42 results on '"Chalopin, Domitille"'
Search Results
2. Transposable Element Expression Profiles in Premalignant Pigment Cell Lesions and Melanoma of Xiphophorus.
- Author
-
Münch, Luca, Helmprobst, Frederik, Volff, Jean-Nicolas, Chalopin, Domitille, Schartl, Manfred, and Kneitz, Susanne
- Subjects
CHROMATOPHORES ,MELANOMA ,CHROMOSOME abnormalities ,CELL physiology ,TRANSPOSONS - Abstract
Transposable elements (TEs) are characterized by their ability to change their genomic position. Through insertion or recombination leading to deletions and other chromosomal aberrations, they can cause genetic instability. The extent to which they thereby exert regulatory influence on cellular functions is unclear. To better characterize TEs in processes such as carcinogenesis, we used the well-established Xiphophorus melanoma model. By transcriptome sequencing, we show that an increasing total number in transposons correlates with progression of malignancy in melanoma samples from Xiphophorus interspecific hybrids. Further, by comparing the presence of TEs in the parental genomes of Xiphophorus maculatus and Xiphophorus hellerii, we could show that even in closely related species, genomic location and spectrum of TEs are considerably different. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
3. Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly
- Author
-
Warren, Wesley C., García-Pérez, Raquel, Xu, Sen, Lampert, Kathrin P., Chalopin, Domitille, Stöck, Matthias, Loewe, Laurence, Lu, Yuan, Kuderna, Lukas, Minx, Patrick, Montague, Michael J., Tomlinson, Chad, Hillier, LaDeana W., Murphy, Daniel N., Wang, John, Wang, Zhongwei, Garcia, Constantino Macias, Thomas, Gregg C. W., Volff, Jean-Nicolas, Farias, Fabiana, Aken, Bronwen, Walter, Ronald B., Pruitt, Kim D., Marques-Bonet, Tomas, Hahn, Matthew W., Kneitz, Susanne, Lynch, Michael, and Schartl, Manfred
- Published
- 2018
- Full Text
- View/download PDF
4. Insights into Sex Chromosome Evolution and Aging from the Genome of a Short-Lived Fish
- Author
-
Reichwald, Kathrin, Petzold, Andreas, Koch, Philipp, Downie, Bryan R., Hartmann, Nils, Pietsch, Stefan, Baumgart, Mario, Chalopin, Domitille, Felder, Marius, Bens, Martin, Sahm, Arne, Szafranski, Karol, Taudien, Stefan, Groth, Marco, Arisi, Ivan, Weise, Anja, Bhatt, Samarth S., Sharma, Virag, Kraus, Johann M., Schmid, Florian, Priebe, Steffen, Liehr, Thomas, Görlach, Matthias, Than, Manuel E., Hiller, Michael, Kestler, Hans A., Volff, Jean-Nicolas, Schartl, Manfred, Cellerino, Alessandro, Englert, Christoph, and Platzer, Matthias
- Published
- 2015
- Full Text
- View/download PDF
5. Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates
- Author
-
Warren, Ian A., Naville, Magali, Chalopin, Domitille, Levin, Perrine, Berger, Chloé Suzanne, Galiana, Delphine, and Volff, Jean-Nicolas
- Published
- 2015
- Full Text
- View/download PDF
6. Transposable elements and early evolution of sex chromosomes in fish
- Author
-
Chalopin, Domitille, Volff, Jean-Nicolas, Galiana, Delphine, Anderson, Jennifer L., and Schartl, Manfred
- Published
- 2015
- Full Text
- View/download PDF
7. Hepatocellular Carcinoma Immune Landscape and the Potential of Immunotherapies
- Author
-
Giraud, Julie, Chalopin, Domitille, Blanc, Jean-Frédéric, Saleh, Maya, Immunology from Concept and Experiments to Translation (ImmunoConcept), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB), Centre de Bioinformatique de Bordeaux (CBIB), CGFB, Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Département d'Oncologie [CHU Bordeaux] (Cancérologie/Oncologie/Digestive), GH Sud Haut-Lévêque [CHU Hôpitaux de Bordeaux] (Centre médico chirurgical Magellan)-Hôpital Saint-André [CHU de Bordeaux], and McGill University = Université McGill [Montréal, Canada]
- Subjects
[SDV]Life Sciences [q-bio] ,digestive system diseases - Abstract
International audience; Hepatocellular carcinoma (HCC) is the most common liver tumor and among the deadliest cancers worldwide. Advanced HCC overall survival is meager and has not improved over the last decade despite approval of several tyrosine kinase inhibitors (TKi) for first and second-line treatments. The recent approval of immune checkpoint inhibitors (ICI) has revolutionized HCC palliative care. Unfortunately, the majority of HCC patients fail to respond to these therapies. Here, we elaborate on the immune landscapes of the normal and cirrhotic livers and of the unique HCC tumor microenvironment. We describe the molecular and immunological classifications of HCC, discuss the role of specific immune cell subsets in this cancer, with a focus on myeloid cells and pathways in anti-tumor immunity, tumor promotion and immune evasion. We also describe the challenges and opportunities of immunotherapies in HCC and discuss new avenues based on harnessing the anti-tumor activity of myeloid, NK and γδ T cells, vaccines, chimeric antigen receptors (CAR)-T or -NK cells, oncolytic viruses, and combination therapies.
- Published
- 2021
8. Evolutionary active transposable elements in the genome of the coelacanth
- Author
-
Chalopin, Domitille, Fan, Shaohua, Simakov, Oleg, Meyer, Axel, Schartl, Manfred, and Volff, Jean-Nicolas
- Published
- 2014
- Full Text
- View/download PDF
9. Transcriptional activity of transposable elements in coelacanth
- Author
-
Forconi, Mariko, Chalopin, Domitille, Barucca, Marco, Biscotti, Maria Assunta, De Moro, Gianluca, Galiana, Delphine, Gerdol, Marco, Pallavicini, Alberto, Canapa, Adriana, Olmo, Ettore, and Volff, Jean-Nicolas
- Published
- 2014
- Full Text
- View/download PDF
10. The African coelacanth genome provides insights into tetrapod evolution
- Author
-
Amemiya, Chris T., Alföldi, Jessica J, Lee, Alison P., Fan, Shaohua S, Philippe, Hervé H, MacCallum, Iain I, Braasch, Ingo I, Manousaki, Tereza T, Schneider, Igor I, Rohner, Nicolas N, Organ, Chris C, Chalopin, Domitille D, Smith, Jeramiah J., Robinson, Mark M, Dorrington, Rosemary A., Gerdol, Marco M, Aken, Bronwen B, Biscotti, Maria Assunta, Barucca, Marco M, Baurain, Denis D, Berlin, Aaron M., Blatch, Gregory L., Buonocore, Francesco F, Burmester, Thorsten T, Campbell, Michael S., Canapa, Adriana A, Cannon, John P., Christoffels, Alan A, De Moro, Gianluca G, Edkins, Adrienne L., Fan, Lin L, Fausto, Anna Maria, Feiner, Nathalie N, Forconi, Mariko M, Gamieldien, Junaid J, Gnerre, Sante S, Gnirke, Andreas A, Goldstone, Jared V., Haerty, Wilfried W, Hahn, Mark E., Hesse, Uljana U, Hoffmann, Steve S, Johnson, Jeremy J, Karchner, Sibel I., Kuraku, Shigehiro S, Lara, Marcia M, Levin, Joshua Z., Litman, Gary W., Mauceli, Evan E, Miyake, Tsutomu T, Mueller, Gail M., Nelson, David R., Nitsche, Anne A, Olmo, Ettore E, Ota, Tatsuya T, Pallavicini, Alberto A, Panji, Sumir S, Picone, Barbara B, Ponting, Chris P., Prohaska, Sonja J., Przybylski, Dariusz D, Saha, Nil Ratan, Ravi, Vydianathan V, Ribeiro, Filipe J., Sauka-Spengler, Tatjana T, Scapigliati, Giuseppe G, Searle, Stephen M. J., Sharpe, Ted T, Simakov, Oleg O, Stadler, Peter F., Stegeman, John J., Sumiyama, Kenta K, Tabbaa, Diana D, Tafer, Hakim H, Turner-Maier, Jason J, van Heusden, Peter P, White, Simon S, Williams, Louise L, Yandell, Mark M, Brinkmann, Henner H, Volff, Jean-Nicolas J, Tabin, Clifford J., Shubin, Neil N, Schartl, Manfred M, Jaffe, David B., Postlethwait, John H., Venkatesh, Byrappa B, Di Palma, Federica F, Lander, Eric S., Meyer, Axel A, and Lindblad-Toh, Kerstin K
- Published
- 2013
- Full Text
- View/download PDF
11. Integrated Genomic Analyses From Low-Depth Sequencing Help Resolve Phylogenetic Incongruence in the Bamboos (Poaceae: Bambusoideae).
