Journal ArticleDOI
Horizontal gene transfer in eukaryotic evolution
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TLDR
The number of well-supported cases of transfer from both prokaryotes and eukaryotes, many with significant functional implications, is now expanding rapidly and major recent trends include the important role of HGT in adaptation to certain specialized niches and the highly variable impact of H GT in different lineages.Abstract:
Horizontal gene transfer (HGT; also known as lateral gene transfer) has had an important role in eukaryotic genome evolution, but its importance is often overshadowed by the greater prevalence and our more advanced understanding of gene transfer in prokaryotes. Recurrent endosymbioses and the generally poor sampling of most nuclear genes from diverse lineages have also complicated the search for transferred genes. Nevertheless, the number of well-supported cases of transfer from both prokaryotes and eukaryotes, many with significant functional implications, is now expanding rapidly. Major recent trends include the important role of HGT in adaptation to certain specialized niches and the highly variable impact of HGT in different lineages.read more
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Book ChapterDOI
Fungal Horizontal Gene Transfer: A History Beyond the Phylogenetic Kingdoms
TL;DR: Evidence suggest that HGT is a relevant mechanism in eukaryotic genome development, as an evolutionary shortcut, triggering the appearance of new capabilities in the involved organisms.
Journal ArticleDOI
LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice
Hao Wang,Zhao Xu,Hongjie Yu +2 more
TL;DR: It is estimated that a significant proportion of the rice genome has experienced inter-subspecies nonreciprocal recombination (ISNR) in as recent as 53,000 years, confirming that recent ISNR is an important factor that molds modern cultivated rice genome.
Journal ArticleDOI
Genome-scale analysis of regulatory protein acetylation enzymes from photosynthetic eukaryotes
R. Glen Uhrig,Pascal Schläpfer,Pascal Schläpfer,Devang Mehta,Matthias Hirsch-Hoffmann,Wilhelm Gruissem +5 more
TL;DR: New evolutionary, structural, and biological insights are revealed into the KAT- and KDAC-families of photosynthetic eukaryotes, including evolutionary parallels to protein kinases and protein phosphatases.
Journal ArticleDOI
Genome degeneration affects both extracellular and intracellular bacterial endosymbionts
Heike Feldhaar,Roy Gross +1 more
TL;DR: The obligate intracellular bacterial endosymbionts of insects are a paradigm for reductive genome evolution and a study demonstrates that similar evolutionary forces shaping genome structure may also apply to extracellular endosYmbions of insects.
Journal ArticleDOI
Divergent bacterial transformation exerted by soil minerals.
TL;DR: Three mechanisms were proposed governing bacterial transformation in mineral systems: adsorption of CSF, gene expression and membrane damage, which have advanced the understanding on the genetic transformation of bacteria as influenced by minerals in a wide range of soils and associated environments.
References
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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
Lateral gene transfer and the nature of bacterial innovation
TL;DR: Unlike eukaryotes, which evolve principally through the modification of existing genetic information, bacteria have obtained a significant proportion of their genetic diversity through the acquisition of sequences from distantly related organisms.
