Xiphophorus maculatus

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Ronald B. Walter - One of the best experts on this subject based on the ideXlab platform.

  • intra strain genetic variation of platyfish Xiphophorus maculatus strains determines tumorigenic trajectory
    Frontiers in Genetics, 2020
    Co-Authors: Manfred Schartl, Mikki Boswell, William T Boswell, Taryn J Olivas, Wes Warren, Ronald B. Walter
    Abstract:

    Xiphophorus interspecies hybrids represent a valuable model system to study heritable tumorigenesis, and the only model system that exhibits both spontaneous and inducible tumors. Types of tumorigenesis depend on the specific pedigree of the parental species, X. maculatus, utilized to produce interspecies hybrids. Although the ancestors of the two currently used X. maculatus parental lines, Jp163 A and Jp163 B, were originally siblings produced by the same mother, backcross interspecies hybrid progeny between X. hellerii and X. maculatus Jp163 A develop spontaneous melanoma initiating at the dorsal fin due to segregation of an oncogene and a regulator encoded by the X. maculatus genome, while the backcross hybrid progeny with X. hellerii or X. couchianus and Jp163 B exhibit melanoma on the flanks of their bodies, especially after treatment with ultraviolet light. Therefore, dissecting the genetic differences between these two closely related lines may lead to better understanding of functional molecular differences associated with tumorigenic mechanisms. For this purpose, comparative genomic analyses were undertaken to establish genetic variants between these two X. maculatus lines. Surprisingly, given the heritage of these two fish lines, we found genetic variants are clustered together in select chromosomal regions. Among these variants are non-synonymous mutations located in 381 genes. The non-random distribution of genetic variants between these two may highlight ancestral chromosomal recombination patterns that became fixed during subsequent inbreeding. Employing comparative transcriptomics, we also determined differences in the skin transcriptional landscape between the two lines. The genetic differences observed are associated with pathways highlighting fundamental cellular functions including inter-cellular and microenvironment-cellular interactions, and DNA repair. These results collectively lead to the conclusion that diverged functional genetic baselines are present between Jp163 A and B strains. Further, disruption of these fixed genetic baselines in the hybrids may give rise to spontaneous or inducible mechanisms of tumorigenesis.

  • exposure to 4100k fluorescent light elicits sex specific transcriptional responses in Xiphophorus maculatus skin
    Comparative Biochemistry and Physiology C-toxicology & Pharmacology, 2018
    Co-Authors: William T Boswell, Mikki Boswell, Markita G Savage, Dylan J Walter, Kaela Navarro, Jordan Chang, Jianjun Shen, Ronald B. Walter
    Abstract:

    It has been reported that exposure to artificial light may affect oxygen intake, heart rate, absorption of vitamins and minerals, and behavioral responses in humans. We have reported specific gene expression responses in the skin of Xiphophorus fish after exposure to ultraviolet light (UV), as well as, both broad spectrum and narrow waveband visible light. In regard to fluorescent light (FL), we have shown that male X. maculatus exposed to 4100K FL (i.e. "cool white") rapidly suppress transcription of many genes involved with DNA replication and repair, chromosomal segregation, and cell cycle progression in skin. We have also detailed sex specific transcriptional responses of Xiphophorus skin after exposure to UVB. However, investigation of gender differences in global gene expression response after exposure to 4100K FL has not been reported, despite common use of this FL source for residential, commercial, and animal facility illumination. Here, we compare RNA-Seq results analyzed to assess changes in the global transcription profiles of female and male X. maculatus skin in response to 4100K FL exposure. Our results suggest 4100K FL exposure incites a sex-biased genetic response including up-modulation of inflammation in females and down modulation of DNA repair/replication in males. In addition, we identify clusters of genes that become oppositely modulated in males and females after FL exposure that are principally involved in cell death and cell proliferation.

  • Waveband specific transcriptional control of select genetic pathways in vertebrate skin (Xiphophorus maculatus)
    BMC Genomics, 2018
    Co-Authors: Ronald B. Walter, Mikki Boswell, William T Boswell, Dylan J Walter, Kaela Navarro, Jordan Chang, Sean M. Walter, Raquel Salinas, Markita Savage
    Abstract:

    Background Evolution occurred exclusively under the full spectrum of sunlight. Conscription of narrow regions of the solar spectrum by specific photoreceptors suggests a common strategy for regulation of genetic pathways. Fluorescent light (FL) does not possess the complexity of the solar spectrum and has only been in service for about 60 years. If vertebrates evolved specific genetic responses regulated by light wavelengths representing the entire solar spectrum, there may be genetic consequences to reducing the spectral complexity of light. Results We utilized RNA-Seq to assess changes in the transcriptional profiles of Xiphophorus maculatus skin after exposure to FL (“cool white”), or narrow wavelength regions of light between 350 and 600 nm (i.e., 50 nm or 10 nm regions, herein termed “wavebands”). Exposure to each 50 nm waveband identified sets of genes representing discrete pathways that showed waveband specific transcriptional modulation. For example, 350–400 or 450–500 nm waveband exposures resulted in opposite regulation of gene sets marking necrosis and apoptosis (i.e., 350–400 nm; necrosis suppression, apoptosis activation, while 450–500 nm; apoptosis suppression, necrosis activation). Further investigation of specific transcriptional modulation employing successive 10 nm waveband exposures between 500 and 550 nm showed; (a) greater numbers of genes may be transcriptionally modulated after 10 nm exposures, than observed for 50 nm or FL exposures, (b) the 10 nm wavebands induced gene sets showing greater functional specificity than 50 nm or FL exposures, and (c) the genetic effects of FL are primarily due to 30 nm between 500 and 530 nm. Interestingly, many genetic pathways exhibited completely opposite transcriptional effects after different waveband exposures. For example, the epidermal growth factor ( EGF ) pathway exhibits transcriptional suppression after FL exposure, becomes highly active after 450–500 nm waveband exposure, and again, exhibits strong transcriptional suppression after exposure to the 520–530 nm waveband. Conclusions Collectively, these results suggest one may manipulate transcription of specific genetic pathways in skin by exposure of the intact animal to specific wavebands of light. In addition, we identify genes transcriptionally modulated in a predictable manner by specific waveband exposures. Such genes, and their regulatory elements, may represent valuable tools for genetic engineering and gene therapy protocols.

