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1. Developmental toxicity of pre-production plastic pellets affects a large swathe of invertebrate taxa

Author

Jimenez-Guri, Eva, Paganos, Periklis, La Vecchia, Claudia, Annona, Giovanni, Caccavale, Filomena, Molina, Maria Dolores, Ferrández-Roldán, Alfonso, Donnellan, Rory Daniel, Salatiello, Federica, Johnstone, Adam, Eliso, Maria Concetta, Spagnuolo, Antonietta, Cañestro, Cristian, Albalat, Ricard, Martín-Durán, José María, Williams, Elizabeth A., D'Aniello, Enrico, and Arnone, Maria Ina

Published
2024
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3. Extreme genome scrambling in marine planktonicOikopleura dioicacryptic species

Author

Plessy, Charles, primary, Mansfield, Michael J., additional, Bliznina, Aleksandra, additional, Masunaga, Aki, additional, West, Charlotte, additional, Tan, Yongkai, additional, Liu, Andrew W., additional, Grašič, Jan, additional, del Río Pisula, María Sara, additional, Sánchez-Serna, Gaspar, additional, Fabrega-Torrus, Marc, additional, Ferrández-Roldán, Alfonso, additional, Roncalli, Vittoria, additional, Navratilova, Pavla, additional, Thompson, Eric M., additional, Onuma, Takeshi, additional, Nishida, Hiroki, additional, Cañestro, Cristian, additional, and Luscombe, Nicholas M., additional

Published
2024
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6. 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, Jeremy, 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 EG, 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 MJ, Aken, Bronwen, Yandell, Mark, Schneider, Igor, Yoder, Jeffrey A, Volff, Jean-Nicolas, Meyer, Axel, Amemiya, Chris T, Venkatesh, Byrappa, Holland, Peter WH, Guiguen, Yann, Bobe, Julien, Shubin, Neil H, Di Palma, Federica, Alföldi, Jessica, Lindblad-Toh, Kerstin, and Postlethwait, John H

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Animals, Evolution, Molecular, Female, Fishes, Genome, Humans, Karyotype, Models, Genetic, Organ Specificity, Sequence Analysis, DNA, Transcriptome, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
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

8. Amphioxus functional genomics and the origins of vertebrate gene regulation

Author

Marlétaz, Ferdinand, Firbas, Panos N., Maeso, Ignacio, Tena, Juan J., Bogdanovic, Ozren, Perry, Malcolm, Wyatt, Christopher D. R., de la Calle-Mustienes, Elisa, Bertrand, Stephanie, Burguera, Demian, Acemel, Rafael D., van Heeringen, Simon J., Naranjo, Silvia, Herrera-Ubeda, Carlos, Skvortsova, Ksenia, Jimenez-Gancedo, Sandra, Aldea, Daniel, Marquez, Yamile, Buono, Lorena, Kozmikova, Iryna, Permanyer, Jon, Louis, Alexandra, Albuixech-Crespo, Beatriz, Le Petillon, Yann, Leon, Anthony, Subirana, Lucie, Balwierz, Piotr J., Duckett, Paul Edward, Farahani, Ensieh, Aury, Jean-Marc, Mangenot, Sophie, Wincker, Patrick, Albalat, Ricard, Benito-Gutiérrez, Èlia, Cañestro, Cristian, Castro, Filipe, D’Aniello, Salvatore, Ferrier, David E. K., Huang, Shengfeng, Laudet, Vincent, Marais, Gabriel A. B., Pontarotti, Pierre, Schubert, Michael, Seitz, Hervé, Somorjai, Ildiko, Takahashi, Tokiharu, Mirabeau, Olivier, Xu, Anlong, Yu, Jr-Kai, Carninci, Piero, Martinez-Morales, Juan Ramon, Crollius, Hugues Roest, Kozmik, Zbynek, Weirauch, Matthew T., Garcia-Fernàndez, Jordi, Lister, Ryan, Lenhard, Boris, Holland, Peter W. H., Escriva, Hector, Gómez-Skarmeta, Jose Luis, and Irimia, Manuel

Published
2018
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9. Extreme genome scrambling in marine planktonic Oikopleura dioicacryptic species

Author

Plessy, Charles, Mansfield, Michael J., Bliznina, Aleksandra, Masunaga, Aki, West, Charlotte, Tan, Yongkai, Liu, Andrew W., Grašič, Jan, del Río Pisula, María Sara, Sánchez-Serna, Gaspar, Fabrega-Torrus, Marc, Ferrández-Roldán, Alfonso, Roncalli, Vittoria, Navratilova, Pavla, Thompson, Eric M., Onuma, Takeshi, Nishida, Hiroki, Cañestro, Cristian, and Luscombe, Nicholas M.