- Author
-
Chalopin, Domitille, Clark, Lynn G., Wysocki, William P., Park, Minkyu, Duvall, Melvin R., and Bennetzen, Jeffrey L.
- Subjects
GENOMICS ,GRASSES ,BAMBOO ,GENOME size ,ANCIENT history - Abstract
The bamboos (Bambusoideae, Poaceae) comprise a major grass lineage with a complex evolutionary history involving ancient hybridization and allopolyploidy. About 1700 described species are classified into three tribes, Olyreae (herbaceous bamboos), Bambuseae (tropical woody bamboos), and Arundinarieae (temperate woody bamboos). Nuclear analyses strongly support monophyly of the woody tribes, whereas plastome analyses strongly support paraphyly, with Bambuseae sister to Olyreae. Our objectives were to clarify the origin(s) of the woody bamboo tribes and resolve the nuclear vs. plastid conflict using genomic tools. For the first time, plastid and nuclear genomic information from the same bamboo species were combined in a single study. We sampled 51 species of bamboos representing the three tribes, estimated their genome sizes and generated low-depth sample sequence data, from which plastomes were assembled and nuclear repeats were analyzed. The distribution of repeat families was found to agree with nuclear gene phylogenies, but also provides novel insights into nuclear evolutionary history. We infer two early, independent hybridization events, one between an Olyreae ancestor and a woody ancestor giving rise to the two Bambuseae lineages, and another between two woody ancestors giving rise to the Arundinarieae. Retention of the Olyreae plastome associated with differential dominance of nuclear genomes and subsequent diploidization in some lineages explains the paraphyly observed in plastome phylogenetic estimations. We confirm ancient hybridization and allopolyploidy in the origins of the extant woody bamboo lineages and propose biased fractionation and diploidization as important factors in their evolution. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
12. Direct evidence for postmeiotic transcription during Drosophila melanogaster spermatogenesis
- Author
-
Vibranovski, Maria D., Chalopin, Domitille S., Lopes, Hedibert F., Long, Manyuan, and Karr, Timothy L.
- Subjects
Drosophila -- Physiological aspects ,Drosophila -- Genetic aspects ,RNA sequencing -- Research ,Spermatogenesis -- Research ,Genetic transcription -- Research ,Biological sciences - Published
- 2010
13. Germ cell and tumor associated piRNAs in the medaka and \(Xiphophorus\) melanoma models
- Author
-
Kneitz, Susanne, Mishra, Rasmi R., Chalopin, Domitille, Postlethwait, John, Warren, Wesley C., Walter, Ronald B., and Schartl, Manfred
- Subjects
Base Composition ,endocrine system ,urogenital system ,Oryzias ,piRNA ,Fish model ,Cyprinodontiformes ,Disease Models, Animal ,Cell Transformation, Neoplastic ,Germ Cells ,Multigene Family ,Small RNA-sequencing ,DNA Transposable Elements ,Genetics ,Animals ,RNA, Small Interfering ,Melanoma ,ddc:611 ,Genetic Association Studies ,Research Article ,Biotechnology - Abstract
Background A growing number of studies report an abnormal expression of Piwi-interacting RNAs (piRNAs) and the piRNA processing enzyme Piwi in many cancers. Whether this finding is an epiphenomenon of the chaotic molecular biology of the fast dividing, neoplastically transformed cells or is functionally relevant to tumorigenesisis is difficult to discern at present. To better understand the role of piRNAs in cancer development small laboratory fish models can make a valuable contribution. However, little is known about piRNAs in somatic and neoplastic tissues of fish. Results To identify piRNA clusters that might be involved in melanoma pathogenesis, we use several transgenic lines of medaka, and platyfish/swordtail hybrids, which develop various types of melanoma. In these tumors Piwi, is expressed at different levels, depending on tumor type. To quantify piRNA levels, whole piRNA populations of testes and melanomas of different histotypes were sequenced. Because no reference piRNA cluster set for medaka or Xiphophorus was yet available we developed a software pipeline to detect piRNA clusters in our samples and clusters were selected that were enriched in one or more samples. We found several loci to be overexpressed or down-regulated in different melanoma subtypes as compared to hyperpigmented skin. Furthermore, cluster analysis revealed a clear distinction between testes, low-grade and high-grade malignant melanoma in medaka. Conclusions Our data imply that dysregulation of piRNA expression may be associated with development of melanoma. Our results also reinforce the importance of fish as a suitable model system to study the role of piRNAs in tumorigenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2697-z) contains supplementary material, which is available to authorized users.