  • the transcriptional response of skin to fluorescent light exposure in viviparous Xiphophorus and oviparous danio oryzias fishes
    Comparative Biochemistry and Physiology C-toxicology & Pharmacology, 2017
    Co-Authors: Mikki Boswell, William T Boswell, Markita G Savage, Jordan Chang, Zachary Mazurek, Jeanot Muster, Ronald B. Walter
    Abstract:

    Differences in light sources are common in animal facilities and potentially can impact experimental results. Here, the potential impact of lighting differences on skin transcriptomes has been tested in three aquatic animal models commonly utilized in biomedical research, (Xiphophorus maculatus (platyfish), Oryzias latipes (medaka) and Danio rerio (zebrafish). Analysis of replicate comparative RNA-Seq data showed the transcriptional response to commonly utilized 4100K or "cool white" fluorescent light (FL) is much greater in platyfish and medaka than in zebrafish. FL induces genes associated with inflammatory and immune responses in both medaka and zebrafish; however, the platyfish exhibit suppression of genes involved with immune/inflammation, as well as genes associated with cell cycle progression. Furthermore, comparative analyses of gene expression data from platyfish UVB exposures, with medaka and zebrafish after exposure to 4100K FL, show comparable effects on the same stress pathways. We suggest the response to light is conserved, but that long-term adaptation to species specific environmental niches has resulted in a shifting of the wavelengths required to incite similar "genetic" responses in skin. We forward the hypothesis that the "genetic perception" of light may have evolved differently than ocular perception and suggest that light type (i.e., wavelengths emitted) is an important parameter to consider in experimental design.

  • Transcriptome analysis of female and male Xiphophorus maculatus Jp 163
    2016
    Co-Authors: Ziping Zhang, Yilei Wang, Shuhong Wang, Makedonka Mitreva, Jingtao Liu, Wesley Warren, Ronald B. Walter
    Abstract:

    Background: Xiphophorus models are important for melanoma, sex determination and differentiation, ovoviviparity and evolution. To gain a global view of the molecular mechanism(s) whereby gene expression may influence sexual dimorphism in Xiphophorus and to develop a database for future studies, we performed a large-scale transcriptome study. Methodology/Principal Findings: The 454-FLX massively parallel DNA sequencing platform was employed to obtain 742,771 and 721,543 reads from 2 normalized cDNA libraries generated from whole adult female and male X. maculatus Jp 163 A, respectively. The reads assembled into 45,538 contigs (here, a "contig " is a set of contiguous sequences), of which, 11,918 shared homology to existing protein sequences. These numbers estimate that the contigs may cover 53 % of the total number of Xiphophorus transcriptome. Putative translations were obtained for 11,918 cDNA contigs, of which, 3,049 amino acid sequences contain Pfam domains and 11,064 contigs encode secretory proteins. A total of 3,898 contigs were associated with 2,781 InterPro (IPR) entries and 5,411 contigs with 132 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. There were 10,446 contigs annotated with 69,778 gene ontology (GO) terms and the three corresponding organizing principles. Fifty-four potential sex differentially expressed genes have been identified from these contigs. Eight and nine of these contigs were confirmed by real-time PCR as female and male predominantly expressed genes respectively. Based on annotation results, 34 contigs were predicted to be differentially expressed in male and female and 17 of the

Manfred Schartl - One of the best experts on this subject based on the ideXlab platform.

  • intra strain genetic variation of platyfish Xiphophorus maculatus strains determines tumorigenic trajectory
    Frontiers in Genetics, 2020
    Co-Authors: Manfred Schartl, Mikki Boswell, William T Boswell, Taryn J Olivas, Wes Warren, Ronald B. Walter
    Abstract:

    Xiphophorus interspecies hybrids represent a valuable model system to study heritable tumorigenesis, and the only model system that exhibits both spontaneous and inducible tumors. Types of tumorigenesis depend on the specific pedigree of the parental species, X. maculatus, utilized to produce interspecies hybrids. Although the ancestors of the two currently used X. maculatus parental lines, Jp163 A and Jp163 B, were originally siblings produced by the same mother, backcross interspecies hybrid progeny between X. hellerii and X. maculatus Jp163 A develop spontaneous melanoma initiating at the dorsal fin due to segregation of an oncogene and a regulator encoded by the X. maculatus genome, while the backcross hybrid progeny with X. hellerii or X. couchianus and Jp163 B exhibit melanoma on the flanks of their bodies, especially after treatment with ultraviolet light. Therefore, dissecting the genetic differences between these two closely related lines may lead to better understanding of functional molecular differences associated with tumorigenic mechanisms. For this purpose, comparative genomic analyses were undertaken to establish genetic variants between these two X. maculatus lines. Surprisingly, given the heritage of these two fish lines, we found genetic variants are clustered together in select chromosomal regions. Among these variants are non-synonymous mutations located in 381 genes. The non-random distribution of genetic variants between these two may highlight ancestral chromosomal recombination patterns that became fixed during subsequent inbreeding. Employing comparative transcriptomics, we also determined differences in the skin transcriptional landscape between the two lines. The genetic differences observed are associated with pathways highlighting fundamental cellular functions including inter-cellular and microenvironment-cellular interactions, and DNA repair. These results collectively lead to the conclusion that diverged functional genetic baselines are present between Jp163 A and B strains. Further, disruption of these fixed genetic baselines in the hybrids may give rise to spontaneous or inducible mechanisms of tumorigenesis.