Abstract

Genome structural variations within species are rare. How selective constraints preserve gene order and chromosome structure is a central question in evolutionary biology that remains unsolved. Our sequencing of several genomes of the appendicularian tunicate Oikopleura dioicaaround the globe reveals extreme genome scrambling caused by thousands of chromosomal rearrangements, although showing no obvious morphological differences between these animals. The breakpoint accumulation rate is an order of magnitude higher than in ascidian tunicates, nematodes, Drosophila,or mammals. Chromosome arms and sex-specific regions appear to be the primary unit of macrosynteny conservation. At the microsyntenic level, scrambling did not preserve operon structures, suggesting an absence of selective pressure to maintain them. The uncoupling of the genome scrambling with morphological conservation in O. dioicasuggests the presence of previously unnoticed cryptic species and provides a new biological system that challenges our previous vision of speciation in which similar animals always share similar genome structures.

Published
2024
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14. The cosmopolitan appendicularian Oikopleura dioica reveals hidden genetic diversity around the globe

Author

Masunaga, Aki, primary, Mansfield, Michael J, additional, Tan, Yongkai, additional, Liu, Andrew W, additional, Bliznina, Aleksandra, additional, Barzaghi, Paolo, additional, Hodgetts, Tamara L, additional, Ferrández-Roldán, Alfonso, additional, Cañestro, Cristian, additional, Onuma, Takeshi A, additional, Plessy, Charles, additional, and Luscombe, Nicholas M, additional

Published
2022
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15. Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate

Author

Denoeud, France, Henriet, Simon, Mungpakdee, Sutada, Aury, Jean-Marc, Da Silva, Corinne, Brinkmann, Henner, Mikhaleva, Jana, Olsen, Lisbeth Charlotte, Jubin, Claire, Cañestro, Cristian, Bouquet, Jean-Marie, Danks, Gemma, Poulain, Julie, Campsteijn, Coen, Adamski, Marcin, Cross, Ismael, Yadetie, Fekadu, Muffato, Matthieu, Louis, Alexandra, Butcher, Stephen, Tsagkogeorga, Georgia, Konrad, Anke, Singh, Sarabdeep, Jensen, Marit Flo, Cong, Evelyne Huynh, Eikeseth-Otteraa, Helen, Noel, Benjamin, Anthouard, Véronique, Porcel, Betina M., Kachouri-Lafond, Rym, Nishino, Atsuo, Ugolini, Matteo, Chourrout, Pascal, Nishida, Hiroki, Aasland, Rein, Huzurbazar, Snehalata, Westhof, Eric, Delsuc, Frédéric, Lehrach, Hans, Reinhardt, Richard, Weissenbach, Jean, Roy, Scott W., Artiguenave, François, Postlethwait, John H., Manak, J. Robert, Thompson, Eric M., Jaillon, Olivier, Du Pasquier, Louis, Boudinot, Pierre, Liberles, David A., Volff, Jean-Nicolas, Philippe, Hervé, Lenhard, Boris, Crollius, Hugues Roest, Wincker, Patrick, and Chourrout, Daniel

Published
2010

23. Additional file 1: of Wnt evolution and function shuffling in liberal and conservative chordate genomes

Author

Somorjai, Ildikó, Martí-Solans, Josep, Diaz-Gracia, Miriam, Nishida, Hiroki, Imai, Kaoru, Escrivà, Hector, Cañestro, Cristian, and Albalat, Ricard

Abstract

Figure S1. Evolution of Wnt5 in ascidians. Figure S2. Expression of WntA in two ascidian species. Figure S3. Chordate Wnt expression. Figure S4. Wnt subfamilies in A. lucayanum, P. marinus, and C. milii. Table S1. Chordate Wnt genes analyzed in this study. Table S2. Branchiostoma lanceolatum and Halocynthia roretzi primer and probe sequences. Table S3. Wnt synteny in lancelets (B. lanceolatum, B. belcheri and B. floridae) and vertebrates (H. sapiens and P. marinus). Text S1.Branchiostoma lanceolatum Wnt expression as shown in Fig. 2. Text S2. References for Figure S3. (PDF 11566 kb)

Published
2018
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25. Evolution of developmental roles of Pax2/5/8 paralogs after independent duplication in urochordate and vertebrate lineages

