this study, 121 domestic guppies were used for genomic analysis (GWAS), and 44 genes were identified. Furthermore, 21 domestic guppies were used for transcriptomic analysis, and 874 differentially expressed genes (DEGs) were identified, including 357 upregulated and 517 downregulated genes. Through GO and KEGG enrichment, we identified some important terms or pathways mainly related to melanin biosynthesis and ion transport. qRT-PCR was also performed to verify the differential expression levels of four important candidate genes (TYR, OCA2, SLC45A2, and SLC24A5) between red-eyed and black-eyed guppies. Based on the results of genomic and transcriptomic analyses, we propose that OCA2 is the most important candidate gene for the red-eyed phenotype in guppies.

The influence of transposable elements on animal colouration

Transposable elements (TEs) are mobile genetic sequences present within host genomes. TEs can contribute to the evolution of host traits, since transposition is mutagenic and TEs often contain host regulatory and protein coding sequences. We review cases where TEs influence animal colouration, reporting major patterns and outstanding questions. TE-induced colouration phenotypes typically arise via introduction of novel regulatory sequences and splice sites, affecting pigment cell development or pigment synthesis. We discuss if particular TE types may be more frequently involved in the evolution of colour variation in animals, given that examples involving long terminal repeat (LTR) elements appear to dominate. Currently, examples of TE-induced colouration phenotypes in animals mainly concern model and domesticated insect and mammal species. However, several influential recent examples, coupled with increases in genome sequencing, suggest cases reported from wild species will increase considerably.

Teratorn and its relatives - a cross-point of distinct mobile elements, transposons and viruses

Mobile genetic elements (e.g., transposable elements and plasmids) and viruses display significant diversity with various life cycles, but how this diversity emerges remains obscure. We previously reported a novel and giant (180 kb long) mobile element, Teratorn, originally identified in the genome of medaka, Oryzias latipes. Teratorn is a composite DNA transposon created by a fusion of a piggyBac-like DNA transposon (piggyBac) and a novel herpesvirus of the Alloherpesviridae family. Genomic survey revealed that Teratorn-like herpesviruses are widely distributed among teleost genomes, the majority of which are also fused with piggyBac, suggesting that fusion with piggyBac is a trigger for the life-cycle shift of authentic herpesviruses to an intragenomic parasite. Thus, Teratorn-like herpesvirus provides a clear example of how novel mobile elements emerge, that is to say, the creation of diversity. In this review, we discuss the unique sequence and life-cycle characteristics of Teratorn, followed by the evolutionary process of piggyBac-herpesvirus fusion based on the distribution of Teratorn-like herpesviruses (relatives) among teleosts. Finally, we provide other examples of evolutionary associations between different classes of elements and propose that recombination could be a driving force generating novel mobile elements.

Evolutionarily conserved role of hps1 in melanin production and blood coagulation in medaka fish

Hermansky–Pudlak syndrome is an autosomal recessive disease characterized by albinism, visual impairment, and blood platelet dysfunction. One of the genes responsible for Hermansky–Pudlak syndrome, hps1, regulates organelle biogenesis and thus plays important roles in melanin production, blood clotting, and the other organelle-related functions in humans and mice. However, the function of hps1 in other species remains poorly understood. In this study, we discovered albino medaka fish during the maintenance of a wild-derived population and identified hps1 as the responsible gene using positional cloning. In addition to the specific absence of melanophore pigmentation, the hps1 mutant showed reduced blood coagulation, suggesting that hps1 is involved in clotting caused by both mammalian platelets and fish thrombocytes. Together, the findings of our study demonstrate that hps1 has an evolutionarily conserved role in melanin production and blood coagulation. In addition, our study presents a useful vertebrate model for understanding the molecular mechanisms of Hermansky–Pudlak syndrome.

Transcriptome Analysis Reveals the Complex Regulatory Pathway of Background Color in Juvenile Plectropomus leopardus Skin Color Variation

Fish skin color is often strongly affected by background color. We hypothesized that the regulatory mechanism of variations in skin color in P. leopardus is linked to the background color. In this study, we conducted transcriptome analysis of Plectropomus leopardus cultured under different background colors to compare gene expression levels and the important signaling pathways. The RNA-seq analysis yielded 26,675 known mRNAs, 3278 novel mRNAs, and 3179 differentially expressed genes (DEGs). The DEGs related to melanin synthesis were screened out. Some key melanin-related genes were identified, specifically tyr, slc7a11, mc1r, ednrb, dct, tat, and wnt1. These DEGs were mainly involved in melanogenesis, including tyrosine metabolism, the Wnt signaling pathway, and the cAMP signaling pathway. The expression levels of some key genes were upregulated when background color deepened, such as α-msh, wnt, and gf. The α-MSH/cAMP-dependent, Wnt/β-catenin, and PI3K/Akt signaling pathways were activated, resulting in the accumulation of intracellular mitf. mitf promoted melanin production by binding to the tyr/tyrp1/dct promoter region. In the present study, we explored the molecular mechanism underlying the darkened skin color pattern of P. leopardus, providing a theoretical basis for the molecular mechanism underlying pigmentation in P. leopardus.