  • molecular genetic response of Xiphophorus maculatus x couchianus interspecies hybrid skin to uvb exposure
    Comparative Biochemistry and Physiology C-toxicology & Pharmacology, 2015
    Co-Authors: Mikki Bowswell, Manfred Schartl, William Bowswell, Kuan Yang, Ronald B. Walter
    Abstract:

    The phenotypic and genetic similarities between Xiphophorus and human melanoma render Xiphophorus a useful animal model for studying the genetic basis of melanoma etiology. In the Xiphophorus model, melanoma has been shown to be inducible by ultraviolet light (UVB) exposure among interspecies hybrids, but not in parental line fish similarly treated. This leads to questions of what genes are responsive to UVB exposure in the skin of the interspecies hybrids, as well as how parental alleles in hybrids may be differentially regulated and the potential roles they may play in induced melanomagenesis. To address these questions, we produced X. maculatus Jp 163 B×X. couchianus (Sp-Couch) F1 hybrid fish, exposed both hybrid and parental fish to UVB, and performed gene expression profiling of the skin using RNA-Seq methodology. We characterized a group of unique UVB-responsive genes in Sp-Couch hybrid including dct, pmela, tyr, tyrp1a, slc2a11b, rab38a, rab27, tspan10, slc45a2, oca2, slc24a5, ptn and mitfa. These genes are associated with melanin production and melanocyte proliferation. They were also up-regulated in Sp-Couch hybrid, indicating that their UVB response is hybridization initiated. In the hybrid, several melanin production and pigmentation related genes, including slc45a2, tspan10, dct, slc2a11b and ptn showed either X. couchianus or X. maculatus allele specific expression. The finding that these genes exhibit allele specific expression regulatory mechanisms in Sp-Couch hybrids, but do not exhibit a corresponding UVB response in either one of the parental fishes, may suggest UVB targets and imply mechanisms regarding the susceptibility of Sp-Couch to induced melanomagenesis.

  • a transcriptome derived female specific marker from the invasive western mosquitofish gambusia affinis
    PLOS ONE, 2015
    Co-Authors: Dunja K Lamatsch, Manfred Schartl, Sofia Adolfsson, Alistair M, Guntram Christiansen, Maria Pichler, Yuichi Ozaki, Linnea Smeds, Shinichi Nakagawa
    Abstract:

    Sex-specific markers are a prerequisite for understanding reproductive biology, genetic factors involved in sex differences, mechanisms of sex determination, and ultimately the evolution of sex chromosomes. The Western mosquitofish, Gambusia affinis, may be considered a model species for sex-chromosome evolution, as it displays female heterogamety (ZW/ZZ), and is also ecologically interesting as a worldwide invasive species. Here, de novo RNA-sequencing on the gonads of sexually mature G. affinis was used to identify contigs that were highly transcribed in females but not in males (i.e., transcripts with ovary-specific expression). Subsequently, 129 primer pairs spanning 79 contigs were tested by PCR to identify sex-specific transcripts. Of those primer pairs, one female-specific DNA marker was identified, Sanger sequenced and subsequently validated in 115 fish. Sequence analyses revealed a high similarity between the identified sex-specific marker and the 3´ UTR of the aminomethyl transferase (amt) gene of the closely related platyfish (Xiphophorus maculatus). This is the first time that RNA-seq has been used to successfully characterize a sex-specific marker in a fish species in the absence of a genome map. Additionally, the identified sex-specific marker represents one of only a handful of such markers in fishes.

  • a rad tag genetic map for the platyfish Xiphophorus maculatus reveals mechanisms of karyotype evolution among teleost fish
    Genetics, 2014
    Co-Authors: Angel Amores, Ronald B. Walter, Wesley C Warren, Manfred Schartl, Julian M Catchen, Indrajit Nanda, John H Postlethwait
    Abstract:

    Mammalian genomes can vary substantially in haploid chromosome number even within a small taxon (e.g., 3-40 among deer alone); in contrast, teleost fish genomes are stable (24-25 in 58% of teleosts), but we do not yet understand the mechanisms that account for differences in karyotype stability. Among perciform teleosts, platyfish (Xiphophorus maculatus) and medaka (Oryzias latipes) both have 24 chromosome pairs, but threespine stickleback (Gasterosteus aculeatus) and green pufferfish (Tetraodon nigroviridis) have just 21 pairs. To understand the evolution of teleost genomes, we made a platyfish meiotic map containing 16,114 mapped markers scored on 267 backcross fish. We tiled genomic contigs along the map to create chromosome-length genome assemblies. Genome-wide comparisons of conserved synteny showed that platyfish and medaka karyotypes remained remarkably similar with few interchromosomal translocations but with numerous intrachromosomal rearrangements (transpositions and inversions) since their lineages diverged ∼120 million years ago. Comparative genomics with platyfish shows how reduced chromosome numbers in stickleback and green pufferfish arose by fusion of pairs of ancestral chromosomes after their lineages diverged from platyfish ∼195 million years ago. Zebrafish and human genomes provide outgroups to root observed changes. These studies identify likely genome assembly errors, characterize chromosome fusion events, distinguish lineage-independent chromosome fusions, show that the teleost genome duplication does not appear to have accelerated the rate of translocations, and reveal the stability of syntenies and gene orders in teleost chromosomes over hundreds of millions of years.