Author

Cañestro Cristian, Bassham Susan, and Postlethwait John H

Subjects
Biology (General), QH301-705.5
Abstract

Abstract Background Gene duplication provides opportunities for lineage diversification and evolution of developmental novelties. Duplicated genes generally either disappear by accumulation of mutations (nonfunctionalization), or are preserved either by the origin of positively selected functions in one or both duplicates (neofunctionalization), or by the partitioning of original gene subfunctions between the duplicates (subfunctionalization). The Pax2/5/8 family of important developmental regulators has undergone parallel expansion among chordate groups. After the divergence of urochordate and vertebrate lineages, two rounds of independent gene duplications resulted in the Pax2, Pax5, and Pax8 genes of most vertebrates (the sister group of the urochordates), and an additional duplication provided the pax2a and pax2b duplicates in teleost fish. Separate from the vertebrate genome expansions, a duplication also created two Pax2/5/8 genes in the common ancestor of ascidian and larvacean urochordates. Results To better understand mechanisms underlying the evolution of duplicated genes, we investigated, in the larvacean urochordate Oikopleura dioica, the embryonic gene expression patterns of Pax2/5/8 paralogs. We compared the larvacean and ascidian expression patterns to infer modular subfunctions present in the single pre-duplication Pax2/5/8 gene of stem urochordates, and we compared vertebrate and urochordate expression to infer the suite of Pax2/5/8 gene subfunctions in the common ancestor of olfactores (vertebrates + urochordates). Expression pattern differences of larvacean and ascidian Pax2/5/8 orthologs in the endostyle, pharynx and hindgut suggest that some ancestral gene functions have been partitioned differently to the duplicates in the two urochordate lineages. Novel expression in the larvacean heart may have resulted from the neofunctionalization of a Pax2/5/8 gene in the urochordates. Expression of larvacean Pax2/5/8 in the endostyle, in sites of epithelial remodeling, and in sensory tissues evokes like functions of Pax2, Pax5 and Pax8 in vertebrate embryos, and may indicate ancient origins for these functions in the chordate common ancestor. Conclusion Comparative analysis of expression patterns of chordate Pax2/5/8 duplicates, rooted on the single-copy Pax2/5/8 gene of amphioxus, whose lineage diverged basally among chordates, provides new insights into the evolution and development of the heart, thyroid, pharynx, stomodeum and placodes in chordates; supports the controversial conclusion that the atrial siphon of ascidians and the otic placode in vertebrates are homologous; and backs the notion that Pax2/5/8 functioned in ancestral chordates to engineer epithelial fusions and perforations, including gill slit openings.

Published
2008
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26. Amphioxus functional genomics and the origins of vertebrate gene regulation

Author

European Research Council, European Commission, Ministerio de Economía y Competitividad (España), Australian Research Council, Marlétaz, Ferdinand, Firbas, Panos, Maeso, Ignacio, Tena, Juan J., Bogdanovic, Ozren, Perry, M., Wyatt, Christopher D. R., Calle-Mustienes, Elisa de la, Bertrand, Stephanie, Burguera, Demian, Acemel, Rafael D., Van Heeringen, Simon J., Naranjo, Silvia, Herrera-Úbeda, Carlos, Skvortsova, Ksenia, Jiménez-Gancedo, Sandra, Aldea, Daniel, Marquez, Yamile, Buono, Lorena, Kozmikova, Iryna, Permanyer, Jon, Louis, Alexandra, Albuixech-Crespo, Beatriz, Petillon, Yann Le, Leon, Anthony, Subirana, Lucie, Balwierz, Piotr J., Duckett, Paul Edward, Farahani, Ensieh, Aury, Jean‐Marc, Mangenot, Sophie, Wincker, Patrick, Albalat, Ricard, Benito-Gutiérrez, Èlia, Cañestro, Cristian, Castro, Filipe, D’Aniello, Salvatore, Ferrier, David E. K., Huang, Shengfeng, Laudet, Vincent, Marais, Gabriel A.B., Pontarotti, Pierre, Schubert, Michael, Seitz, Hervé, Somorjai, Ildiko, Takahashi, Tokiharu, Mirabeau, Olivier, Xu, Anlong, Yu, Jr-Kai, Carninci, Piero, Martínez-Morales, Juan Ramón, Roest Crollius, Hugues, Kozmik, Zbynek, Weirauch, Matthew T., Garcia-Fernàndez, Jordi, Lister, Ryan, Lenhard, Boris, Holland, Peter W. H., Escrivá, Héctor, Gómez-Skarmeta, José Luis, Irimia, Manuel, European Research Council, European Commission, Ministerio de Economía y Competitividad (España), Australian Research Council, Marlétaz, Ferdinand, Firbas, Panos, Maeso, Ignacio, Tena, Juan J., Bogdanovic, Ozren, Perry, M., Wyatt, Christopher D. R., Calle-Mustienes, Elisa de la, Bertrand, Stephanie, Burguera, Demian, Acemel, Rafael D., Van Heeringen, Simon J., Naranjo, Silvia, Herrera-Úbeda, Carlos, Skvortsova, Ksenia, Jiménez-Gancedo, Sandra, Aldea, Daniel, Marquez, Yamile, Buono, Lorena, Kozmikova, Iryna, Permanyer, Jon, Louis, Alexandra, Albuixech-Crespo, Beatriz, Petillon, Yann Le, Leon, Anthony, Subirana, Lucie, Balwierz, Piotr J., Duckett, Paul Edward, Farahani, Ensieh, Aury, Jean‐Marc, Mangenot, Sophie, Wincker, Patrick, Albalat, Ricard, Benito-Gutiérrez, Èlia, Cañestro, Cristian, Castro, Filipe, D’Aniello, Salvatore, Ferrier, David E. K., Huang, Shengfeng, Laudet, Vincent, Marais, Gabriel A.B., Pontarotti, Pierre, Schubert, Michael, Seitz, Hervé, Somorjai, Ildiko, Takahashi, Tokiharu, Mirabeau, Olivier, Xu, Anlong, Yu, Jr-Kai, Carninci, Piero, Martínez-Morales, Juan Ramón, Roest Crollius, Hugues, Kozmik, Zbynek, Weirauch, Matthew T., Garcia-Fernàndez, Jordi, Lister, Ryan, Lenhard, Boris, Holland, Peter W. H., Escrivá, Héctor, Gómez-Skarmeta, José Luis, and Irimia, Manuel