Identification of Male-Specific Molecular Markers by Recombination of RhoGEF10 Gene in Spotted Knifejaw (Oplegnathus punctatus)

The spotted knifejaw (Oplegnathus punctatus) is a marine economic fish with high ecological value, food value, and fishing value, and its growth has obvious sex dimorphism. The rapid identification of its sex is beneficial to the development of sex determination and breeding. In this study, the method of comparative genomics and PCR amplification was used to further establish a rapid detection method for the recombinant RhoGEF10 gene in O. punctatus, which can quickly, accurately, and efficiently identify the sex of the O. punctatus to be tested. The homologous comparison results of male and female individuals showed that the DNA fragment length of the RhoGEF10 gene on the X1 chromosome was 326 bp, and the DNA fragment length on the Y chromosome was 879 bp. Therefore, it can be concluded that there is an insert fragment of 553 bp on the Y chromosome. PCR amplification results showed that the two DNA fragments of 879 bp and 326 bp were amplified in the Y chromosome and X1 chromosome of the male O. punctatus (X1X2Y), respectively, and the 879 bp fragment was a unique marker fragment of the recombinant RhoGEF10 gene; The female O. punctatus (X1X1X2X2) only a single DNA fragment of 326 bp was amplified. At the same time, the inserted fragment of the male individual resulted in partial inactivation of the RhoGEF10 protein, which in turn resulted in a slowing of peripheral nerve conduction velocity and thinning of the myelin sheath in male O. punctatus. The method shortens the time for accurate identification of the O. punctatus RhoGEF10 gene recombination and improves the detection efficiency. It is of great significance and application value in the research of nerve conduction and myelin development, male and female sex identification, the preparation of high male seedlings, and family selection based on the RhoGEF10 gene in the O. punctatus.

The crucial role of model systems in understanding the complexity of cell signaling in human neurocristopathies

Animal models are useful to study the molecular, cellular, and morphogenetic mechanisms underlying normal and pathological development. Cell-based study models have emerged as an alternative approach to study many aspects of human embryonic development and disease. The neural crest (NC) is a transient, multipotent, and migratory embryonic cell population that generates a diverse group of cell types that arises during vertebrate development. The abnormal formation or development of the NC results in neurocristopathies (NCPs), which are characterized by a broad spectrum of functional and morphological alterations. The impaired molecular mechanisms that give rise to these multiphenotypic diseases are not entirely clear yet. This fact, added to the high incidence of these disorders in the newborn population, has led to the development of systematic approaches for their understanding. In this article, we have systematically reviewed the ways in which experimentation with different animal and cell model systems has improved our knowledge of NCPs, and how these advances might contribute to the development of better diagnostic and therapeutic tools for the treatment of these pathologies. This article is categorized under: Congenital Diseases > Genetics/Genomics/Epigenetics Congenital Diseases > Stem Cells and Development Congenital Diseases > Molecular and Cellular Physiology Neurological Diseases > Genetics/Genomics/Epigenetics.

Comparative study of stress responses, laterality and familiarity recognition between albino and pigmented fish

Oculocutaneous albinism is the result of a combination of homozygous recessive mutations that block the synthesis of the tyrosine and melatonin hormones. This disability is associated with physiological limitations, e.g., visual impairment expressed by lower visual acuity and movement perception, and eventually leads to acrophobia and/or photophobia, suggesting a potentially higher stress level associated with the behavioral responses of individuals with albinism to external stimuli compared to their pigmented conspecifics. However, in fish, differences in behavioral and/or physiological responses and stress levels between these phenotypes have been poorly documented. While acoustic perception of albino individuals is well known, the use of olfactory sensors for social communication, e.g., for the preference for familiar conspecifics, remains poorly understood. We performed two laboratory experiments with albino and pigmented European catfish Silurus glanis to observe: i) their behavioral and physiological responses to short-term stress induced by a combination of air exposure and novel environmental stressors and ii) their ability to use odor keys to recognize of familiar conspecifics and the influence of lateralization on this preference. In response to stress stimuli, albino fish showed higher movement activities and ventilatory frequencies and more often changed their swimming directions compared to their pigmented conspecifics. Blood plasma analysis showed significantly higher values of stress-, deprivation-, and emotional arousal-associated substances, e.g., glucose and lactate, as well as of substances released during intensive muscle activity of hyperventilation and tissue hypoxia, e.g., hemoglobin, mean corpuscular hemoglobin, erythrocytes, and neutrophil granulocytes. A preference test between environments with and without scented water showed the preference by both albino and pigmented catfish for environments with scent of familiar conspecifics, and both groups of fish displayed left-side lateralization associated with the observation of conspecifics and group coordination. The results tended to show higher physiological and behavioral responses of albinos to stress stimuli compared to the responses of their pigmented conspecifics, but the uses of olfactory sensors and lateralization were not differentiated between the two groups.

The medaka fish Tol2 transposable element is in an early stage of decay: identification of a nonautonomous copy

The majority of DNA-based transposable elements comprise autonomous and nonautonomous copies, or only nonautonomous copies, where the autonomous copy contains an intact gene for a transposase protein and the nonautonomous copy does not. Even if autonomous copies coexist, they are generally less frequent. The Tol2 element of medaka fish is one of the few elements for which a nonautonomous copy has not yet been found. Here we report the presence of a nonautonomous Tol2 copy that was identified by surveying the medaka genome sequence database. This copy contained 3 local sequence alterations that affected the deduced amino acid sequence of the transposase: a deletion of 15 nucleotides resulting in a deletion of 5 amino acids, a base substitution causing a single amino acid change, and another base substitution giving rise to a stop codon. Transposition assays using cultured human cells revealed that the transposase activity was reduced by the 15-nucleotide deletion and abolished by the nonsense mutation. This is the first example of a nonautonomous Tol2 copy. Thus, Tol2 is in an early stage of decay in the medaka genome, and is therefore a unique element to observe an almost whole decay process that progresses in natural populations.