  • the genome of the platyfish Xiphophorus maculatus provides insights into evolutionary adaptation and several complex traits
    Nature Genetics, 2013
    Co-Authors: Manfred Schartl, Ronald B. Walter, Angel Amores, Julian M Catchen, Yingjia Shen, Tzintzuni Garcia, Ingo Braasch, Domitille Chalopin, Jean-nicolas Volff
    Abstract:

    Wesley Warren and colleagues report the whole-genome sequence of the platyfish, Xiphophorus maculatus, providing the first genome of a poeciliid fish. They provide a resource for this model organism used to study traits including viviparity, complex behaviors, pigmentation and cancer, and their comparative analysis provides insights into evolutionary adaptations in natural teleost populations.

Volff Jean-nicolas - One of the best experts on this subject based on the ideXlab platform.

  • A multicopy Y-chromosomal SGNH hydrolase gene expressed in the testis of the platyfish has been captured and mobilized by a Helitron transposon
    'Springer Science and Business Media LLC', 2014
    Co-Authors: Tomaszkiewicz Marta, Chalopin Domitille, Schartl Manfred, Galiana Delphine, Volff Jean-nicolas
    Abstract:

    Background: Teleost fish present a high diversity of sex determination systems, with possible frequent evolutionary turnover of sex chromosomes and sex-determining genes. In order to identify genes involved in male sex determination and differentiation in the platyfish Xiphophorus maculatus, bacterial artificial chromosome contigs from the sex-determining region differentiating the Y from the X chromosome have been assembled and analyzed. Results: A novel three-copy gene called teximY (for testis-expressed in Xiphophorus maculatus on the Y) was identified on the Y but not on the X chromosome. A highly related sequence called texim1, probably at the origin of the Y-linked genes, as well as three more divergent texim genes were detected in (pseudo) autosomal regions of the platyfish genome. Texim genes, for which no functional data are available so far in any organism, encode predicted esterases/lipases with a SGNH hydrolase domain. Texim proteins are related to proteins from very different origins, including proteins encoded by animal CR1 retrotransposons, animal platelet-activating factor acetylhydrolases (PAFah) and bacterial hydrolases. Texim gene distribution is patchy in animals. Texim sequences were detected in several fish species including killifish, medaka, pufferfish, sea bass, cod and gar, but not in zebrafish. Texim-like genes are also present in Oikopleura (urochordate), Amphioxus (cephalochordate) and sea urchin (echinoderm) but absent from mammals and other tetrapods. Interestingly, texim genes are associated with a Helitron transposon in different fish species but not in urochordates, cephalochordates and echinoderms, suggesting capture and mobilization of an ancestral texim gene in the bony fish lineage. RT-qPCR analyses showed that Y-linked teximY genes are preferentially expressed in testis, with expression at late stages of spermatogenesis (late spermatids and spermatozeugmata). Conclusions: These observations suggest either that TeximY proteins play a role in Helitron transposition in the male germ line in fish, or that texim genes are spermatogenesis genes mobilized and spread by transposable elements in fish genomes

  • The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits
    'Springer Science and Business Media LLC', 2013
    Co-Authors: Schartl Manfred, Volff Jean-nicolas, Braasch Ingo, Chalopin Domitille, Walter, Ronald B., Shen Yingjia, Garcia Tzintzuni, Catchen Julian, Amores Angel, Lesch Klaus-peter
    Abstract:

    The authors would like to thank the staff of the Xiphophorus Genetic Stock Center (XGSC) and the Biocenter Fish Facility for maintaining the pedigreed fish lines used in this study. We gratefully acknowledge the sequencing efforts of C. Fronick, K. Delehaunty and the production sequencing group at the Genome Institute. This work was supported by US National Institutes of Health, National Center for Research Resources (NCRR) and Office of Research Infrastructure Programs (ORIP), Division of Comparative Medicine grants R24 RR024790 and R24 OD011120 (R. B. W.), including an American Recovery and Reinvestment Act supplement to this award, and R24OD011199 (R. B. W.), R24 RR032658 and R24 OD011198 (W. C. W.), R01 RR020833 and R01 OD011116 (J.H.P.), by the Deutsche Forschungsgemeinschaft, TRR 58/A5 (K. P. L.) and TRR 17 (M. S.) VolkswagenStiftung, grant I/84 815 (I. B.) and by the Agence Nationale de Recherche (J.-N.V.).International audienceSeveral attributes intuitively considered to be typical mammalian features, such as complex behavior, live birth and malignant disease such as cancer, also appeared several times independently in lower vertebrates. The genetic mechanisms underlying the evolution of these elaborate traits are poorly understood. The platyfish, X. maculatus, offers a unique model to better understand the molecular biology of such traits. We report here the sequencing of the platyfish genome. Integrating genome assembly with extensive genetic maps identified an unexpected evolutionary stability of chromosomes in fish, in contrast to in mammals. Genes associated with viviparity show signatures of positive selection, identifying new putative functional domains and rare cases of parallel evolution. We also find that genes implicated in cognition show an unexpectedly high rate of duplicate gene retention after the teleost genome duplication event, suggesting a hypothesis for the evolution of the behavioral complexity in fish, which exceeds that found in amphibians and reptiles