- Published
- 2016
14. Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons
- Author
-
Braasch, Ingo, Gehrke, Andrew R., Smith, Jeramiah J., Kawasaki, Kazuhiko, Manousaki, Tereza, Pasquier, Jérémy, Amores, Angel, Desvignes, Thomas, Batzel, Peter, Catchen, Julian, Berlin, Aaron M., Campbell, Michael S., Barrell, Daniel, Martin, Kyle J., Mulley, John F., Ravi, Vydianathan, Lee, Alison P., Nakamura, Tetsuya, Chalopin, Domitille, Fan, Shaohua, Wcisel, Dustin, Cañestro, Cristian, Sydes, Jason, Beaudry, Felix E.G., Sun, Yi, Hertel, Jana, Beam, Michael J., Fasold, Mario, Ishiyama, Mikio, Johnson, Jeremy, Kehr, Steffi, Lara, Marcia, Letaw, John H., Litman, Gary W., Litman, Ronda T., Mikami, Masato, Ota, Tatsuya, Saha, Nil Ratan, Williams, Louise, Stadler, Peter F., Wang, Han, Taylor, John S., Fontenot, Quenton, Ferrara, Allyse, Searle, Stephen M.J., Aken, Bronwen, Yandell, Mark, Schneider, Igor, Yoder, Jeffrey A, Volff, Jean-Nicolas, Meyer, Axel, Amemiya, Chris T, Venkatesh, Byrappa, Holland, Peter W.H., Guiguen, Yann, Bobe, Julien, Shubin, Neil H., Di Palma, Federica, Alföldi, Jessica, Lindblad-Toh, Kerstin, Postlethwait, John H., Institute of Neuroscience, National Research Council [Italy] (CNR), Department of Integrative Biology [Berkeley] (IB), University of California [Berkeley], University of California-University of California, Department of Organismal Biology and Anatomy, University of Chicago, Department of Biology, Northern Arizona University [Flagstaff], Department of Anthropology, University of California, Pennsylvania State University (Penn State), Penn State System, Hellenic Centre for Marine Research, Hellenic Center for Marine Research (HCMR), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Department of Animal Biology, University of Pennsylvania [Philadelphia], Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Eccles Institute of Human Genetics, University of Utah, Cold Spring Harbor, Cold Spring Harbor Laboratory, Wellcome Trust Genome Campus, The Wellcome Trust Sanger Institute [Cambridge], European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Department of Zoology, Auburn University (AU), Department of Animal and Plant Sciences [Sheffield], University of Sheffield [Sheffield], School of Biological Sciences [Bangor], Bangor University, Comparative Genomics Laboratory, Agency for Science, Technology and Research (A*STAR), International Institute of Molecular and Cell Biology, Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Department of Genetics, The University of Texas M.D. Anderson Cancer Center [Houston], Department of Molecular Biomedical Sciences Raleigh, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), Center for Comparative Medicine and Translational Research Raleigh, Departament de Genètica, Universitat Autònoma de Barcelona [Barcelona] (UAB), Institut de Recerca de la Biodiversitat, University of Barcelona, University of Victoria, Center for Circadian Clocks, Soochow University, School of Biology and Basic Medical Sciences, Medical College, Bioinformatics Group, Department of Computer Science, Universität Leipzig [Leipzig], Young Investigators Group Bioinformatics and Transcriptomics, Department of Proteomics, Helmholtz Centre for Environmental Research (UFZ), Department of Dental Hygiene, Nippon Dental University, Morsani College of Medicine, Department of Pediatrics, University of South Florida (USF), Department of Microbiology, Department of Evolutionary Studies of Biosystems, SOKENDAI, Graduate University for Advanced Studies, Molecular Genetics Program, Benaroya Research Institute, Department of Biological Sciences, The Open University [Milton Keynes] (OU), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, European Bioinformatics Institute, Instituto de Ciências Biológicas, Federal University of Para - Universidade Federal do Para [Belem - Brésil], Department of Molecular Biomedical Sciences, University of North Carolina System (UNC)-University of North Carolina System (UNC)-College of Veterinary Medicine Raleigh, Center for Comparative Medicine and Translational Research, International Max Planck Research School for Organismal Biology (IMPRS), University of Konstanz, Genome Analysis Center, Vertebrate and Health Genomics, Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), Hellenic Centre for Marine Research (HCMR), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Universitat Autònoma de Barcelona (UAB), University of Victoria [Canada] (UVIC), Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), University of South Florida [Tampa] (USF), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), University of California (UC), University of Pennsylvania, École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Universität Leipzig, and Federal University of Para - Universidade Federal do Pará - UFPA [Belém, Brazil] (UFPA)
- Subjects
[SDV]Life Sciences [q-bio] ,analyse phylogénétique ,reproduction ,poisson ,analyse génomique ,human ,chromosome ,analyse du transcriptome ,genome ,duplication des génomes ,miRNA ,fish ,teleost ,physiologie animale ,séquence régulatrice ,vertébré ,homme ,lepisosteus oculatus ,interaction animal homme ,lépisosté tacheté ,évolution du génome ,fonction des gènes ,teleosteen ,regulatory sequence ,vertebrates ,immunité ,expression des gènes - Abstract
The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons (vol 48, pg 427, 2016); As we intended, other researchers have been able to use the draft spotted gar genome sequence available from the Broad Institute website since December 2011, the assembly LepOcu1 publicly available from NCBI since 13 January 2012 under accession code GCA000242695.1, and the Ensembl gene annotation (version 74, December 2013; http://www.ensembl.org/Lepisosteus_oculatus/Info/Annotation) and recent annotation by NCBI on 15 May 2014 guided by RNA sequence data from ten tissues. While this article was in review, a paper (Nature 526, 108–111, 2015) was published that arrives at conclusions similar to some of our own analyses, and we wish to acknowledge that publication, which used our unpublished data and genome annotations, emphasizing the importance of the strategy of early release of sequence data. The correction has been made to the HTML and PDF versions of the article.
- Published
- 2016
15. Guidelines for the Nomenclature of Genetic Elements in Tunicate Genomes
- Author
-
Stolfi, Alberto, Sasakura, Yasunori, Chalopin, Domitille, Satou, Yutaka, Christiaen, Lionel, Dantec, Christelle, Endo, Toshinori, Naville, Magali, Nishida, Hiroki, Swalla, Billie J., Volff, Jean-Nicolas, Voskoboynik, Ayelet, Dauga, Delphine, Lemaire, Patrick, Shimoda Marine Research Center, University of Tsukuba, École normale supérieure - Lyon (ENS Lyon), Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Kyoto University [Kyoto], Department of Molecular & Cell Biology [Berkeley], University of California [Berkeley], University of California-University of California, Centre de recherche en Biologie Cellulaire (CRBM), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Osaka University [Osaka], Friday Harbor Laboratories, University of Washington [Seattle], HOPKINS MARINE STATION, Stanford University [Stanford], Bioself Communication [Marseille], Université de Tsukuba = University of Tsukuba, École normale supérieure de Lyon (ENS de Lyon), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Kyoto University, University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Centre de recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hopkins Marine Station [Stanford], Stanford University, National Science Foundation Postdoctoral Research Fellowship in Biology NSF-1161835 National Bioresource Project (Japan) NIGMS/NIH R01GM096032 NHLBI/NIH R01HL108643 R01GM100315 1R01AG037968 PIME from CNRS National Science Foundation DBI-0939454, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
EXPRESSION ,Transcription, Genetic ,genome annotation ,DATABASE ,tunicates ,Guidelines as Topic ,SEQUENCE ,Article ,cis-regulatory sequences ,Terminology as Topic ,LHX3 ,Genes, Overlapping ,Animals ,Urochordata ,PLASTICITY ,gene ,Phylogeny ,Genome ,Chromosome Mapping ,Genomics ,transposable element ,CHORDATE ,ASCIDIAN CIONA-INTESTINALIS ,Antisense Elements (Genetics) ,Genetic Loci ,[SCCO.PSYC]Cognitive science/Psychology ,SYSTEM - Abstract
International audience; Tunicates are invertebrate members of the chordate phylum, and are considered to be the sister group of vertebrates. Tunicates are composed of ascidians, thaliaceans, and appendicularians. With the advent of inexpensive high-throughput sequencing, the number of sequenced tunicate genomes is expected to rise sharply within the coming years. To facilitate comparative genomics within the tunicates, and between tunicates and vertebrates, standardized rules for the nomenclature of tunicate genetic elements need to be established. Here we propose a set of nomenclature rules, consensual within the community, for predicted genes, pseudogenes, transcripts, operons, transcriptional cis-regulatory regions, transposable elements, and transgenic constructs. In addition, the document proposes guidelines for naming transgenic and mutant lines. genesis 53:65-78, 2015. (c) 2014 Wiley Periodicals, Inc.
- Published
- 2015
16. Individual knock out of glycine receptor alpha subunits identifies a specific requirement of glra1 for motor function in zebrafish.