Transcriptome analysis identifies candidate genes associated with skin color variation in Triplophysa siluroides

In vertebrates, skin pigmentation is the most diverse phenotypic trait, and it is produced by a complex biological process that is often genetically controlled. Recently, two different colors (the typical brown and orange varieties) of Triplophysa siluroides, a species restricted to Yellow River drainage in China, were discovered. In the present study, the skin, brain and liver transcriptomes of T. siluroides of both colors were sequenced to search for genes related to skin pigmentation. Transcriptome sequencing generated 1,484,197,774 clean reads, resulting in a total of 222.6 Gb of sequence. The reads were assembled into 470,788 unigenes with a mean length of 1550 bp and an N50 size of 2944 bp. Functional annotation of the unigene dataset showed that 214,507, 304,161, 112,886, 179,074, 180,064, 184,837 and 82,081 unigenes were significantly matched to entries in the Nr protein, Nt, KO, Swiss-Prot, Pfam, GO and KOG databases, respectively. A differential expression analysis revealed that 2774, 3552 and 1529 unigenes were upregulated and 2720, 2663 and 1103 unigenes were downregulated in the skin, brain and liver of orange-skinned T. siluroides, respectively. Several genes that play key roles in pigmentation, i.e., Agouti, Slc45a2, Cbs, Mift and Slc7a11, showed significantly differential expression between brown and orange fish. In addition, we detected 158,863 simple sequence repeats (SSRs) in the T. siluroides transcriptome, and a total of 201,338 single-nucleotide polymorphisms (SNPs) were discovered in the different transcriptomes. The present results will facilitate further study of the molecular mechanisms of skin pigmentation and marker-assisted breeding of fish with valuable skin colors.

Potential adverse effect of tyrosinase inhibitors on teleosts:A review

Coloration plays a crucial role in the social communication and survival of organisms. Multidisciplinary studies have been conducted to elucidate the correlation between coloration and melanin biosynthesis (referred as melanogenesis). The multi-copper enzyme tyrosinase catalyzes the first two steps of melanogenesis for coloration in teleosts. Due to the increasing demand of tyrosinase inhibitors for the production of skin whitening cosmetics, hypopigmentation pharmaceuticals, and anti-browning agents, a large number of natural and synthetic inhibitors have been developed over the past few decades. Although a number of previous studies have focused on human use and toxicity, such as the increased cytotoxic effects of ROS-generating compounds, their ecotoxicological impacts on aquatic organisms are still poorly understood. Hence, the focus of the present review is to describe the role of coloration in teleosts as well as potential ecotoxicological effects elicited by exposure to tyrosinase inhibitors. Furthermore, this review introduces our recently registered adverse outcome pathway (AOP) related to tyrosinase inhibition and population decline in teleosts.

The untapped potential of medaka and its wild relatives

The medaka is a fish that has served as a model organism for over a century, yet there is still much to learn about its life in the wild. Here we summarize the current knowledge, highlight recent progress and outline remaining gaps in our understanding of the natural history of medaka. It has also become clear over time that rather than being a single species, medaka comprises an entire species complex, so disentangling the species boundaries is an important goal for future research. Moreover, medaka and other ricefishes exhibit striking functional diversity, little of which has been investigated to date. As such, there are opportunities to use the resources developed for medaka to study other ricefishes, and to learn more about medaka itself in an evolutionary context.

Five alternative splicing variants of the TYR gene and their different roles in melanogenesis in the Muchuan black-boned chicken

1. The TYR gene encodes tyrosinase, a multifunctional enzyme that is essential for melanin biosynthesis in melanocytes. This experiment involved the cloning and characterisation of the TYR gene in chicken. Five alternative splice variants were identified in the black feather bulb and designated as TYR-AS1, TYR-AS2, TYR-AS3, TYR-AS4 and TYR-AS5. 2. Among the 11 chicken tissues examined, the feather bulb, comb and skin showed higher levels of all TYR variants. All TYR variants were expressed at significantly different levels in black and white feather bulbs (P < 0.05) and may be involved in melanin formation in plumage. Only TYR-AS1, which plays an important role in muscle melanogenesis, was significantly differentially expressed between black and white muscle (P < 0.01). All TYR variants were expressed at significantly different levels in black and white skin (P < 0.01). 3. The mRNA expression levels of the 5 variants were closely associated with skin melanogenesis in the chicken. These findings provide new clues to the molecular mechanism of melanin formation in the Muchuan black-boned chicken.

pnp4a Is the Causal Gene of the Medaka Iridophore Mutant guanineless

See-through medaka lines are suitable for observing internal organs throughout life. They were bred by crossing multiple color mutants. However, some of the causal genes for these mutants have not been identified. The medaka has four pigment cell types: black melanophores, yellow xanthophores, white leucophores, and silvery iridophores. The causal genes of melanophore, xanthophore, and leucophore mutants have been elucidated, but the causal gene for the iridophore mutant remains unknown. Here, we describe the iridophore mutant, guanineless (gu), which exhibits a strong reduction in visible iridophores throughout its larval to adult stages. The gu locus was previously mapped to chromosome 5, but was located near the telomeric region, making it difficult to integrate into the chromosome. We sought the causal gene of gu using synteny analysis with the zebrafish genome and found a strong candidate, purine nucleoside phosphorylase 4a (pnp4a). Gene targeting and complementation testing showed that pnp4a is the causal gene of gu. This result will allow the establishment of inbred medaka strains or other useful strains with see-through phenotypes without major disruption in the genetic background of each strain.

