Literature DB >> 21097902

Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate.

France Denoeud1, Simon Henriet, Sutada Mungpakdee, Jean-Marc Aury, Corinne Da Silva, Henner Brinkmann, Jana Mikhaleva, Lisbeth Charlotte Olsen, Claire Jubin, Cristian Cañestro, Jean-Marie Bouquet, Gemma Danks, Julie Poulain, Coen Campsteijn, Marcin Adamski, Ismael Cross, Fekadu Yadetie, Matthieu Muffato, Alexandra Louis, Stephen Butcher, Georgia Tsagkogeorga, Anke Konrad, Sarabdeep Singh, Marit Flo Jensen, Evelyne Huynh Cong, Helen Eikeseth-Otteraa, Benjamin Noel, Véronique Anthouard, Betina M Porcel, Rym Kachouri-Lafond, Atsuo Nishino, Matteo Ugolini, Pascal Chourrout, Hiroki Nishida, Rein Aasland, Snehalata Huzurbazar, Eric Westhof, Frédéric Delsuc, Hans Lehrach, Richard Reinhardt, Jean Weissenbach, Scott W Roy, François Artiguenave, John H Postlethwait, J Robert Manak, Eric M Thompson, Olivier Jaillon, Louis Du Pasquier, Pierre Boudinot, David A Liberles, Jean-Nicolas Volff, Hervé Philippe, Boris Lenhard, Hugues Roest Crollius, Patrick Wincker, Daniel Chourrout.   

Abstract

Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain.

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Year:  2010        PMID: 21097902      PMCID: PMC3760481          DOI: 10.1126/science.1194167

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  25 in total

1.  The frailty of adaptive hypotheses for the origins of organismal complexity.

Authors:  Michael Lynch
Journal:  Proc Natl Acad Sci U S A       Date:  2007-05-09       Impact factor: 11.205

2.  Mystery of intron gain: new data and new models.

Authors:  Scott William Roy; Manuel Irimia
Journal:  Trends Genet       Date:  2008-12-11       Impact factor: 11.639

Review 3.  Fruit flies and humans respond differently to retrotransposons.

Authors:  Thomas H Eickbush; Anthony V Furano
Journal:  Curr Opin Genet Dev       Date:  2002-12       Impact factor: 5.578

4.  Retrohoming of a bacterial group II intron: mobility via complete reverse splicing, independent of homologous DNA recombination.

Authors:  B Cousineau; D Smith; S Lawrence-Cavanagh; J E Mueller; J Yang; D Mills; D Manias; G Dunny; A M Lambowitz; M Belfort
Journal:  Cell       Date:  1998-08-21       Impact factor: 41.582

5.  Retroelement dynamics and a novel type of chordate retrovirus-like element in the miniature genome of the tunicate Oikopleura dioica.

Authors:  Jean-Nicolas Volff; Hans Lehrach; Richard Reinhardt; Daniel Chourrout
Journal:  Mol Biol Evol       Date:  2004-07-14       Impact factor: 16.240

6.  The pattern of evolution of smaller-scale gene duplicates in mammalian genomes is more consistent with neo- than subfunctionalisation.

Authors:  Timothy Hughes; David A Liberles
Journal:  J Mol Evol       Date:  2007-10-24       Impact factor: 2.395

7.  The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans genome.

Authors:  Vaishali Katju; Michael Lynch
Journal:  Genetics       Date:  2003-12       Impact factor: 4.562

8.  The Trichoplax genome and the nature of placozoans.

Authors:  Mansi Srivastava; Emina Begovic; Jarrod Chapman; Nicholas H Putnam; Uffe Hellsten; Takeshi Kawashima; Alan Kuo; Therese Mitros; Asaf Salamov; Meredith L Carpenter; Ana Y Signorovitch; Maria A Moreno; Kai Kamm; Jane Grimwood; Jeremy Schmutz; Harris Shapiro; Igor V Grigoriev; Leo W Buss; Bernd Schierwater; Stephen L Dellaporta; Daniel S Rokhsar
Journal:  Nature       Date:  2008-08-21       Impact factor: 49.962