  • Caractérisation moléculaire de la région du déterminisme du sexe liée au chromosome Y du platy Xiphophorus maculatus
    2012
    Co-Authors: Tomaszkiewicz Marta, Volff Jean-nicolas
    Abstract:

    De par leur diversité de mécanismes de déterminisme du sexe et de chromosomes sexuels, les poissons téléostéens représentent d excellents modèles pour mieux comprendre les bases moléculaires et évolutives du contrôle du développement sexuel chez les vertébrés. Grâce à l analyse de chromosomes artificiels bactériens couvrant les chromosomes sexuels du platy Xiphophorus maculatus, trois copies d un nouveau gène nommé teximY ont été découvertes dans la région de déterminisme du sexe du chromosome Y mais pas du chromosome X. Un gène texim1 très apparenté à teximY ainsi que trois gènes plus divergents ont été identifiés sur les autosomes. Les gènes teximY sont préférentiellement exprimés dans les testicules, au niveau des cellules germinales lors des étapes tardives de la spermatogénèse, alors que texim1 est également transcrit dans les gonades femelles. Des gènes texim ont été détectés chez d'autres poissons téléostéens mais pas chez le poisson-zèbre, ainsi que chez des céphalocordés, des urocordés et des échinodermes mais pas chez les tétrapodes. Les gènes texim codent pour des estérases putatives à domaine SGNH apparentées à des protéines cellulaires procaryotes et eucaryotes ou codées par des retrotransposons animaux. Les gènes texim sont associés à des transposons Helitron chez les poissons mais pas chez les autres animaux, suggérant capture et mobilisation du gène ancestral texim par un transposon à la base de la radiation des téléostéens. TeximY pourrait jouer un rôle dans la transposition du transposon Helitron dans la lignée germinale mâle, ou correspondre à un gène de spermatogenèse mobilisé par le transposon Helitron sur les nouveaux chromosomes sexuels de poissons.The molecular and evolutionary basis of sex determination in vertebrates needs to be unveiled via comparison of different systems. Fish exhibit hypervariability of sex determination mechanisms. Thanks to the analysis of the Bacterial Artificial Chromosome (BAC) library covering the sex chromosomes of the platyfish Xiphophorus maculatus (Rio Jamapa population, XX /XY), three copies of a new gene have been identified in the sex-determining region of the Y but not the X chromosome, and named teximY. Four autosomal counterparts of teximY have been also detected in the genome of the platyfish with one of them, texim1 presenting 95% of cDNA sequence identity with the Y-linked copies. RT-qPCR expression analyses have been performed for each copy in male and female tissues. Two Y-linked teximY copies were preferentially expressed in testis, whereas the autosomal copy texim1 showed preferential expression in male and female gonads. In situ hybridizations with a teximY/1 probe revealed expression in late spermatids and spermatozeugmata. Texim sequences were detected in several fish species, but not in zebrafish, as well as in cephalochordates, urochordates and sea echinoderms but not in tetrapods. Predicted Texim proteins are related to proteins from different origins. Interestingly, texim genes are associated with a Helitron transposon in fish but neither in cephalochordates nor in echinoderms, suggesting capture and mobilization of an ancestral texim gene at the base of the bony fish lineage. TeximY proteins may play a role in Helitron transposition in the male germ line in fish, or texim genes are spermatogenesis genes mobilized and spread by transposable elements in fish genomes.LYON-ENS Sciences (693872304) / SudocSudocFranceF

  • Analyse moléculaire de la région du déterminisme du sexe chez le platy Xiphophorus maculatus
    2010
    Co-Authors: BÖhne Astrid, Volff Jean-nicolas
    Abstract:

    This work aimed to identify the sex-determining gene of the platyfish Xiphophorus maculatus. I characterized the gene Zisupton present on the Y but absent from the X chromosome. Zisupton encodes a new protein type, with domains involved in nucleic acid binding and protein-protein interaction. A testis-specific isoform carries further domains involved in ubiquitin/SUMO posttranslational protein modification. Further analysis revealed five other Zisupton copies in the platyfish genome. Analyses of these copies led to the identification of conserved boundaries delimited by inverted repeats. Different target site duplications and flanking sequences were found around each copy. These sequences are characteristics of transposons. Zisupton presents a new order of DNA transposons without sequence similarities to known transposons. Zisupton was recently active in the genus Xiphophorus and possibly subject to horizontal transfer. Zisupton might correspond to a mobile sex-determining gene.Le but de ce travail était d'identifier le gène maître du déterminisme du sexe chez le platy Xiphophorus maculatus. J'ai caractérisé le gène Zisupton présent sur le chromosome Y mais absent du X. Zisupton code pour une nouvelle protéine impliquée dans les interactions avec des acides nucléiques et des protéines. Un isoforme spécifique des testicules porte des domaines supplémentaires impliqués dans la modification post-traductionnelles via les voies ubiquitin/SUMO. Le génome du platy contient cinq autres copies de Zisupton. Les copies sont délimitées par les mêmes séquences répétées et inversées. Différentes duplications du site d'insertion et régions flanquantes entourent chaque copie. Ces séquences sont caractéristiques des transposons. Nous proposons que Zisupton est membre d'une nouvelle classe de transposons. Zisupton a transposé récemment dans le genre Xiphophorus et a pu subir des transferts horizontaux. Zisupton pourrait être un gène mobile de déterminisme du sexe.LYON-ENS Sciences (693872304) / SudocSudocFranceF

Jean-nicolas Volff - One of the best experts on this subject based on the ideXlab platform.