Identification of nuclear localization signal within goldfish Tgf2 transposase

The structure of goldfish (Carassius auratus) Tgf2 transposase is still poorly understood, although it can mediate efficient gene transfer in teleost fish. We hypothesized the existence of a nuclear localization signal (NLS) within Tgf2 transposase to assist transport into the nucleus. To explore this, 15 consecutive amino acid residues (656-670 aa) within the C-terminus of Tgf2 transposase were predicted in silico to be a NLS domain. The pEGFP-C1-Tgf2TP(△31C) plasmid encoding the NLS-domain-deleted Tgf2 transposase fused to EGFP was constructed, and transfected into 293T cells. After transfection with pEGFP-C1-Tgf2TP(△31C), EGFP was not detected in the nucleus alone, while 67.0% of cells expressed EGFP only in the cytoplasm. In contrast, after transfection with control plasmids containing C- or N-terminal truncated Tgf2 transposases with an intact NLS domain, EGFP was not detected in the cytoplasm alone, while approximately 40% of cells expressed EGFP only in the nucleus, and the remaining 60% expressed EGFP in both the nucleus and cytoplasm. Our results demonstrated that loss of the NLS domain results in expression in the cytoplasm but not in the nucleus. These findings suggest that 15 aa residues located from 656 to 670 aa within the C-terminus of Tgf2 transposase can function as a NLS to assist the transfer of the transposase into the nucleus where it mediates DNA transposition.

DNA Transposition at Work

DNA transposons are defined segments of DNA that are able to move from one genomic location to another. Movement is facilitated by one or more proteins, called the transposase, typically encoded by the mobile element itself. Here, we first provide an overview of the classification of such mobile elements in a variety of organisms. From a mechanistic perspective, we have focused on one particular group of DNA transposons that encode a transposase with a DD(E/D) catalytic domain that is topologically similar to RNase H. For these, a number of three-dimensional structures of transpososomes (transposase-nucleic acid complexes) are available, and we use these to describe the basics of their mechanisms. The DD(E/D) group, in addition to being the largest and most common among all DNA transposases, is the one whose members have been used for a wide variety of genomic applications. Therefore, a second focus of the article is to provide a nonexhaustive overview of transposon applications. Although several non-transposon-based approaches to site-directed genome modifications have emerged in the past decade, transposon-based applications are highly relevant when integration specificity is not sought. In fact, for many applications, the almost-perfect randomness and high frequency of integration make transposon-based approaches indispensable.

Disruption of dmc1 Produces Abnormal Sperm in Medaka (Oryzias latipes)

DMC1 is a recombinase that is essential for meiotic synapsis. Experiments in extensive species of eukaryotes have indicated the independent role of DMC1 in repairing double strand breaks (DSBs) produced during meiosis I. Mutation of dmc1 in mice and human often leads to obstacles in spermatogenesis and male sterility. Here, we report on the disruption of dmc1 in male medaka (Oryzias latipes). Synapsis was disturbed in the mutant medaka testis nuclei, as observed in mice and other organisms. Unexpectedly, the mutant medaka could produce a few sperm and, although most of these had multiple tail or multiple head malformations, some of them could swim, and few of them even had insemination ability. Our transcriptome analysis showed that there was not a remarkable change in the expression of most of the genes involved in the pathways associated with the meiotic DNA repair and flagella assembly. Our results provided an indication of the accessory mechanisms that might be involved in the repair of DSBs during meiosis. In a species besides humans, we provided evidence that disorders in meiosis recombination might lead to the malformation of sperm.

Identification and characterization of a LTR retrotransposon from the genome of Cyprinus carpio var. Jian

A Ty3/gypsy-retrotransposon-type transposon was found in the genome of the Jian carp (Cyprinus carpio var. Jian) in a previous study (unpublished), and was designated a JRE retrotransposon (Jian retrotransposon). The full-length JRE retrotransposon is 5126 bp, which includes two long terminal repeats of 470 bp at the 5' end and 453 bp at the 3' end, and two open reading frames between them: 4203 bp encoding the group-specific antigen (GAG) and polyprotein (POL). The pol gene has a typical Ty3/gypsy retrotransposon structure, and the gene order is protease, reverse transcriptase, RNase H, and integrase (PR-RT-RH-IN). A phylogenetic analysis of the pol gene showed that it has similarities of 40.7, 40, and 32.8 %, to retrotransposons of Azumapecten farreri, Mizuhopecten yessoensis, and Xiphophorus maculatus, respectively. Therefore, JRE might belong to the JULE retrotransposon family. The copy number of the JRE transposon in the genome of the Jian carp is 124, determined with real-time quantitative PCR. The mRNA of the JRE retrotransposon is expressed in five Jian carp tissues, the liver, kidney, blood, muscle, and gonad, and slightly higher in the kidney and liver than in the other tissues.

Establishment of Gal4 transgenic zebrafish lines for analysis of development of cerebellar neural circuitry

The cerebellum is involved in some forms of motor coordination and motor learning. Here we isolated transgenic (Tg) zebrafish lines that express a modified version of Gal4-VP16 (GFF) in the cerebellar neural circuits: granule, Purkinje, or eurydendroid cells, Bergmann glia, or the neurons in the inferior olive nuclei (IO) which send climbing fibers to Purkinje cells, with the transposon Tol2 system. By combining GFF lines with Tg lines carrying a reporter gene located downstream of Gal4 binding sequences (upstream activating sequence: UAS), we investigated the anatomy and developmental processes of the cerebellar neural circuitry. Combining an IO-specific Gal4 line with a UAS reporter line expressing the photoconvertible fluorescent protein Kaede demonstrated the contralateral projections of climbing fibers. Combining a granule cell-specific Gal4 line with a UAS reporter line expressing wheat germ agglutinin (WGA) confirmed direct and/or indirect connections of granule cells with Purkinje cells, eurydendroid cells, and IO neurons in zebrafish. Time-lapse analysis of a granule cell-specific Gal4 line revealed initial random movements and ventral migration of granule cell nuclei. Transgenesis of a reporter gene with another transposon Tol1 system visualized neuronal structure at a single cell resolution. Our findings indicate the usefulness of these zebrafish Gal4 Tg lines for studying the development and function of cerebellar neural circuits.