Abstract

Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus (Branchiostoma lanceolatum) and characterize DNA methylation, chromatin accessibility, histone modifications and transcriptomes across multiple developmental stages and adult tissues to investigate the evolution of the regulation of the chordate genome. Comparisons with vertebrates identify an intermediate stage in the evolution of differentially methylated enhancers, and a high conservation of gene expression and its cis-regulatory logic between amphioxus and vertebrates that occurs maximally at an earlier mid-embryonic phylotypic period. We analyse regulatory evolution after whole-genome duplications, and find that—in vertebrates—over 80% of broadly expressed gene families with multiple paralogues derived from whole-genome duplications have members that restricted their ancestral expression, and underwent specialization rather than subfunctionalization. Counter-intuitively, paralogues that restricted their expression increased the complexity of their regulatory landscapes. These data pave the way for a better understanding of the regulatory principles that underlie key vertebrate innovations.

Published
2018

29. 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

31. Pth4, an ancient parathyroid hormone lost in eutherian mammals, reveals a new brain‐to‐bone signaling pathway

Author

Suarez‐Bregua, Paula, primary, Torres‐Nuñez, Eva, additional, Saxena, Ankur, additional, Guerreiro, Pedro, additional, Braasch, Ingo, additional, Prober, David A., additional, Moran, Paloma, additional, Cerda‐Reverter, Jose Miguel, additional, Du, Shao Jun, additional, Adrio, Fatima, additional, Power, Deborah M., additional, Canario, Adelino V. M., additional, Postlethwait, John H., additional, Bronner, Marianne E., additional, Cañestro, Cristian, additional, and Rotllant, Josep, additional

Published
2016
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33. Erratum: Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

Author

Braasch, Ingo, primary, Gehrke, Andrew R, additional, Smith, Jeramiah J, additional, Kawasaki, Kazuhiko, additional, Manousaki, Tereza, additional, Pasquier, Jeremy, additional, Amores, Angel, additional, Desvignes, Thomas, additional, Batzel, Peter, additional, Catchen, Julian, additional, Berlin, Aaron M, additional, Campbell, Michael S, additional, Barrell, Daniel, additional, Martin, Kyle J, additional, Mulley, John F, additional, Ravi, Vydianathan, additional, Lee, Alison P, additional, Nakamura, Tetsuya, additional, Chalopin, Domitille, additional, Fan, Shaohua, additional, Wcisel, Dustin, additional, Cañestro, Cristian, additional, Sydes, Jason, additional, Beaudry, Felix E G, additional, Sun, Yi, additional, Hertel, Jana, additional, Beam, Michael J, additional, Fasold, Mario, additional, Ishiyama, Mikio, additional, Johnson, Jeremy, additional, Kehr, Steffi, additional, Lara, Marcia, additional, Letaw, John H, additional, Litman, Gary W, additional, Litman, Ronda T, additional, Mikami, Masato, additional, Ota, Tatsuya, additional, Saha, Nil Ratan, additional, Williams, Louise, additional, Stadler, Peter F, additional, Wang, Han, additional, Taylor, John S, additional, Fontenot, Quenton, additional, Ferrara, Allyse, additional, Searle, Stephen M J, additional, Aken, Bronwen, additional, Yandell, Mark, additional, Schneider, Igor, additional, Yoder, Jeffrey A, additional, Volff, Jean-Nicolas, additional, Meyer, Axel, additional, Amemiya, Chris T, additional, Venkatesh, Byrappa, additional, Holland, Peter W H, additional, Guiguen, Yann, additional, Bobe, Julien, additional, Shubin, Neil H, additional, Di Palma, Federica, additional, Alfo¨ldi, Jessica, additional, Lindblad-Toh, Kerstin, additional, and Postlethwait, John H, additional