9.  Phase distribution of spliceosomal introns: implications for intron origin.

Authors:  Hung D Nguyen; Maki Yoshihama; Naoya Kenmochi
Journal:  BMC Evol Biol       Date:  2006-09-08       Impact factor: 3.260

10.  Culture optimization for the emergent zooplanktonic model organism Oikopleura dioica.

Authors:  Jean-Marie Bouquet; Endy Spriet; Christofer Troedsson; Helen Otterå; Daniel Chourrout; Eric M Thompson
Journal:  J Plankton Res       Date:  2009-01-16       Impact factor: 2.455

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  111 in total

1.  Forming a tough shell via an intracellular matrix and cellular junctions in the tail epidermis of Oikopleura dioica (Chordata: Tunicata: Appendicularia).

Authors:  Keisuke Nakashima; Atsuo Nishino; Euichi Hirose
Journal:  Naturwissenschaften       Date:  2011-06-12

2.  The evolutionary landscape of the Rab family in chordates.

Authors:  Ugo Coppola; Filomena Ristoratore; Ricard Albalat; Salvatore D'Aniello
Journal:  Cell Mol Life Sci       Date:  2019-04-26       Impact factor: 9.261

3.  Maternal and zygotic transcriptomes in the appendicularian, Oikopleura dioica: novel protein-encoding genes, intra-species sequence variations, and trans-spliced RNA leader.

Authors:  Kai Wang; Tatsuya Omotezako; Kanae Kishi; Hiroki Nishida; Takeshi A Onuma
Journal:  Dev Genes Evol       Date:  2015-06-02       Impact factor: 0.900

4.  Coelimination and Survival in Gene Network Evolution: Dismantling the RA-Signaling in a Chordate.

Authors:  Josep Martí-Solans; Olga V Belyaeva; Nuria P Torres-Aguila; Natalia Y Kedishvili; Ricard Albalat; Cristian Cañestro
Journal:  Mol Biol Evol       Date:  2016-07-12       Impact factor: 16.240

5.  The phylogenetic distribution and evolution of enzymes within the thymidine kinase 2-like gene family in metazoa.

Authors:  Anke Konrad; Jason Lai; Zeeshan Mutahir; Jure Piškur; David A Liberles
Journal:  J Mol Evol       Date:  2014-02-06       Impact factor: 2.395

Review 6.  No more non-model species: the promise of next generation sequencing for comparative immunology.

Authors:  Nolwenn M Dheilly; Coen Adema; David A Raftos; Benjamin Gourbal; Christoph Grunau; Louis Du Pasquier
Journal:  Dev Comp Immunol       Date:  2014-02-06       Impact factor: 3.636

7.  Retroduplication and loss of parental genes is a mechanism for the generation of intronless genes in Ciona intestinalis and Ciona savignyi.

Authors:  Dong Seon Kim; Yao Wang; Hye Ji Oh; Dongjin Choi; Kangseok Lee; Yoonsoo Hahn
Journal:  Dev Genes Evol       Date:  2014-07-19       Impact factor: 0.900

8.  Emerging Frontiers in the Study of Molecular Evolution.

Authors:  David A Liberles; Belinda Chang; Kerry Geiler-Samerotte; Aaron Goldman; Jody Hey; Betül Kaçar; Michelle Meyer; William Murphy; David Posada; Andrew Storfer
Journal:  J Mol Evol       Date:  2020-04       Impact factor: 2.395

9.  Frequency of intron loss correlates with processed pseudogene abundance: a novel strategy to test the reverse transcriptase model of intron loss.

Authors:  Tao Zhu; Deng-Ke Niu
Journal:  BMC Biol       Date:  2013-03-05       Impact factor: 7.431

10.  RNA interference in the appendicularian Oikopleura dioica reveals the function of the Brachyury gene.

Authors:  Tatsuya Omotezako; Atsuo Nishino; Takeshi A Onuma; Hiroki Nishida
Journal:  Dev Genes Evol       Date:  2013-03-15       Impact factor: 0.900

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