Appearance traits in fish farming: progress from classical genetics to genomics, providing insight into current and potential genetic improvement

Appearance traits in fish, those external body characteristics that influence consumer acceptance at point of sale, have come to the forefront of commercial fish farming, as culture profitability is closely linked to management of these traits. Appearance traits comprise mainly body shape and skin pigmentation. Analysis of the genetic basis of these traits in different fish reveals significant genetic variation within populations, indicating potential for their genetic improvement. Work into ascertaining the minor or major genes underlying appearance traits for commercial fish is emerging, with substantial progress in model fish in terms of identifying genes that control body shape and skin colors. In this review, we describe research progress to date, especially with regard to commercial fish, and discuss genomic findings in model fish in order to better address the genetic basis of the traits. Given that appearance traits are important in commercial fish, the genomic information related to this issue promises to accelerate the selection process in coming years.

Leucophores are similar to xanthophores in their specification and differentiation processes in medaka

Animal body color is generated primarily by neural crest-derived pigment cells in the skin. Mammals and birds have only melanocytes on the surface of their bodies; however, fish have a variety of pigment cell types or chromatophores, including melanophores, xanthophores, and iridophores. The medaka has a unique chromatophore type called the leucophore. The genetic basis of chromatophore diversity remains poorly understood. Here, we report that three loci in medaka, namely, leucophore free (lf), lf-2, and white leucophore (wl), which affect leucophore and xanthophore differentiation, encode solute carrier family 2, member 15b (slc2a15b), paired box gene 7a (pax7a), and solute carrier family 2 facilitated glucose transporter, member 11b (slc2a11b), respectively. Because lf-2, a loss-of-function mutant for pax7a, causes defects in the formation of xanthophore and leucophore precursor cells, pax7a is critical for the development of the chromatophores. This genetic evidence implies that leucophores are similar to xanthophores, although it was previously thought that leucophores were related to iridophores, as these chromatophores have purine-dependent light reflection. Our identification of slc2a15b and slc2a11b as genes critical for the differentiation of leucophores and xanthophores in medaka led to a further finding that the existence of these two genes in the genome coincides with the presence of xanthophores in nonmammalian vertebrates: birds have yellow-pigmented irises with xanthophore-like intracellular organelles. Our findings provide clues for revealing diverse evolutionary mechanisms of pigment cell formation in animals.

Spontaneous germline excision of Tol1, a DNA-based transposable element naturally occurring in the medaka fish genome

DNA-based transposable elements are ubiquitous constituents of eukaryotic genomes. Vertebrates are, however, exceptional in that most of their DNA-based elements appear to be inactivated. The Tol1 element of the medaka fish, Oryzias latipes, is one of the few elements for which copies containing an undamaged gene have been found. Spontaneous transposition of this element in somatic cells has previously been demonstrated, but there is only indirect evidence for its germline transposition. Here, we show direct evidence of spontaneous excision in the germline. Tyrosinase is the key enzyme in melanin biosynthesis. In an albino laboratory strain of medaka fish, which is homozygous for a mutant tyrosinase gene in which a Tol1 copy is inserted, we identified de novo reversion mutations related to melanin pigmentation. The gamete-based reversion rate was as high as 0.4%. The revertant fish carried the tyrosinase gene from which the Tol1 copy had been excised. We previously reported the germline transposition of Tol2, another DNA-based element that is thought to be a recent invader of the medaka fish genome. Tol1 is an ancient resident of the genome. Our results indicate that even an old element can contribute to genetic variation in the host genome as a natural mutator.

Efficient RNA/Cas9-mediated genome editing in Xenopus tropicalis

For the emerging amphibian genetic model Xenopus tropicalis targeted gene disruption is dependent on zinc-finger nucleases (ZFNs) or transcription activator-like effector nucleases (TALENs), which require either complex design and selection or laborious construction. Thus, easy and efficient genome editing tools are still highly desirable for this species. Here, we report that RNA-guided Cas9 nuclease resulted in precise targeted gene disruption in all ten X. tropicalis genes that we analyzed, with efficiencies above 45% and readily up to 100%. Systematic point mutation analyses in two loci revealed that perfect matches between the spacer and the protospacer sequences proximal to the protospacer adjacent motif (PAM) were essential for Cas9 to cleave the target sites in the X. tropicalis genome. Further study showed that the Cas9 system could serve as an efficient tool for multiplexed genome engineering in Xenopus embryos. Analysis of the disruption of two genes, ptf1a/p48 and tyrosinase, indicated that Cas9-mediated gene targeting can facilitate direct phenotypic assessment in X. tropicalis embryos. Finally, five founder frogs from targeting of either elastase-T1, elastase-T2 or tyrosinase showed highly efficient transmission of targeted mutations into F1 embryos. Together, our data demonstrate that the Cas9 system is an easy, efficient and reliable tool for multiplex genome editing in X. tropicalis.