- Author
-
Samarut, Eric, Chalopin, Domitille, Riché, Raphaëlle, Allard, Marc, Liao, Meijiang, and Drapeau, Pierre
- Subjects
- *
GLYCINE receptors , *CHLORIDE channels , *COMPUTATIONAL biology , *DEVELOPMENTAL biology , *BRAIN stem , *PHYSICAL sciences - Abstract
Glycine receptors (GlyRs) are ligand-gated chloride channels mediating inhibitory neurotransmission in the brain stem and spinal cord. They function as pentamers composed of alpha and beta subunits for which 5 genes have been identified in human (GLRA1, GLRA2, GLRA3, GLRA4, GLRB). Several in vitro studies showed that the pentameric subtype composition as well as its stoichiometry influence the distribution and the molecular function of the receptor. Moreover, mutations in some of these genes are involved in different human conditions ranging from tinnitus to epilepsy and hyperekplexia, suggesting distinct functions of the different subunits. Although the beta subunit is essential for synaptic clustering of the receptor, the specific role of each alpha subtype is still puzzling in vivo. The zebrafish genome encodes for five glycine receptor alpha subunits (glra1, glra2, glra3, glra4a, glra4b) thus offering a model of choice to investigate the respective role of each subtype on general motor behaviour. After establishing a phylogeny of GlyR subunit evolution between human and zebrafish, we checked the temporal expression pattern of these transcripts during embryo development. Interestingly, we found that glra1 is the only maternally transmitted alpha subunit. We also showed that the expression of the different GlyR subunits starts at different time points during development. Lastly, in order to decipher the role of each alpha subunit on the general motor behaviour of the fish, we knocked out individually each alpha subunit by CRISPR/Cas9-targeted mutagenesis. Surprisingly, we found that knocking out any of the alpha2, 3, a4a or a4b subunit did not lead to any obvious developmental or motor phenotype. However, glra1-/- (hitch) embryos depicted a strong motor dysfunction from 3 days, making them incapable to swim and thus leading to their premature death. Our results infer a strong functional redundancy between alpha subunits and confirm the central role played by glra1 for proper inhibitory neurotransmission controlling locomotion. The genetic tools we developed here will be of general interest for further studies aiming at dissecting the role of GlyRs in glycinergic transmission in vivo and the hitch mutant (hic) is of specific relevance as a new model of hyperekplexia. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
17. Insights into vertebrate whole-genome duplications from the rainbow trout genome
- Author
-
Berthelot, Camille, Brunet , Frédéric, Chalopin, Domitille, Juanchich, Amélie, Bernard, Maria, Jaillon, Olivier, Roest Crollius, Hugues, Guiguen, Yann, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), École normale supérieure de Lyon (ENS de Lyon), Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Universidad de Puerto Rico. PRI., École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, École normale supérieure - Lyon (ENS Lyon), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), ProdInra, Archive Ouverte, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), AgroParisTech-Institut National de la Recherche Agronomique (INRA), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
salmonidae ,Reproductive Biology ,poisson ,génome ,[SDV.BDD] Life Sciences [q-bio]/Development Biology ,Biologie de la reproduction ,Biologie du développement ,[SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology ,Development Biology ,duplication des génomes ,[SDV.BDD]Life Sciences [q-bio]/Development Biology ,[SDV.BDLR] Life Sciences [q-bio]/Reproductive Biology ,truite arc en ciel - Abstract
absent
- Published
- 2014
18. Génomique comparative de l'évolution et de l'impact évolutif des éléments transposables chez les poissons et autres vertébrés
- Author
-
Chalopin, Domitille, Institut de Génomique Fonctionnelle de Lyon (IGFL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Ecole normale supérieure de lyon - ENS LYON, Jean-Nicolas Volff, École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and STAR, ABES
- Subjects
Diversity ,Nouveautés génétiques ,Génomes de vertébrés ,Molecular domestication ,Genetic novelties ,[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology ,Vertebrate genomes ,[SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology ,Domestication moléculaire ,Contenu ,Content ,Diversité ,Transposable elements ,Eléments transposables - Abstract
Transposable elements (TEs) are mobile genetic elements - able to move and to multiply within genomes - identified in almost all living organisms including bacteria. Considered as junk DNA for long, nowadays they are undeniably major players of gene, genome and host evolution. TEs can be deleterious causing diseases but these “parasites” can also be source of new genetic materials as promoters or even new genes bringing new functions for hosts. The objectives of my thesis was to determine the presence or not of the different TE families in vertebrate genomes, as well as their respective content to understand their evolutionary history. I performed a large-Scale comparative analysis to highlight the various evolutionary strategies of TEs. I showed that TE content is highly variable in vertebrate genomes, the smallest and the largest being found in fish, and may contribute to their genome sizes especially in fish. These superfamilies underwent differential waves of activity in vertebrate species highlighting TE dynamics. On another hand, I focused on the study of a vertebrate-Specific TE-Derived gene, named Gin-2, to understand its origin, evolution, and its potential function in vertebrates. In silico analyses showed that Gin-2 is a very ancient gene (500 My, only absent from placentals) derived from GIN transposons. Further analyses present a particular expression in brain and gonads during adulthood, while a strong expression during gastrulation suggests a potential role of Gin-2 in zebrafish development. All together, the different analyses contribute to a better view of TE evolution and their evolutionary impacts in vertebrate genomes., Les éléments transposables (ETs) sont des éléments génétiques mobiles capables de se déplacer et de se multiplier au sein d’un génome. Identifiés dans la plupart des espèces vivantes incluant les bactéries, mais longtemps considérés comme de l’ADN poubelle, aujourd’hui les ETs sont indéniablement des acteurs majeurs impliqués dans l’évolution des gènes, des génomes et des organismes. Si à l’échelle des individus les ETs peuvent avoir des effets délétères pouvant entrainer des maladies, à plus grande échelle ils sont de puissants agents évolutifs impliqués dans la plasticité génomique. Ces « parasites » peuvent également être sources de nouveaux matériels génétiques comme des promoteurs ou même de nouveaux gènes avec de nouvelles fonctions pour l’hôte. Les objectifs majeurs de mon travail de thèse ont été de déterminer les différentes familles d’ETs présentes dans les génomes de poissons, la part que chacune d’entre elles occupe dans ces génomes et enfin de comprendre l’histoire évolutive des familles d’ETs dans les génomes de poissons en comparaison avec les autres génomes de vertébrés. Cette comparaison à grande échelle permettra de comprendre les différentes stratégies évolutives des ETs. D’autre part, j’ai étudié deux gènes de vertébrés, Gin-1 et Gin-2 dérivés d’ETs, dans le but de comprendre leurs origines et évolution au sein des vertébrés ainsi que d’émettre des hypothèses quant à leur fonction moléculaire potentielle encore inconnue. Pour cela, des analyses in silico ont permis de mieux comprendre les origines de ces gènes. Gin-1, présent chez les amniotes, et Gin-2, absent uniquement des mammifères placentaires, dérivent tous deux de transposons GIN.
- Published
- 2014
19. Analysis of the spotted gar genome suggests absence of causative link between ancestral genome duplication and transposable element diversification in teleost fish.