  • the genome of the platyfish Xiphophorus maculatus provides insights into evolutionary adaptation and several complex traits
    Nature Genetics, 2013
    Co-Authors: Manfred Schartl, Ronald B. Walter, Angel Amores, Julian M Catchen, Yingjia Shen, Tzintzuni Garcia, Ingo Braasch, Domitille Chalopin, Jean-nicolas Volff
    Abstract:

    Wesley Warren and colleagues report the whole-genome sequence of the platyfish, Xiphophorus maculatus, providing the first genome of a poeciliid fish. They provide a resource for this model organism used to study traits including viviparity, complex behaviors, pigmentation and cancer, and their comparative analysis provides insights into evolutionary adaptations in natural teleost populations.

  • The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits
    Nature Genetics, 2013
    Co-Authors: Manfred Schartl, Ronald B. Walter, Jean-nicolas Volff, Angel Amores, Julian M Catchen, Yingjia Shen, Tzintzuni Garcia, Ingo Braasch, Domitille Chalopin, Klaus-peter Lesch
    Abstract:

    Several attributes intuitively considered to be typical mammalian features, such as complex behavior, live birth and malignant disease such as cancer, also appeared several times independently in lower vertebrates. The genetic mechanisms underlying the evolution of these elaborate traits are poorly understood. The platyfish, X. maculatus, offers a unique model to better understand the molecular biology of such traits. We report here the sequencing of the platyfish genome. Integrating genome assembly with extensive genetic maps identified an unexpected evolutionary stability of chromosomes in fish, in contrast to in mammals. Genes associated with viviparity show signatures of positive selection, identifying new putative functional domains and rare cases of parallel evolution. We also find that genes implicated in cognition show an unexpectedly high rate of duplicate gene retention after the teleost genome duplication event, suggesting a hypothesis for the evolution of the behavioral complexity in fish, which exceeds that found in amphibians and reptiles.

  • Tissue-specific expression of dmrt genes in embryos and adults of the platyfish Xiphophorus maculatus.
    Zebrafish, 2006
    Co-Authors: Anne-marie Veith, Matthias Schäfer, Nils Klüver, Cornelia Schmidt, Christina Schultheis, Manfred Schartl, Christoph Winkler, Jean-nicolas Volff
    Abstract:

    The vertebrate dmrt gene family encodes transcription factors with a characteristic DNA-binding motif called the DM domain. The best studied member is dmrt1, which is involved in sexual development...

  • cloning of the dmrt1 gene of Xiphophorus maculatus dmy dmrt1y is not the master sex determining gene in the platyfish
    Gene, 2003
    Co-Authors: Anne-marie Veith, Manfred Schartl, Indrajit Nanda, Michael Schmid, Alexander Froschauer, Cornelia Korting, Reinhold Hanel, Jean-nicolas Volff
    Abstract:

    In contrast to the situation observed in mammals and birds, a switching between different sex determination systems frequently occurred during the evolution of the teleost fish lineage. This might be due to a frequent turnover of sex-determining signals at the top of the sex determination cascade (master sex-determining genes in the case of genetic sex determination). Alternatively, different variations of a same master gene might decide the sex of individuals in different sex determination systems. In the medaka Oryzias latipes, a Y-specific copy of the putative transcription factor gene dmrt1 very likely corresponds to the master sex-determining gene inducing male formation [Nature 417 (2002) 559; Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 11778]. This gene, alternately called dmY and dmrt1Y, has been formed by duplication of the autosomal dmrt1. In order to determine if an orthologue of dmrt1Y was also located in the sex determination region of the related platyfish Xiphophorus maculatus, Southern blot analysis was performed on genomic DNA from XY and YY males and WY and XX females using both medaka and human dmrt1 cDNA as probes. Using different restriction enzymes, no evidence for sex-specific dmrt-containing genomic fragments could be found in the platyfish. No dmrt gene could be detected by low-stringency Southern blot analysis of genomic inserts from 60 bacterial artificial chromosome (BAC) clones linked to the sex-determining locus on the X and Y chromosomes. Six different groups of BAC clones containing dmrt genes were isolated from a platyfish genomic library. X. maculatus dmrt1 gene and cDNA were characterised. In adult, expression of dmrt1 was detected only in testis. Phylogenetic analysis indicated that the duplication of dmrt1 that led to the formation of dmY/dmrt1Y within the medaka lineage clearly occurred after its divergence from the platyfish lineage. Hence, a dmY/dmrt1Y orthologue generated by this particular event of duplication does not correspond to the master sex-determining gene in the platyfish.