Published
2016
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37. Oikopleura dioicaculturing made easy: A Low-Cost facility for an emerging animal model in EvoDevo

Author

Martí-Solans, Josep, primary, Ferrández-Roldán, Alfonso, additional, Godoy-Marín, Hector, additional, Badia-Ramentol, Jordi, additional, Torres-Aguila, Nuria P., additional, Rodríguez-Marí, Adriana, additional, Bouquet, Jean Marie, additional, Chourrout, Daniel, additional, Thompson, Eric M., additional, Albalat, Ricard, additional, and Cañestro, Cristian, additional

Published
2014
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40. Roles of brca2 (fancd1) in Oocyte Nuclear Architecture, Gametogenesis, Gonad Tumors, and Genome Stability in Zebrafish

Author

Rodríguez-Marí, Adriana, primary, Wilson, Catherine, additional, Titus, Tom A., additional, Cañestro, Cristian, additional, BreMiller, Ruth A., additional, Yan, Yi-Lin, additional, Nanda, Indrajit, additional, Johnston, Adam, additional, Kanki, John P., additional, Gray, Erin M., additional, He, Xinjun, additional, Spitsbergen, Jan, additional, Schindler, Detlev, additional, and Postlethwait, John H., additional

Published
2011
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41. The first non-LTR retrotransposon characterised in the cephalochordate amphioxus, BfCR1, shows similarities to CR1-like elements

Author

Albalat, Ricard, Permanyer, J., Cañestro, Cristian, Martínez Mir, Amalia, González-Angulo, O., González-Duarte, Roser, Albalat, Ricard, Permanyer, J., Cañestro, Cristian, Martínez Mir, Amalia, González-Angulo, O., and González-Duarte, Roser

Abstract

BfCR1 is the first non-long terminal repeat retrotransposon to be characterised in the amphioxus genome. Sequence alignment of the predicted translation product reveals that BfCR1 belongs to the CR1-like retroposon class, a family widely distributed in vertebrate and invertebrate lineages. Structural analysis shows conservation of the specific motifs of the ORF2-CR1 elements: the N-terminal endonuclease, the reverse transcriptase and the C-terminal domains. The BfCR1 element possesses an atypical 3' terminus consisting of the tandem repeat (AAG)6. We gathered evidence supporting the mobility of this element and report an estimated 15 copies of BfCR1, mostly truncated, per haploid genome, a remarkably low number when compared to that of vertebrates. Phylogenetic analysis, including the amphioxus element, seems to indicate that (i) CR1-like retroposons cluster in a monophyletic group and (ii) the CR1-like family was already present in the chordate ancestor. Our data provide further support for the horizontal transmission of CR1-like elements during early vertebrate evolution.

Published
2003

47. Characterization of the amphioxus presenilin gene in a high gene-density genomic region illustrates duplication during the vertebrate lineage

Author

Martínez Mir, Amalia, Cañestro, Cristian, González-Duarte, Roser, Albalat, Ricard, Martínez Mir, Amalia, Cañestro, Cristian, González-Duarte, Roser, and Albalat, Ricard

Abstract

Molecular studies on the pathology of Alzheimer's disease (AD) have revealed that mutations in presenilin genes (PS) account for some familial cases. Although the contribution of these genes to the etiology is clear, their biological function remains obscure. Approaches using model organisms have been hampered by the fact that rodents contain two PS copies in the genome and do not develop the hallmark features associated with AD upon aging. To understand PS function and evolution, we have searched for PS homologous sequences in the genome of a lower chordate, Branchiostoma floridae. We report the structure of a single copy Branchiostoma floridae PS gene, named BfPS, and describe new features at the molecular level. Moreover, molecular phylogenetic analysis suggests that BfPS is orthologous to the vertebrate PS-1 and PS-2 forms. Finally, the analysis of more than 16 kb of genomic DNA encompassing BfPS identified three novel genes, which cluster with BfPS in a high gene-density region.

Published
2001

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