- Author
-
Chalopin, Domitille and Volff, Jean‐Nicolas
- Subjects
GARS ,VERTEBRATES ,OSTEICHTHYES ,CHROMOSOME duplication ,CHROMOSOMES ,GENOMES - Abstract
Teleost fish have been shown to contain many superfamilies of transposable elements (TEs) that are absent from most tetrapod genomes. Since theories predict an increase in TE activity following polyploidization, such diversity might be linked to the 3R whole-genome duplication that occurred approximately 300 million years ago before the teleost radiation. To test this hypothesis, we have analyzed the genome of the spotted gar Lepisosteus oculatus, which diverged from the teleost lineage before the 3R duplication. Our results indicate that TE diversity and copy numbers are similar in gar and teleost genomes, suggesting that TE diversity was ancestral and not linked to the 3R whole-genome duplication. We propose that about 25 distinct superfamilies of TEs were present in the last ancestor of gars and teleost fish about 300 million years ago in the ray-finned fish lineage. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
20. Identification and FISH mapping of different families of transposons in the Atlantic eel (Anguilla anguilla) genome
- Author
-
Coluccia, E., Chalopin, Domitille, Deiana, A. M., Salvadori, S., Deidda, F., Galiana, Delphine, Volff, Jean-Nicolas, University of Cagliari, Institut de Génomique Fonctionnelle de Lyon (IGFL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Université de Lyon, École normale supérieure - Lyon (ENS Lyon), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Cagliari = University of Cagliari (UniCa), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and École normale supérieure de Lyon (ENS de Lyon)
- Subjects
[SDV]Life Sciences [q-bio] ,[INFO]Computer Science [cs] ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2012
21. Initial characterization of transposable elements in the pseudo-tetraploid genome of the rainbow trout
- Author
-
Chalopin, Domitille, Genet, Carine, Brunet, Frédéric, Galiana-Arnoux, Delphine, Boehne, Astrid, Guiguen, Yann, Volff, Jean-Nicolas, Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Station commune de Recherches en Ichtyophysiologie, Biodiversité et Environnement (SCRIBE), Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), and École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL)
- Subjects
[SDV]Life Sciences [q-bio] - Abstract
absent
- Published
- 2010
22. In vivo measurement of ethoxyresorufin biotransformation by zebrafish prolarva to evaluate cytchrome P450 1A induction: application to fresh waters and environmental sediment extracts
- Author
-
Noury, P., Chalopin, Domitille, Garric, Jeanne, and Irstea Publications, Migration
- Subjects
[SDE] Environmental Sciences ,FISH ,ZEBRAFISH ,BIOMARKERS ,SEDIMENT ,EROD IN VIVO ,ComputingMilieux_MISCELLANEOUS - Published
- 2008
23. X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species.
- Author
-
Yingjia Shen, Chalopin, Domitille, Garcia, Tzintzuni, Boswell, Mikki, Boswell, William, Shiryev, Sergey A., Agarwala, Richa, Volff, Jean-Nicolas, Postlethwait, John H., Schartl, Manfred, Minx, Patrick, Warren, Wesley C., and Walter, Ronald B.
- Subjects
- *
FISH genomes , *XIPHOPHORUS helleri , *PHENOTYPES , *NUCLEOTIDE sequencing , *GENETIC regulation - Abstract
Background: Xiphophorus fishes are represented by 26 live-bearing species of tropical fish that express many attributes (e.g., viviparity, genetic and phenotypic variation, ecological adaptation, varied sexual developmental mechanisms, ability to produce fertile interspecies hybrids) that have made attractive research models for over 85 years. Use of various interspecies hybrids to investigate the genetics underlying spontaneous and induced tumorigenesis has resulted in the development and maintenance of pedigreed Xiphophorus lines specifically bred for research. The recent availability of the X. maculatus reference genome assembly now provides unprecedented opportunities for novel and exciting comparative research studies among Xiphophorus species. Results: We present sequencing, assembly and annotation of two new genomes representing Xiphophorus couchianus and Xiphophorus hellerii. The final X. couchianus and X. hellerii assemblies have total sizes of 708 Mb and 734 Mb and correspond to 98 % and 102 % of the X. maculatus Jp 163 A genome size, respectively. The rates of single nucleotide change range from 1 per 52 bp to 1 per 69 bp among the three genomes and the impact of putatively damaging variants are presented. In addition, a survey of transposable elements allowed us to deduce an ancestral TE landscape, uncovered potential active TEs and document a recent burst of TEs during evolution of this genus. Conclusions: Two new Xiphophorus genomes and their corresponding transcriptomes were efficiently assembled, the former using a novel guided assembly approach. Three assembled genome sequences within this single vertebrate order of new world live-bearing fishes will accelerate our understanding of relationship between environmental adaptation and genome evolution. In addition, these genome resources provide capability to determine allele specific gene regulation among interspecies hybrids produced by crossing any of the three species that are known to produce progeny predisposed to tumor development. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
24. The coelacanth: Can a “living fossil” have active transposable elements in its genome?
- Author
-
Naville, Magali, Chalopin, Domitille, Casane, Didier, Laurenti, Patrick, and Volff, Jean-Nicolas
- Subjects
- *
COELACANTHIFORMES , *LIVING fossils , *TRANSPOSONS , *GENOMES , *TETRAPODS - Abstract
The coelacanth has long been regarded as a “living fossil,” with extant specimens looking very similar to fossils dating back to the Cretaceous period. The hypothesis of a slowly or even not evolving genome has been proposed to account for this apparent morphological stasis. While this assumption seems to be sustained by different evolutionary analyses on protein-coding genes, recent studies on transposable elements have provided more conflicting results. Indeed, the coelacanth genome contains many transposable elements and has been shaped by several major bursts of transposition during evolution. In addition, comparison of orthologous genomic regions from the genomes of the 2 extant coelacanth speciesL. chalumnaeandL. menadoensisrevealed multiple species-specific insertions, indicating transposable element recent activity and contribution to post-speciation genome divergence. These observations, which do not support the genome stasis hypothesis, challenge either the impact of transposable elements on organismal evolution or the status of the coelacanth as a “living fossil.” Closer inspection of fossil and molecular data indicate that, even if coelacanths might evolve more slowly than some other lineages due to demographic and/or ecological factors, this variation is still in the range of a “non-fossil” vertebrate species. [ABSTRACT FROM PUBLISHER]
- Published
- 2015
- Full Text
- View/download PDF
25. Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates.
- Author
-
Chalopin, Domitille, Naville, Magali, Plard, Floriane, Galiana, Delphine, and Volff, Jean-Nicolas
- Subjects
- *
CHORDATA , *VERTEBRATES , *COMPARATIVE studies , *TRANSPOSONS , *CROSSOPTERYGIANS - Abstract
Transposable elements (TEs) are major components of vertebrate genomes, with major roles in genome architecture and evolution. In order to characterize both common patterns and lineage-specific differences in TE content and TE evolution, we have compared the mobilomes of 23 vertebrate genomes, including 10 actinopterygian fish, 11 sarcopterygians, and 2 nonbony vertebrates. We found important variations in TE content (from 6% in the pufferfish tetraodon to 55% in zebrafish), with a more important relative contribution of TEs to genome size in fish than in mammals. Some TE superfamilies were found to be widespread in vertebrates, but most elements showed a more patchy distribution, indicative of multiple events of loss or gain. Interestingly, loss of major TE families was observed during the evolution of the sarcopterygian lineage, with a particularly strong reduction in TE diversity in birds and mammals. Phylogenetic trends in TE composition and activity were detected: Teleost fish genomes are dominated by DNA transposons and contain few ancient TE copies, while mammalian genomes have been predominantly shaped by nonlong terminal repeat retrotransposons, along with the persistence of older sequences. Differences were also found within lineages: The medaka fish genome underwent more recent TE amplification than the related platyfish, as observed for LINE retrotransposons in the mouse compared with the human genome. This study allows the identification of putative cases of horizontal transfer of TEs, and to tentatively infer the composition of the ancestral vertebrate mobilome. Taken together, the results obtained highlight the importance of TEs in the structure and evolution of vertebrate genomes, and demonstrate their major impact on genome diversity both between and within lineages. [ABSTRACT FROM PUBLISHER]