  • construction and initial analysis of bacterial artificial chromosome bac contigs from the sex determining region of the platyfish Xiphophorus maculatus
    Gene, 2002
    Co-Authors: Alexander Froschauer, Manfred Schartl, Cornelia Korting, Takayuki Katagiri, Takashi Aoki, Shuichi Asakawa, Nobuyoshi Shimizu, Jean-nicolas Volff
    Abstract:

    Despite the major importance of sex determination in aquaculture, no master sex-determining gene has been identified so far in teleost fish. In the platyfish Xiphophorus maculatus, this master gene is flanked by two receptor tyrosine kinase genes, the Xmrk oncogene responsible for melanoma formation in some Xiphophorus interspecific hybrids, and its proto-oncogenic counterpart. Both Xmrk genes, which have already been characterised at the molecular level, delimit a region of about 1 Mb that contains other gene loci involved in sexual maturity, pigmentation and melanoma formation. We have constructed a genomic bacterial artificial chromosome (BAC) library of X. maculatus with a tenfold coverage of the haploid genome and walked on both X and Y sex chromosomes starting from both Xmrk genes. This led to the assembly of BAC contigs from the sex-determining region covering approximately 950 kb of the X and 750 kb of the Y chromosome. To our knowledge, these are the largest contigs reported so far for sex chromosomes in fish. Molecular analysis suggests that the sex-determining region of X. maculatus frequently undergoes retrotranspositions and other kinds of rearrangements. This genomic plasticity might be related to the high genetic variability observed in Xiphophorus for sex determination, sexual maturity, pigmentation and melanoma formation, which are encoded by gene loci located in the sex-determining region.

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  • intra strain genetic variation of platyfish Xiphophorus maculatus strains determines tumorigenic trajectory
    Frontiers in Genetics, 2020
    Co-Authors: Manfred Schartl, Mikki Boswell, William T Boswell, Taryn J Olivas, Wes Warren, Ronald B. Walter
    Abstract:

    Xiphophorus interspecies hybrids represent a valuable model system to study heritable tumorigenesis, and the only model system that exhibits both spontaneous and inducible tumors. Types of tumorigenesis depend on the specific pedigree of the parental species, X. maculatus, utilized to produce interspecies hybrids. Although the ancestors of the two currently used X. maculatus parental lines, Jp163 A and Jp163 B, were originally siblings produced by the same mother, backcross interspecies hybrid progeny between X. hellerii and X. maculatus Jp163 A develop spontaneous melanoma initiating at the dorsal fin due to segregation of an oncogene and a regulator encoded by the X. maculatus genome, while the backcross hybrid progeny with X. hellerii or X. couchianus and Jp163 B exhibit melanoma on the flanks of their bodies, especially after treatment with ultraviolet light. Therefore, dissecting the genetic differences between these two closely related lines may lead to better understanding of functional molecular differences associated with tumorigenic mechanisms. For this purpose, comparative genomic analyses were undertaken to establish genetic variants between these two X. maculatus lines. Surprisingly, given the heritage of these two fish lines, we found genetic variants are clustered together in select chromosomal regions. Among these variants are non-synonymous mutations located in 381 genes. The non-random distribution of genetic variants between these two may highlight ancestral chromosomal recombination patterns that became fixed during subsequent inbreeding. Employing comparative transcriptomics, we also determined differences in the skin transcriptional landscape between the two lines. The genetic differences observed are associated with pathways highlighting fundamental cellular functions including inter-cellular and microenvironment-cellular interactions, and DNA repair. These results collectively lead to the conclusion that diverged functional genetic baselines are present between Jp163 A and B strains. Further, disruption of these fixed genetic baselines in the hybrids may give rise to spontaneous or inducible mechanisms of tumorigenesis.

  • exposure to 4100k fluorescent light elicits sex specific transcriptional responses in Xiphophorus maculatus skin
    Comparative Biochemistry and Physiology C-toxicology & Pharmacology, 2018
    Co-Authors: William T Boswell, Mikki Boswell, Markita G Savage, Dylan J Walter, Kaela Navarro, Jordan Chang, Jianjun Shen, Ronald B. Walter
    Abstract:

    It has been reported that exposure to artificial light may affect oxygen intake, heart rate, absorption of vitamins and minerals, and behavioral responses in humans. We have reported specific gene expression responses in the skin of Xiphophorus fish after exposure to ultraviolet light (UV), as well as, both broad spectrum and narrow waveband visible light. In regard to fluorescent light (FL), we have shown that male X. maculatus exposed to 4100K FL (i.e. "cool white") rapidly suppress transcription of many genes involved with DNA replication and repair, chromosomal segregation, and cell cycle progression in skin. We have also detailed sex specific transcriptional responses of Xiphophorus skin after exposure to UVB. However, investigation of gender differences in global gene expression response after exposure to 4100K FL has not been reported, despite common use of this FL source for residential, commercial, and animal facility illumination. Here, we compare RNA-Seq results analyzed to assess changes in the global transcription profiles of female and male X. maculatus skin in response to 4100K FL exposure. Our results suggest 4100K FL exposure incites a sex-biased genetic response including up-modulation of inflammation in females and down modulation of DNA repair/replication in males. In addition, we identify clusters of genes that become oppositely modulated in males and females after FL exposure that are principally involved in cell death and cell proliferation.

