58 results on '"Chalopin, Domitille"'
Search Results
52. The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits
- Author
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Schartl, Manfred, primary, Walter, Ronald B, additional, Shen, Yingjia, additional, Garcia, Tzintzuni, additional, Catchen, Julian, additional, Amores, Angel, additional, Braasch, Ingo, additional, Chalopin, Domitille, additional, Volff, Jean-Nicolas, additional, Lesch, Klaus-Peter, additional, Bisazza, Angelo, additional, Minx, Pat, additional, Hillier, LaDeana, additional, Wilson, Richard K, additional, Fuerstenberg, Susan, additional, Boore, Jeffrey, additional, Searle, Steve, additional, Postlethwait, John H, additional, and Warren, Wesley C, additional
- Published
- 2013
- Full Text
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53. X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species.
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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
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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
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54. Genetic Innovation in Vertebrates: Gypsy Integrase Genes and Other Genes Derived from Transposable Elements
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Chalopin, Domitille, primary, Galiana, Delphine, additional, and Volff, Jean-Nicolas, additional
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- 2012
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55. Analysis of the African coelacanth genome sheds light on tetrapod evolution
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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.
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- 2013
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56. Insights into Sex Chromosome Evolution and Aging from the Genome of a Short-Lived Fish
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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
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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
57. Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.
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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
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58. Guidelines for the nomenclature of genetic elements in tunicate genomes.
- Author
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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
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