- Published
- 2015
- Full Text
- View/download PDF
26. Interspecies Insertion Polymorphism Analysis Reveals Recent Activity of Transposable Elements in Extant Coelacanths.
- Author
-
Naville, Magali, Chalopin, Domitille, and Volff, Jean-Nicolas
- Subjects
- *
COELACANTHIFORMES , *TRANSPOSONS , *FISH ecology , *GENETIC polymorphisms , *FISH morphology , *FISHES - Abstract
Coelacanths are lobe-finned fish represented by two extant species, Latimeria chalumnae in South Africa and Comoros and L. menadoensis in Indonesia. Due to their intermediate phylogenetic position between ray-finned fish and tetrapods in the vertebrate lineage, they are of great interest from an evolutionary point of view. In addition, extant specimens look similar to 300 million-year-old fossils; because of their apparent slowly evolving morphology, coelacanths have been often described as « living fossils ». As an underlying cause of such a morphological stasis, several authors have proposed a slow evolution of the coelacanth genome. Accordingly, sequencing of the L. chalumnae genome has revealed a globally low substitution rate for protein-coding regions compared to other vertebrates. However, genome and gene evolution can also be influenced by transposable elements, which form a major and dynamic part of vertebrate genomes through their ability to move, duplicate and recombine. In this work, we have searched for evidence of transposition activity in coelacanth genomes through the comparative analysis of orthologous genomic regions from both Latimeria species. Comparison of 5.7 Mb (0.2%) of the L. chalumnae genome with orthologous Bacterial Artificial Chromosome clones from L. menadoensis allowed the identification of 27 species-specific transposable element insertions, with a strong relative contribution of CR1 non-LTR retrotransposons. Species-specific homologous recombination between the long terminal repeats of a new coelacanth endogenous retrovirus was also detected. Our analysis suggests that transposon activity is responsible for at least 0.6% of genome divergence between both Latimeria species. Taken together, this study demonstrates that coelacanth genomes are not evolutionary inert: they contain recently active transposable elements, which have significantly contributed to post-speciation genome divergence in Latimeria. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
27. The cavefish genome reveals candidate genes for eye loss.
- Author
-
McGaugh, Suzanne E., Gross, Joshua B., Aken, Bronwen, Blin, Maryline, Borowsky, Richard, Chalopin, Domitille, Hinaux, Hélène, Jeffery, William R., Keene, Alex, Ma, Li, Minx, Patrick, Murphy, Daniel, O’Quin, Kelly E., Rétaux, Sylvie, Rohner, Nicolas, Searle, Steve M. J., Stahl, Bethany A., Tabin, Cliff, Volff, Jean-Nicolas, and Masato Yoshizawa
- Published
- 2014
- Full Text
- View/download PDF
28. LTR Retroelement-Derived Protein-Coding Genes and Vertebrate Evolution.
- Author
-
Chalopin, Domitille, Tomaszkiewicz, Marta, Galiana, Delphine, and Volff, Jean-Nicolas
- Published
- 2012
- Full Text
- View/download PDF
29. A multicopy Y-chromosomal SGNH hydrolase gene expressed in the testis of the platyfish has been captured and mobilized by a Helitron transposon.
- Author
-
Tomaszkiewicz, Marta, Chalopin, Domitille, Schartl, Manfred, Galiana, Delphine, and Volff, Jean-Nicolas
- Subjects
- *
PLATIES , *HYDROLASES , *GENE expression , *TRANSPOSONS , *CHROMOSOMES , *KILLIFISHES - 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. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
30. Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle.
- Author
-
Chen, Songlin, Zhang, Guojie, Shao, Changwei, Huang, Quanfei, Liu, Geng, Zhang, Pei, Song, Wentao, An, Na, Chalopin, Domitille, Volff, Jean-Nicolas, Hong, Yunhan, Li, Qiye, Sha, Zhenxia, Zhou, Heling, Xie, Mingshu, Yu, Qiulin, Liu, Yang, Xiang, Hui, Wang, Na, and Wu, Kui
- Subjects
GENOMES ,CYNOGLOSSUS ,GENETICS ,SEX chromosomes ,MATERIAL plasticity - Abstract
Genetic sex determination by W and Z chromosomes has developed independently in different groups of organisms. To better understand the evolution of sex chromosomes and the plasticity of sex-determination mechanisms, we sequenced the whole genomes of a male (ZZ) and a female (ZW) half-smooth tongue sole (Cynoglossus semilaevis). In addition to insights into adaptation to a benthic lifestyle, we find that the sex chromosomes of these fish are derived from the same ancestral vertebrate protochromosome as the avian W and Z chromosomes. Notably, the same gene on the Z chromosome, dmrt1, which is the male-determining gene in birds, showed convergent evolution of features that are compatible with a similar function in tongue sole. Comparison of the relatively young tongue sole sex chromosomes with those of mammals and birds identified events that occurred during the early phase of sex-chromosome evolution. Pertinent to the current debate about heterogametic sex-chromosome decay, we find that massive gene loss occurred in the wake of sex-chromosome 'birth'. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
31. The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits.
- Author
-
Schartl, Manfred, Walter, Ronald B, Shen, Yingjia, Garcia, Tzintzuni, Catchen, Julian, Amores, Angel, Braasch, Ingo, Chalopin, Domitille, Volff, Jean-Nicolas, Lesch, Klaus-Peter, Bisazza, Angelo, Minx, Pat, Hillier, LaDeana, Wilson, Richard K, Fuerstenberg, Susan, Boore, Jeffrey, Searle, Steve, Postlethwait, John H, and Warren, Wesley C
- Subjects
PLATIES ,XIPHOPHORUS maculatus ,BIOLOGICAL adaptation ,FISH genetics ,MOLECULAR biology ,GENE mapping - 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. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