Journal ArticleDOI
The Genome of the African Trypanosome Trypanosoma brucei
Matthew Berriman,Elodie Ghedin,Elodie Ghedin,Christiane Hertz-Fowler,Gaëlle Blandin,Hubert Renauld,Daniella Castanheira Bartholomeu,Nicola Lennard,Elisabet Caler,N. Hamlin,Brian J. Haas,Ulrike Böhme,Linda Hannick,Martin Aslett,Joshua Shallom,Lucio Marcello,Lihua Hou,Bill Wickstead,U. Cecilia M. Alsmark,Claire Arrowsmith,Rebecca Atkin,Andrew Barron,Frédéric Bringaud,Karen Brooks,Mark Carrington,Inna Cherevach,Tracey-Jane Chillingworth,Carol Churcher,Louise Clark,Craig Corton,Ann Cronin,Robert L. Davies,Jonathon Doggett,Appolinaire Djikeng,Tamara Feldblyum,Mark C. Field,Audrey Fraser,Ian Goodhead,Zahra Hance,David Harper,Barbara Harris,Heidi Hauser,Jessica B. Hostetler,Al Ivens,Kay Jagels,David W. Johnson,Justin Johnson,Kristine Jones,Arnaud Kerhornou,Hean Koo,Natasha Larke,Scott M. Landfear,Christopher Larkin,Vanessa Leech,Alexandra Line,Angela Lord,Annette MacLeod,P. Mooney,Sharon Moule,David M. A. Martin,Gareth W. Morgan,Karen Mungall,Halina Norbertczak,Doug Ormond,Grace Pai,Christopher S. Peacock,Jeremy Peterson,Michael A. Quail,Ester Rabbinowitsch,Marie-Adèle Rajandream,Chris P Reitter,Steven L. Salzberg,Mandy Sanders,Seth Schobel,Sarah Sharp,Mark Simmonds,Anjana J. Simpson,Luke J. Tallon,C. Michael R. Turner,Andrew Tait,Adrian Tivey,Susan Van Aken,Danielle Walker,David Wanless,Shiliang Wang,Brian White,Owen White,Sally Whitehead,John Woodward,Jennifer R. Wortman,Mark Raymond Adams,T. Martin Embley,Keith Gull,Elisabetta Ullu,J. David Barry,Alan H. Fairlamb,Fred R. Opperdoes,Barclay G. Barrell,John E. Donelson,Neil Hall,Neil Hall,Claire M. Fraser,Sara E. Melville,Najib M. El-Sayed,Najib M. El-Sayed +104 more
TL;DR: Comparisons of the cytoskeleton and endocytic trafficking systems of Trypanosoma brucei with those of humans and other eukaryotic organisms reveal major differences.
Journal ArticleDOI
Genome evolution in yeasts
Bernard Dujon,David James Sherman,Gilles Fischer,Pascal Durrens,Serge Casaregola,Ingrid Lafontaine,Jacky de Montigny,Christian Marck,Cécile Neuvéglise,Emmanuel Talla,Nicolas Goffard,Lionel Frangeul,Michel Aigle,Véronique Anthouard,Anna Babour,Valérie Barbe,Stéphanie Barnay,Sylvie Blanchin,Jean-Marie Beckerich,Emmanuelle Beyne,Claudine Bleykasten,Anita Boisramé,Jeanne Boyer,Laurence Cattolico,Fabrice Confanioleri,Antoine de Daruvar,Laurence Despons,Emmanuelle Fabre,Cécile Fairhead,Hélène Ferry-Dumazet,Alexis Groppi,Florence Hantraye,Christophe Hennequin,Nicolas Jauniaux,Philippe Joyet,Rym Kachouri,Alix Kerrest,Romain Koszul,Marc Lemaire,Isabelle Lesur,Laurence Ma,Héloïse Muller,Jean-Marc Nicaud,Macha Nikolski,Sophie Oztas,Odile Ozier-Kalogeropoulos,Stefan Pellenz,Serge Potier,Guy-Franck Richard,Marie-Laure Straub,Audrey Suleau,Dominique Swennen,Fredj Tekaia,Micheline Wésolowski-Louvel,Eric Westhof,Bénédicte Wirth,Maria Zeniou-Meyer,Ivan Zivanovic,Monique Bolotin-Fukuhara,Agnès Thierry,Christiane Bouchier,Bernard Caudron,Claude Scarpelli,Claude Gaillardin,Jean Weissenbach,Patrick Wincker,Jean-Luc Souciet +66 more
TL;DR: Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss.
Journal ArticleDOI
Phylogenetic Classification and the Universal Tree
TL;DR: Molecular phylogeneticists will have failed to find the “true tree,” not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree.