Journal ArticleDOI
Yesterday's polyploids and the mystery of diploidization
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TLDR
Sequence-level studies on model organisms whose genomes show clearer evidence of ancient polyploidy are invaluable because they indicate what the evolutionary products of genome duplication can look like.Abstract:
Thirty years after Susumu Ohno proposed that vertebrate genomes are degenerate polyploids, the extent to which genome duplication contributed to the evolution of the vertebrate genome, if at all, is still uncertain. Sequence-level studies on model organisms whose genomes show clearer evidence of ancient polyploidy are invaluable because they indicate what the evolutionary products of genome duplication can look like. The greatest mystery is the molecular basis of diploidization, the evolutionary process by which a polyploid genome turns into a diploid one.read more
Citations
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Journal ArticleDOI
Evolution by gene duplication: an update
TL;DR: Detailed molecular characterization of individual gene families, computational analysis of genomic sequences and population genetic modeling can all be used to help uncover the mechanisms behind the evolution by gene duplication.
Journal ArticleDOI
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype
Olivier Jaillon,Jean-Marc Aury,Frédéric Brunet,Jean-Louis Petit,Nicole Stange-Thomann,Evan Mauceli,Laurence Bouneau,Cécile Fischer,Catherine Ozouf-Costaz,Alain Bernot,Sophie Nicaud,David M. Jaffe,Sheila Fisher,Georges Lutfalla,Carole Dossat,Béatrice Segurens,Corinne Dasilva,Marcel Salanoubat,Michael Levy,Nathalie Boudet,Sergi Castellano,Véronique Anthouard,Claire Jubin,Vanina Castelli,Michael Katinka,Benoit Vacherie,Christian Biémont,Zineb Skalli,Laurence Cattolico,Julie Poulain,Véronique de Berardinis,Corinne Cruaud,Simone Duprat,Philippe Brottier,Jean-Pierre Coutanceau,Jérôme Gouzy,Genís Parra,Guillaume Lardier,Charles Chapple,Kevin McKernan,Paul A. McEwan,Stephanie Bosak,Manolis Kellis,Jean-Nicolas Volff,Roderic Guigó,Michael C. Zody,Jill P. Mesirov,Kerstin Lindblad-Toh,Bruce W. Birren,Chad Nusbaum,Daniel Kahn,Marc Robinson-Rechavi,Vincent Laudet,Vincent Schächter,Francis Quetier,William Saurin,Claude Scarpelli,Patrick Wincker,Eric S. Lander,Eric S. Lander,Jean Weissenbach,Hugues Roest Crollius,Hugues Roest Crollius +62 more
TL;DR: Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish, and reconstructs much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype.
Journal ArticleDOI
The snail superfamily of zinc-finger transcription factors.
TL;DR: The Snail superfamily of zinc-finger transcription factors is involved in processes that imply pronounced cell movements, both during embryonic development and in the acquisition of invasive and migratory properties during tumour progression.
Journal ArticleDOI
The genome sequence of the filamentous fungus Neurospora crassa
James E. Galagan,Sarah E. Calvo,Katherine A. Borkovich,Eric U. Selker,Nick O. Read,David B. Jaffe,William Fitzhugh,Li-Jun Ma,Serge Smirnov,Seth Purcell,Bushra Rehman,Timothy Elkins,Reinhard Engels,Shunguang Wang,Cydney B. Nielsen,Jonathan Butler,Matthew G. Endrizzi,Dayong Qui,Peter Ianakiev,Deborah Bell-Pedersen,Mary Anne Nelson,Margaret Werner-Washburne,Claude P. Selitrennikoff,John A. Kinsey,Edward L. Braun,Alex Zelter,Alex Zelter,Ulrich Schulte,Gregory O. Kothe,Gregory Jedd,Werner Mewes,Chuck Staben,Edward M. Marcotte,David Greenberg,Alice Roy,Karen Foley,Jerome Naylor,Nicole Stange-Thomann,Robert Barrett,Sante Gnerre,Michael Kamal,Manolis Kamvysselis,Evan Mauceli,Cord Bielke,Stephen Rudd,Dmitrij Frishman,Svetlana Krystofova,Carolyn G. Rasmussen,Robert L. Metzenberg,David D. Perkins,Scott Kroken,Carlo Cogoni,Giuseppe Macino,David E. A. Catcheside,Weixi Li,Robert J. Pratt,Stephen A. Osmani,Colin P.C. DeSouza,Louise Glass,Marc J. Orbach,J. Andrew Berglund,Rodger B. Voelker,Oded Yarden,Michael Plamann,Stephan Seiler,Jay C. Dunlap,Alan Radford,Rodolfo Aramayo,Donald O. Natvig,Lisa A. Alex,Gertrud Mannhaupt,Daniel J. Ebbole,Michael Freitag,Ian T. Paulsen,Matthew S. Sachs,Eric S. Lander,Chad Nusbaum,Bruce W. Birren +77 more
TL;DR: A high-quality draft sequence of the N. crassa genome is reported, suggesting that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.
Journal ArticleDOI
The amphioxus genome and the evolution of the chordate karyotype
Nicholas H. Putnam,Thomas Butts,David E. K. Ferrier,Rebecca F. Furlong,Uffe Hellsten,Takeshi Kawashima,Takeshi Kawashima,Marc Robinson-Rechavi,Marc Robinson-Rechavi,Eiichi Shoguchi,Eiichi Shoguchi,Astrid Terry,Jr-Kai Yu,E grave,lia Benito-Gutiérrez,Inna Dubchak,Jordi Garcia-Fernàndez,Jeremy J. Gibson-Brown,Igor V. Grigoriev,Amy C. Horton,Pieter J. de Jong,Jerzy Jurka,Vladimir V. Kapitonov,Yuji Kohara,Yoko Kuroki,Erika Lindquist,Susan Lucas,Kazutoyo Osoegawa,Len A. Pennacchio,Asaf Salamov,Yutaka Satou,Tatjana Sauka-Spengler,Jeremy Schmutz,Tadasu Shin-I,Atsushi Toyoda,Marianne Bronner-Fraser,Asao Fujiyama,Linda Z. Holland,Peter W. H. Holland,Nori Satoh,Nori Satoh,Daniel S. Rokhsar,Daniel S. Rokhsar +42 more
TL;DR: Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization.
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TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Journal ArticleDOI
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TL;DR: Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems are indicated.
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Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
TL;DR: This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.
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Sequence the Human Genome
TL;DR: This book aims to provide a history of Chinese modern art from 17th Century to the present day through the lens of 20th Century critics, practitioners, journalists, and mediaeval and modern-day critics.