32. Genetic Innovation in Vertebrates: Gypsy Integrase Genes and Other Genes Derived from Transposable Elements.
- Author
-
Chalopin, Domitille, Galiana, Delphine, and Volff, Jean-Nicolas
- Subjects
- *
TRANSPOSONS , *VERTEBRATE genetics , *GENE rearrangement , *GENETIC barcoding , *MOLECULAR evolution , *GENE expression , *MOLECULAR genetics - Abstract
Due to their ability to drive DNA rearrangements and to serve as a source of new coding and regulatory sequences, transposable elements (TEs) are considered as powerful evolutionary agents within genomes. In this paper, we review the mechanism of molecular domestication, which corresponds to the formation of new genes derived from TE sequences. Many genes derived from retroelements and DNA transposons have been identified in mammals and other vertebrates, some of them fulfilling essential functions for the development and survival of their host organisms. We will particularly focus on the evolution and expression of Gypsy integrase (GIN) genes, which have been formed from ancient event(s) of molecular domestication and have evolved differentially in some vertebrate sublineages. What we describe here is probably only the tip of the evolutionary iceberg, and future genome analyses will certainly uncover new TE-derived genes and biological functions driving genetic innovation in vertebrates and other organisms [ABSTRACT FROM AUTHOR]
- Published
- 2012
- Full Text
- View/download PDF
33. Analysis of the African coelacanth genome sheds light on tetrapod evolution
- Author
-
Amemiya, Chris T., Alföldi, Jessica, Lee, Alison P., Fan, Shaohua, Philippe, Hervé, MacCallum, Iain, Braasch, Ingo, Manousaki, Tereza, Schneider, Igor, Rohner, Nicolas, Organ, Chris, Chalopin, Domitille, Smith, Jeramiah J., Robinson, Mark, Dorrington, Rosemary A., Gerdol, Marco, Aken, Bronwen, Biscotti, Maria Assunta, Barucca, Marco, Baurain, Denis, Berlin, Aaron M., Blatch, Gregory L., Buonocore, Francesco, Burmester, Thorsten, Campbell, Michael S., Canapa, Adriana, Cannon, John P., Christoffels, Alan, De Moro, Gianluca, Edkins, Adrienne L., Fan, Lin, Fausto, Anna Maria, Feiner, Nathalie, Forconi, Mariko, Gamieldien, Junaid, Gnerre, Sante, Gnirke, Andreas, Goldstone, Jared V., Haerty, Wilfried, Hahn, Mark E., Hesse, Uljana, Hoffmann, Steve, Johnson, Jeremy, Karchner, Sibel I., Kuraku, Shigehiro, Lara, Marcia, Levin, Joshua Z., Litman, Gary W., Mauceli, Evan, Miyake, Tsutomu, Mueller, M. Gail, Nelson, David R., Nitsche, Anne, Olmo, Ettore, Ota, Tatsuya, Pallavicini, Alberto, Panji, Sumir, Picone, Barbara, Ponting, Chris P., Prohaska, Sonja J., Przybylski, Dariusz, Saha, Nil Ratan, Ravi, Vydianathan, Ribeiro, Filipe J., Sauka-Spengler, Tatjana, Scapigliati, Giuseppe, Searle, Stephen M. J., Sharpe, Ted, Simakov, Oleg, Stadler, Peter F., Stegeman, John J., Sumiyama, Kenta, Tabbaa, Diana, Tafer, Hakim, Turner-Maier, Jason, van Heusden, Peter, White, Simon, Williams, Louise, Yandell, Mark, Brinkmann, Henner, Volff, Jean-Nicolas, Tabin, Clifford J., Shubin, Neil, Schartl, Manfred, Jaffe, David, Postlethwait, John H., Venkatesh, Byrappa, Di Palma, Federica, Lander, Eric S., Meyer, Axel, and Lindblad-Toh, Kerstin
- Abstract
It was a zoological sensation when a living specimen of the coelacanth was first discovered in 1938, as this lineage of lobe-finned fish was thought to have gone extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features . Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain, and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues demonstrate the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.
- Published
- 2013
- Full Text
- View/download PDF
34. The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates.
- Author
-
Berthelot, Camille, Brunet, Frédéric, Chalopin, Domitille, Juanchich, Amélie, Bernard, Maria, Noël, Benjamin, Bento, Pascal, Da Silva, Corinne, Labadie, Karine, Alberti, Adriana, Aury, Jean-Marc, Louis, Alexandra, Dehais, Patrice, Bardou, Philippe, Montfort, Jérôme, Klopp, Christophe, Cabau, Cédric, Gaspin, Christine, Thorgaard, Gary H., and Boussaha, Mekki
- Published
- 2014
- Full Text
- View/download PDF
35. A High-Quality Reference Genome for the Invasive Mosquitofish Gambusia affinis Using a Chicago Library.
- Author
-
Hoffberg, Sandra L., Troendle, Nicholas J., Glenn, Travis C., Mahmud, Ousman, Louha, Swarnali, Chalopin, Domitille, Bennetzen, Jeffrey L., and Mauricio, Rodney
- Subjects
- *
WESTERN mosquitofish , *POECILIIDAE - Abstract
The western mosquitofish, Gambusia affinis, is a freshwater poecilid fish native to the southeastern United States but with a global distribution due to widespread human introduction. Gambusia affinis has been used as a model species for a broad range of evolutionary and ecological studies. We sequenced the genome of a male G. affinis to facilitate genetic studies in diverse fields including invasion biology and comparative genetics. We generated Illumina short read data from paired-end libraries and in vitro proximity-ligation libraries. We obtained 54.9×coverage, N50 contig length of 17.6 kb, and N50 scaffold length of 6.65 Mb. Compared to two other species in the Poeciliidae family, G. affinis has slightly fewer genes that have shorter total, exon, and intron length on average. Using a set of universal single-copy orthologs in fish genomes, we found 95.5% of these genes were complete in the G. affinis assembly. The number of transposable elements in the G. affinis assembly is similar to those of closely related species. The high-quality genome sequence and annotations we report will be valuable resources for scientists to map the genetic architecture of traits of interest in this species. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
36. Insights into Sex Chromosome Evolution and Aging from the Genome of a Short-Lived Fish
- Author
-
Alessandro Cellerino, Stefan Taudien, Ivan Arisi, Arne Sahm, Samarth Bhatt, Domitille Chalopin, Thomas Liehr, Marius Felder, Karol Szafranski, Steffen Priebe, Hans A. Kestler, Christoph Englert, Virag Sharma, Michael Hiller, Anja Weise, Matthias Platzer, Florian Schmid, Jean-Nicolas Volff, Marco Groth, Manfred Schartl, Johann M. Kraus, Andreas Petzold, Kathrin Reichwald, Martin Bens, Bryan R. Downie, Nils Hartmann, Stefan Pietsch, Matthias Görlach, Manuel E Than, Mario Baumgart, Philipp Koch, Reichwald, Kathrin, Petzold, Andrea, Koch, Philipp, Downie, Bryan R, Hartmann, Nil, Pietsch, Stefan, Baumgart, Mario, Chalopin, Domitille, Felder, Mariu, Bens, Martin, Sahm, Arne, Szafranski, Karol, Taudien, Stefan, Groth, Marco, Arisi, Ivan, Weise, Anja, Bhatt, Samarth S, Sharma, Virag, Kraus, Johann M, Schmid, Florian, Priebe, Steffen, Liehr, Thoma, Görlach, Matthia, Than, Manuel E, Hiller, Michael, Kestler, Hans A, Volff, Jean Nicola, Schartl, Manfred, Cellerino, Alessandro, Englert, Christoph, and Platzer, Matthias
- Subjects
Male ,Aging ,Molecular Sequence Data ,ved/biology.organism_classification_rank.species ,Y chromosome ,Genome ,General Biochemistry, Genetics and Molecular Biology ,Nothobranchius furzeri ,Animals ,Killifish ,Model organism ,Gene ,Caenorhabditis elegans ,Genetics ,Whole genome sequencing ,Sex Chromosomes ,biology ,Biochemistry, Genetics and Molecular Biology(all) ,ved/biology ,Killifishes ,Sex Determination Processes ,biology.organism_classification ,Biological Evolution ,Living matter ,Female - Abstract
Summary The killifish Nothobranchius furzeri is the shortest-lived vertebrate that can be bred in the laboratory. Its rapid growth, early sexual maturation, fast aging, and arrested embryonic development (diapause) make it an attractive model organism in biomedical research. Here, we report a draft sequence of its genome that allowed us to uncover an intra-species Y chromosome polymorphism representing—in real time—different stages of sex chromosome formation that display features of early mammalian XY evolution "in action." Our data suggest that gdf6Y , encoding a TGF-β family growth factor, is the master sex-determining gene in N. furzeri . Moreover, we observed genomic clustering of aging-related genes, identified genes under positive selection, and revealed significant similarities of gene expression profiles between diapause and aging, particularly for genes controlling cell cycle and translation. The annotated genome sequence is provided as an online resource (http://www.nothobranchius.info/NFINgb).