Molecular and developmental contributions to divergent pigment patterns in marine and freshwater sticklebacks

Pigment pattern variation across species or populations offers a tractable framework in which to investigate the evolution of development. Juvenile threespine sticklebacks (Gasterosteus aculeatus) from marine and freshwater environments exhibit divergent pigment patterns that are associated with ecological differences. Juvenile marine sticklebacks have a silvery appearance, whereas sticklebacks from freshwater environments exhibit a pattern of vertical bars. We investigated both the developmental and molecular basis of this population-level variation in pigment pattern. Time course imaging during the transition from larval to juvenile stages revealed differences between marine and freshwater fish in spatial patterns of chromatophore differentiation as well as in pigment amount and dispersal. In freshwater fish, melanophores appear primarily within dark bars whereas iridophores appear within light bars. By contrast, in marine fish, these chromatophores are interspersed across the flank. In addition to spatially segregated chromatophore differentiation, pigment amount and dispersal within melanophores varies spatially across the flank of freshwater, but not marine fish. To gain insight into the molecular pathways that underlie the differences in pigment pattern development, we evaluated differential gene expression in the flanks of developing fish using high-throughput cDNA sequencing (RNA-seq) and quantitative PCR. We identified several genes that were differentially expressed across dark and light bars of freshwater fish, and between freshwater and marine fish. Together, these experiments begin to shed light on the process of pigment pattern evolution in sticklebacks.

Highly efficient bi-allelic mutation rates using TALENs in Xenopus tropicalis

In the past decade, Xenopus tropicalis has emerged as a powerful new amphibian genetic model system, which offers all of the experimental advantages of its larger cousin, Xenopus laevis. Here we investigated the efficiency of transcription activator-like effector nucleases (TALENs) for generating targeted mutations in endogenous genes in X. tropicalis. For our analysis we targeted the tyrosinase (oculocutaneous albinism IA) (tyr) gene, which is required for the production of skin pigments, such as melanin. We injected mRNA encoding TALENs targeting the first exon of the tyr gene into two-cell-stage embryos. Surprisingly, we found that over 90% of the founder animals developed either partial or full albinism, suggesting that the TALENs induced bi-allelic mutations in the tyr gene at very high frequency in the F0 animals. Furthermore, mutations tyr gene were efficiently transmitted into the F1 progeny, as evidenced by the generation of albino offspring. These findings have far reaching implications in our quest to develop efficient reverse genetic approaches in this emerging amphibian model.

Identification of a transparent mutant tiger barb Puntius tetrazona and its use for in vivo observation of a Pleistophora sp. (Microsporidia) infection

A transparent mutant tiger barb Puntius tetrazona was identified and characterized by its transparent body, which allows clear visualization of internal organs. Hybridization of this mutant with the albino variant produces a transparent and albinoid double phenotype, and the transparency of this mutant is controlled by a recessive allele. Light microscopic and ultrastructural examinations show that in contrast to normal individuals, transparent mutants lack iridophores, and light penetrates unimpeded through the body. Pleistophora sp. infection was observed in vivo, allowing live observation of parasite dissemination and the consequent pathological alterations in the fish body as well as the simultaneous acquisition of data on the dynamics and spatial pattern of pathogenic invasion. It is superior to common fish models, as dynamic experimental data can be obtained from individual fish.

Retargeting transposon insertions by the adeno-associated virus Rep protein

The Sleeping Beauty (SB), piggyBac (PB) and Tol2 transposons are promising instruments for genome engineering. Integration site profiling of SB, PB and Tol2 in human cells showed that PB and Tol2 insertions were enriched in genes, whereas SB insertions were randomly distributed. We aimed to introduce a bias into the target site selection properties of the transposon systems by taking advantage of the locus-specific integration system of adeno-associated virus (AAV). The AAV Rep protein binds to Rep recognition sequences (RRSs) in the human genome, and mediates viral integration into nearby sites. A series of fusion constructs consisting of the N-terminal DNA-binding domain of Rep and the transposases or the N57 domain of SB were generated. A plasmid-based transposition assay showed that Rep/SB yielded a 15-fold enrichment of transposition at a particular site near a targeted RRS. Genome-wide insertion site analysis indicated that an approach based on interactions between the SB transposase and Rep/N57 enriched transgene insertions at RRSs. We also provide evidence of biased insertion of the PB and Tol2 transposons. This study provides a comparative insight into target site selection properties of transposons, as well as proof-of-principle for targeted chromosomal transposition by composite protein–protein and protein–DNA interactions.

The genetic basis of divergent pigment patterns in juvenile threespine sticklebacks

Animal pigment patterns are important for a range of functions, including camouflage and communication. Repeating pigment patterns, such as stripes, bars and spots have been of particular interest to developmental and theoretical biologists, but the genetic basis of natural variation in such patterns is largely unexplored. In this study, we identify a difference in a periodic pigment pattern among juvenile threespine sticklebacks (Gasterosteus aculeatus) from different environments. Freshwater sticklebacks exhibit prominent vertical bars that visually break up the body shape, but sticklebacks from marine populations do not. We hypothesize that these distinct pigment patterns are tuned to provide crypsis in different habitats. This phenotypic difference is widespread and appears in most of the freshwater populations that we sampled. We used quantitative trait locus (QTL) mapping in freshwater-marine F2 hybrids to elucidate the genetic architecture underlying divergence in this pigmentation pattern. We identified two QTL that were significantly associated with variation in barring. Interestingly, these QTL were associated with two distinct aspects of the pigment pattern: melanophore number and overall pigment level. We compared the QTL locations with positions of known pigment candidate genes in the stickleback genome. We also identified two major QTL for juvenile body size, providing new insights into the genetic basis of juvenile growth rates in natural populations. In summary, although there is a growing literature describing simple genetic bases for adaptive coloration differences, this study emphasizes that pigment patterns can also possess a more complex genetic architecture.

The art of medaka genetics and genomics: what makes them so unique?

The medaka fish, Oryzias latipes, is an emerging vertebrate model and now has a high quality draft genome and a number of unique mutants. The long history of medaka research in Japan has provided medaka with unique features, which are complementary to other vertebrate models. A large collection of spontaneous mutants collected over a century, the presence of highly polymorphic inbred lines established over decades, and the recently completed genome sequence all give the medaka a big boost. This review focuses on the state of the art in medaka genetics and genomics, such as the first isolation of active transposons in vertebrates, the influence of chromatin structure on sequence variation, fine quantitative trait locus (QTL) analysis, and versatile mutants as human disease models.