  • Waveband specific transcriptional control of select genetic pathways in vertebrate skin (Xiphophorus maculatus)
    BMC Genomics, 2018
    Co-Authors: Ronald B. Walter, Mikki Boswell, William T Boswell, Dylan J Walter, Kaela Navarro, Jordan Chang, Sean M. Walter, Raquel Salinas, Markita Savage
    Abstract:

    Background Evolution occurred exclusively under the full spectrum of sunlight. Conscription of narrow regions of the solar spectrum by specific photoreceptors suggests a common strategy for regulation of genetic pathways. Fluorescent light (FL) does not possess the complexity of the solar spectrum and has only been in service for about 60 years. If vertebrates evolved specific genetic responses regulated by light wavelengths representing the entire solar spectrum, there may be genetic consequences to reducing the spectral complexity of light. Results We utilized RNA-Seq to assess changes in the transcriptional profiles of Xiphophorus maculatus skin after exposure to FL (“cool white”), or narrow wavelength regions of light between 350 and 600 nm (i.e., 50 nm or 10 nm regions, herein termed “wavebands”). Exposure to each 50 nm waveband identified sets of genes representing discrete pathways that showed waveband specific transcriptional modulation. For example, 350–400 or 450–500 nm waveband exposures resulted in opposite regulation of gene sets marking necrosis and apoptosis (i.e., 350–400 nm; necrosis suppression, apoptosis activation, while 450–500 nm; apoptosis suppression, necrosis activation). Further investigation of specific transcriptional modulation employing successive 10 nm waveband exposures between 500 and 550 nm showed; (a) greater numbers of genes may be transcriptionally modulated after 10 nm exposures, than observed for 50 nm or FL exposures, (b) the 10 nm wavebands induced gene sets showing greater functional specificity than 50 nm or FL exposures, and (c) the genetic effects of FL are primarily due to 30 nm between 500 and 530 nm. Interestingly, many genetic pathways exhibited completely opposite transcriptional effects after different waveband exposures. For example, the epidermal growth factor ( EGF ) pathway exhibits transcriptional suppression after FL exposure, becomes highly active after 450–500 nm waveband exposure, and again, exhibits strong transcriptional suppression after exposure to the 520–530 nm waveband. Conclusions Collectively, these results suggest one may manipulate transcription of specific genetic pathways in skin by exposure of the intact animal to specific wavebands of light. In addition, we identify genes transcriptionally modulated in a predictable manner by specific waveband exposures. Such genes, and their regulatory elements, may represent valuable tools for genetic engineering and gene therapy protocols.

  • the transcriptional response of skin to fluorescent light exposure in viviparous Xiphophorus and oviparous danio oryzias fishes
    Comparative Biochemistry and Physiology C-toxicology & Pharmacology, 2017
    Co-Authors: Mikki Boswell, William T Boswell, Markita G Savage, Jordan Chang, Zachary Mazurek, Jeanot Muster, Ronald B. Walter
    Abstract:

    Differences in light sources are common in animal facilities and potentially can impact experimental results. Here, the potential impact of lighting differences on skin transcriptomes has been tested in three aquatic animal models commonly utilized in biomedical research, (Xiphophorus maculatus (platyfish), Oryzias latipes (medaka) and Danio rerio (zebrafish). Analysis of replicate comparative RNA-Seq data showed the transcriptional response to commonly utilized 4100K or "cool white" fluorescent light (FL) is much greater in platyfish and medaka than in zebrafish. FL induces genes associated with inflammatory and immune responses in both medaka and zebrafish; however, the platyfish exhibit suppression of genes involved with immune/inflammation, as well as genes associated with cell cycle progression. Furthermore, comparative analyses of gene expression data from platyfish UVB exposures, with medaka and zebrafish after exposure to 4100K FL, show comparable effects on the same stress pathways. We suggest the response to light is conserved, but that long-term adaptation to species specific environmental niches has resulted in a shifting of the wavelengths required to incite similar "genetic" responses in skin. We forward the hypothesis that the "genetic perception" of light may have evolved differently than ocular perception and suggest that light type (i.e., wavelengths emitted) is an important parameter to consider in experimental design.

  • sex specific molecular genetic response to uvb exposure in Xiphophorus maculatus skin
    Comparative Biochemistry and Physiology C-toxicology & Pharmacology, 2015
    Co-Authors: William T Boswell, Mikki Boswell, Markita G Savage, Jianjun Shen, James K Titus, Ronald B. Walter
    Abstract:

    In both Xiphophorus fishes and humans, males are reported to have a higher incidence of melanoma than females. To better understand sex-specific differences in the molecular genetic response to UVB, we performed RNA-Seq experiments in skin of female and male Xiphophorus maculatus Jp 163 B following UVB doses of 8 or 16kJ/m(2) exposure. Male X. maculatus differentially express a significantly larger number of transcripts following exposure to 16kJ/m(2) UVB (1293 genes) compared to 8kJ/m(2) UVB (324 genes). Female skin showed differential gene expression in a larger number of transcripts following 8kJ/m(2) UVB (765) than did males; however, both females and males showed similar numbers of differentially expressed genes at 16kJ/m(2) UVB (1167 and1293, respectively). Although most modulated transcripts after UVB exposure represented the same dominant pathways in both females and males (e.g., DNA repair, circadian rhythm, and fatty acid biosynthesis), we identified genes in several pathways that exhibited opposite modulation in female vs. male skin (e.g., synaptic development, cell differentiation, wound healing, and glucose metabolism). The oppositely modulated genes appear related through uncoupling protein 3 (UCP3) that is involved with the regulation of fatty acid oxidation and serves to balance glucose and lipid metabolism. Overall, these results identify gender-specific differences in UVB-induced genetic profiles in the skin of females and males and show female and male X. maculatus respond to UVB differently through pathways involved in reactive oxygen species, wound healing, and energy homeostasis.

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