- Published
- 2015
37. The genomes of all lungfish inform on genome expansion and tetrapod evolution.
- Author
-
Schartl M, Woltering JM, Irisarri I, Du K, Kneitz S, Pippel M, Brown T, Franchini P, Li J, Li M, Adolfi M, Winkler S, de Freitas Sousa J, Chen Z, Jacinto S, Kvon EZ, Correa de Oliveira LR, Monteiro E, Baia Amaral D, Burmester T, Chalopin D, Suh A, Myers E, Simakov O, Schneider I, and Meyer A
- Abstract
The genomes of living lungfishes can inform on the molecular-developmental basis of the Devonian sarcopterygian fish-tetrapod transition. We de novo sequenced the genomes of the African (Protopterus annectens) and South American lungfishes (Lepidosiren paradoxa). The Lepidosiren genome (about 91 Gb, roughly 30 times the human genome) is the largest animal genome sequenced so far and more than twice the size of the Australian (Neoceratodus forsteri)
1 and African2 lungfishes owing to enlarged intergenic regions and introns with high repeat content (about 90%). All lungfish genomes continue to expand as some transposable elements (TEs) are still active today. In particular, Lepidosiren's genome grew extremely fast during the past 100 million years (Myr), adding the equivalent of one human genome every 10 Myr. This massive genome expansion seems to be related to a reduction of PIWI-interacting RNAs and C2H2 zinc-finger and Krüppel-associated box (KRAB)-domain protein genes that suppress TE expansions. Although TE abundance facilitates chromosomal rearrangements, lungfish chromosomes still conservatively reflect the ur-tetrapod karyotype. Neoceratodus' limb-like fins still resemble those of their extinct relatives and remained phenotypically static for about 100 Myr. We show that the secondary loss of limb-like appendages in the Lepidosiren-Protopterus ancestor was probably due to loss of sonic hedgehog limb-specific enhancers., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)- Published
- 2024
- Full Text
- View/download PDF
38. Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.
- Author
-
Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FE, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SM, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PW, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alfo Ldi J, Lindblad-Toh K, and Postlethwait JH
- Published
- 2016
- Full Text
- View/download PDF
39. Germ cell and tumor associated piRNAs in the medaka and Xiphophorus melanoma models.
- Author
-
Kneitz S, Mishra RR, Chalopin D, Postlethwait J, Warren WC, Walter RB, and Schartl M
- Subjects
- Animals, Base Composition, Cyprinodontiformes, DNA Transposable Elements, Disease Models, Animal, Multigene Family, Oryzias, RNA, Small Interfering chemistry, Cell Transformation, Neoplastic genetics, Genetic Association Studies, Germ Cells metabolism, Melanoma genetics, RNA, Small Interfering genetics
- Abstract
Background: A growing number of studies report an abnormal expression of Piwi-interacting RNAs (piRNAs) and the piRNA processing enzyme Piwi in many cancers. Whether this finding is an epiphenomenon of the chaotic molecular biology of the fast dividing, neoplastically transformed cells or is functionally relevant to tumorigenesisis is difficult to discern at present. To better understand the role of piRNAs in cancer development small laboratory fish models can make a valuable contribution. However, little is known about piRNAs in somatic and neoplastic tissues of fish., Results: To identify piRNA clusters that might be involved in melanoma pathogenesis, we use several transgenic lines of medaka, and platyfish/swordtail hybrids, which develop various types of melanoma. In these tumors Piwi, is expressed at different levels, depending on tumor type. To quantify piRNA levels, whole piRNA populations of testes and melanomas of different histotypes were sequenced. Because no reference piRNA cluster set for medaka or Xiphophorus was yet available we developed a software pipeline to detect piRNA clusters in our samples and clusters were selected that were enriched in one or more samples. We found several loci to be overexpressed or down-regulated in different melanoma subtypes as compared to hyperpigmented skin. Furthermore, cluster analysis revealed a clear distinction between testes, low-grade and high-grade malignant melanoma in medaka., Conclusions: Our data imply that dysregulation of piRNA expression may be associated with development of melanoma. Our results also reinforce the importance of fish as a suitable model system to study the role of piRNAs in tumorigenesis.
- Published
- 2016
- Full Text
- View/download PDF
40. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.
- Author
-
Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FE, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SM, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PW, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alföldi J, Lindblad-Toh K, and Postlethwait JH
- Subjects
- Animals, Evolution, Molecular, Female, Fishes metabolism, Genome, Humans, Karyotype, Models, Genetic, Organ Specificity, Sequence Analysis, DNA, Transcriptome, Fishes genetics
- Abstract
To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.
- Published
- 2016
- Full Text
- View/download PDF
41. X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species.
- Author
-
Shen Y, Chalopin D, Garcia T, Boswell M, Boswell W, Shiryev SA, Agarwala R, Volff JN, Postlethwait JH, Schartl M, Minx P, Warren WC, and Walter RB
- Subjects
- Animals, Gene Expression Regulation, Genomics, Species Specificity, Cyprinodontiformes genetics, Genetic Variation, Genome, Transcriptome genetics
- Abstract
Background: Xiphophorus fishes are represented by 26 live-bearing species of tropical fish that express many attributes (e.g., viviparity, genetic and phenotypic variation, ecological adaptation, varied sexual developmental mechanisms, ability to produce fertile interspecies hybrids) that have made attractive research models for over 85 years. Use of various interspecies hybrids to investigate the genetics underlying spontaneous and induced tumorigenesis has resulted in the development and maintenance of pedigreed Xiphophorus lines specifically bred for research. The recent availability of the X. maculatus reference genome assembly now provides unprecedented opportunities for novel and exciting comparative research studies among Xiphophorus species., Results: We present sequencing, assembly and annotation of two new genomes representing Xiphophorus couchianus and Xiphophorus hellerii. The final X. couchianus and X. hellerii assemblies have total sizes of 708 Mb and 734 Mb and correspond to 98 % and 102 % of the X. maculatus Jp 163 A genome size, respectively. The rates of single nucleotide change range from 1 per 52 bp to 1 per 69 bp among the three genomes and the impact of putatively damaging variants are presented. In addition, a survey of transposable elements allowed us to deduce an ancestral TE landscape, uncovered potential active TEs and document a recent burst of TEs during evolution of this genus., Conclusions: Two new Xiphophorus genomes and their corresponding transcriptomes were efficiently assembled, the former using a novel guided assembly approach. Three assembled genome sequences within this single vertebrate order of new world live-bearing fishes will accelerate our understanding of relationship between environmental adaptation and genome evolution. In addition, these genome resources provide capability to determine allele specific gene regulation among interspecies hybrids produced by crossing any of the three species that are known to produce progeny predisposed to tumor development.
- Published
- 2016
- Full Text
- View/download PDF
42. Guidelines for the nomenclature of genetic elements in tunicate genomes.
- Author
-
Stolfi A, Sasakura Y, Chalopin D, Satou Y, Christiaen L, Dantec C, Endo T, Naville M, Nishida H, Swalla BJ, Volff JN, Voskoboynik A, Dauga D, and Lemaire P
- Subjects
- Animals, Chromosome Mapping, Genes, Overlapping, Genetic Loci, Genomics, Guidelines as Topic, Phylogeny, Terminology as Topic, Transcription, Genetic, Antisense Elements (Genetics), Genome, Urochordata classification, Urochordata genetics
- Abstract
Tunicates are invertebrate members of the chordate phylum, and are considered to be the sister group of vertebrates. Tunicates are composed of ascidians, thaliaceans, and appendicularians. With the advent of inexpensive high-throughput sequencing, the number of sequenced tunicate genomes is expected to rise sharply within the coming years. To facilitate comparative genomics within the tunicates, and between tunicates and vertebrates, standardized rules for the nomenclature of tunicate genetic elements need to be established. Here we propose a set of nomenclature rules, consensual within the community, for predicted genes, pseudogenes, transcripts, operons, transcriptional cis-regulatory regions, transposable elements, and transgenic constructs. In addition, the document proposes guidelines for naming transgenic and mutant lines., (© 2014 Wiley Periodicals, Inc.)
- Published
- 2015
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.