Essential techniques for introducing medaka to a zebrafish laboratory--towards the combined use of medaka and zebrafish for further genetic dissection of the function of the vertebrate genome

The medaka, Oryzias latipes, a small egg-laying freshwater fish, is one of the three vertebrate model organisms in which genome-wide phenotype-driven mutant screens have been carried out. Despite a number of large-scale screens in zebrafish, a substantial number of mutants with new distinct phenotypes were identified in similar large-scale screens in the medaka. This observed difference in phenotype is due to the two species having a unique combination of genetic, biological and evolutional properties. The two genetic models share a whole-genome duplication event over that of tetrapods; however, each has independently specialized or lost the function of one of the two paralogues. The two fish species complement each other as genetic systems as straightforward comparison of phenotypes, ease of side-by-side analysis using the same techniques and simple and inexpensive husbandry of mutants make these small teleosts quite powerful in combination. Furthermore, both have draft genome sequences and bioinformatic tools available that facilitate further genetic dissection including whole-genome approaches. Together with the gene-driven approach to generate gene knockout mutants of the fish models, the two fish models complement the mouse in genetically dissecting vertebrate genome functions. The external embryogenesis and transparent embryos of the fish allow systematic isolation of embryonic lethal mutations, the most difficult targets in mammalian mutant screens. This chapter will describe how to work with both medaka and zebrafish almost as one species in a lab, focusing on medaka and highlighting the differences between the medaka and zebrafish systems.

Occurrence of a short variant of the Tol2 transposable element in natural populations of the medaka fish

Tol2 is a member of the hAT (hobo/Activator/Tam3) transposable element family, residing as 10-30 copies per diploid genome in the medaka fish. We previously reported that this element is highly homogeneous in structure at both the restriction map level and the nucleotide sequence level. It was, however, possible that there is variation of such a low frequency as not to have been detected in our previous surveys, in which samples from 12 geographical locations were used. In the present study, we first conducted searches of genome sequence databases of medaka, and found a 119-bp-long internal deletion. We then conducted a survey of samples from 58 locations for this deletion by performing PCR preceded by restriction enzyme digestion to increase the sensitivity to this deletion. We found that copies suffering this deletion have spread, or have been generated by multiple origins, in the northern-to-central part of mainland Japan. Thus, although the high homogeneity in structure is a distinct feature of Tol2, variation does exist at low frequencies in natural populations of medaka. The current status of Tol2 is expected to provide information with which results of future surveys can be compared for clarification of determinants of population dynamics of this DNA-based element.

Gene transfer efficiency and genome-wide integration profiling of Sleeping Beauty, Tol2, and piggyBac transposons in human primary T cells

In this study, we compared the genomic integration efficiencies and transposition site preferences of Sleeping Beauty (SB or SB11), Tol2, and piggyBac (PB) transposon systems in primary T cells derived from peripheral blood lymphocytes (PBL) and umbilical cord blood (UCB). We found that PB demonstrated the highest efficiency of stable gene transfer in PBL-derived T cells, whereas SB11 and Tol2 mediated intermediate and lowest efficiencies, respectively. Southern hybridization analysis demonstrated that PB generated the highest number of integrants when compared to SB and Tol2 in both PBL and UCB T cells. Tol2 and PB appeared more likely to promote clonal expansion than SB, which may be in part due to the dysregulated expression of cancer-related genes near the insertion sites. Genome-wide integration analysis demonstrated that SB, Tol2, and PB integrations occurred in all the chromosomes without preference. Additionally, Tol2 and PB integration sites were mainly localized near transcriptional start sites (TSSs), CpG islands and DNaseI hypersensitive sites, whereas SB integrations were randomly distributed. These results suggest that SB may be a preferential choice of the delivery vector in T cells due to its random integration site preference and relatively high efficiency, and support continuing development of SB-mediated T-cell phase I trials.

Accessibility of host cell lineages to medaka stem cells depends on genetic background and irradiation of recipient embryos

Chimera formation is a powerful tool for analyzing pluripotency in vivo. It has been widely accepted that host cell lineages are generally accessible to embryonic stem (ES) cells with the actual contribution depending solely on the intrinsic pluripotency of transplanted donor cells. Here, we show in the fish medaka (Oryzias latipes) that the host accessibility to ES cell contribution exhibits dramatic differences. Specifically, of three albino host strains tested (i (1) , i (3) and af), only strain i (1) generated pigmented chimeras. Strikingly, this accessibility is completely lost in i (1) but acquired in i (3) after host gamma-irradiation. Host irradiation also differentially affected ES cell contribution to somatic organs and gonad. Therefore, the accessibility of various host cell lineages can vary considerably depending on host strains and cell lineages as well as on irradiation. Our findings underscore the importance of host genotypes for interpreting donor cell pluripotency and for improving ES-derived chimera production.

Distribution of complete and defective copies of the Tol1 transposable element in natural populations of the medaka fish Oryzias latipes

DNA-based transposable elements are present in the genomes of various organisms, and generally occur in autonomous and nonautonomous forms, with a good correspondence to complete and defective copies, respectively. In vertebrates, however, the vast majority of DNA-based elements occur only in the nonautonomous form. Until now, the only clear exception known has been the Tol2 element of the medaka fish, which still causes mutations in genes of the host species. Here, we report another exception: the Tol1 element of the same species. This element was thought likely to be a "dead" element like the vast majority of vertebrate elements, but recent identification of an autonomous Tol1 copy in a laboratory medaka strain gave rise to the possibility that the element is still "alive" in medaka natural populations. We examined variation in the structure of Tol1 copies through genomic Southern blot analysis, and revealed that 10 of the 32 fish samples examined contained full-length Tol1 copies in their genomes. The frequency at which these copies occur among Tol1 copies is at most 0.5%, yet some of them still have the ability to produce a functional transposase. The medaka fish thus harbors two active DNA-based elements in its genome, and is in this respect unique among vertebrates.

Pigmentary function and evolution of tyrp1 gene duplicates in fish

The function of the tyrosinase-related protein 1 (Tyrp1) has not yet been investigated in vertebrates basal to tetrapods. Teleost fishes have two duplicates of the tyrp1 gene. Here, we show that the teleost tyrp1 duplicates have distributed the ancestral gene expression in the retinal pigment epithelium (RPE) and melanophores in a species-specific manner. In medaka embryos, tyrp1a expression is found in the RPE and in melanophores while tyrp1b is only expressed in melanophores. In zebrafish embryos, expression of tyrp1 paralogs overlaps in the RPE and in melanophores. Knockdown of each zebrafish tyrp1 duplicate alone does not show pigmentary defects, but simultaneous knockdown of both tyrp1 genes results in the formation of brown instead of black eumelanin accompanied by severe melanosome defects. Our study suggests that the brown melanosome color in Tyrp1-deficient vertebrates is an effect of altered eumelanin synthesis. Black eumelanin formation essentially relies on the presence of Tyrp1 and some of its function is most likely conserved from the common ancestor of bony vertebrates.

Natural variation of male ornamental traits of the guppy, Poecilia reticulata

Male ornamental traits of the guppy, Poecilia reticulata, provide an outstanding example of natural variation in sex-linked male-advantageous traits that are shaped by both sexual and environmental selection. A substantial fraction of the underlying genes is known to be genetically linked to the sex-determining region on the differentiating Y-chromosome. Intercrosses between parental populations originating from geographically distant locations in East Trinidad and Cumaná (Venezuela) were used to study segregation of ornamental traits in male progeny. In addition, we performed backcrosses to compare segregation of ornaments in presence or absence of prominent traits linked to the Y-chromosome. Another backcross strategy involving XY females from the laboratory strain zebrinus maculatus allowed studying additive and dominant effects of alleles on two different Y-chromosomes on pattern formation. For genetic mapping, we have previously developed nuclear SNP markers linked to expressed genes, including several genes known to be important for pattern formation in other species. Of these candidate genes 15 were placed on 11 different linkage groups. Our phenotypic and genotypic analysis of progeny from mapping crosses and backcrosses suggests several genetic mechanisms that enhance natural variation, namely, additive effects of codominant alleles, suppressive actions of dominant alleles, and a complex interplay between sex-linked and autosomal cofactors.

Transposon tools hopping in vertebrates

In the past decade, tools derived from DNA transposons have made major contributions to vertebrate genetic studies from gene delivery to gene discovery. Multiple, highly complementary systems have been developed, and many more are in the pipeline. Judging which DNA transposon element will work the best in diverse uses from zebrafish genetic manipulation to human gene therapy is currently a complex task. We have summarized the major transposon vector systems active in vertebrates, comparing and contrasting known critical biochemical and in vivo properties, for future tool design and new genetic applications.

Germline transgenesis of zebrafish using the medaka Tol1 transposon system

Tol1 is a DNA-based transposable element first identified from an albino mutant medaka fish. It has been demonstrated to function as an efficient gene transfer vector in mammalian cells. We now demonstrate Tol1 germline transgenesis in zebrafish. A construct containing the green fluorescence protein (GFP) reporter gene inserted between the Tol1 arms was microinjected together with Tol1 transposase mRNA into fertilized eggs. Sustained GFP expression was observed in 88% of 1-month-old fish, suggesting efficient transposon integration into somatic cells. Eleven of 24 adult GFP-positive fish yielded GFP-positive progeny. Sequencing analysis of Tol1 insertion sites in GFP-positive progeny confirmed Tol1 transposition-mediated integrations into zebrafish chromosomes. We also observed functional independence of the Tol1 transposase-substrate system from that of Tol2, another medaka-derived transposon. Coupled with its previously demonstrated maximal cargo capacity of >20 kb, Tol1 could serve as a useful addition to the zebrafish genetic engineering toolbox.

The Tol1 element of the medaka fish, a member of the hAT transposable element family, jumps in Caenorhabditis elegans

Tol1 is a DNA-based transposable element residing in the genome of the medaka fish Oryzias latipes, and has been proven to be transposed in various vertebrate species, including mammals. This element belongs to the hAT (hobo/Activator/Tam3) transposable element family, whose members are distributed in a wide range of organisms. It is thus possible that Tol1 is mobile in organisms other than vertebrates. We here show that transposition of this element occurs in the nematode Caenorhabditis elegans. A donor plasmid containing a Tol1 element and a helper plasmid carrying the transposase gene were delivered into gonad cells and, after several generations of culturing, were recovered from worms. PCR analysis of the donor plasmid, using primers that encompassed the Tol1 element, revealed excision of the Tol1 portion from the plasmid. Analysis of genomic DNA of the worms by the inverse PCR method provided evidence that Tol1 had been integrated into the C. elegans chromosomes. Vertebrates and C. elegans are phylogenetically distantly related organisms in that the former are deuterostomes and the latter a protostome animal. Our results indicate (1) the transposition reaction of the Tol1 element requires, besides the transposase, no factors from host cells, or (2) the host factors, even if required, are those that are common to protostomes and deuterostomes. The results also have significance for the development of a gene transfer vector and other biotechnology tools for C. elegans.