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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Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals.
Till Bayer,Manuel Aranda,Shinichi Sunagawa,Lauren K. Yum,Michael K. DeSalvo,Erika Lindquist,Mary Alice Coffroth,Christian R. Voolstra,Mónica Medina +8 more
TL;DR: In this paper, the authors used 454 sequencing to generate transcriptome data from two Symbiodinium species from different clades (clade A and clade B) with more than 56,000 assembled sequences per species, these data represent the largest transcriptomic resource for dinoflagellates to date.
Journal ArticleDOI
Insights into the Evolution of Vitamin B12 Auxotrophy from Sequenced Algal Genomes
Katherine E. Helliwell,Glen L. Wheeler,Kyriacos C. Leptos,Raymond E. Goldstein,Alison G. Smith +4 more
TL;DR: Investigating elements of B(12) metabolism in the sequenced genomes of 15 different algal species, with representatives of the red, green, and brown algae, diatoms, and coccolithophores, including both macro- and microalgae, and from marine and freshwater environments found a strong correlation between the absence of a functional METE gene and B( 12) auxotrophy.
Journal ArticleDOI
Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes
Thomas A. Richards,Thomas A. Richards,Darren M. Soanes,Meredith D. M. Jones,Meredith D. M. Jones,Olga Vasieva,Guy Leonard,Guy Leonard,Konrad Paszkiewicz,Peter G. Foster,Neil Hall,Nicholas J. Talbot +11 more
TL;DR: Using whole-genome, gene-by-gene phylogenetic analysis, an extensive pattern of cross-kingdom HGT between fungi and oomycetes is demonstrated, consistent with the hypothesis that some oomyCetes became successful plant parasites by multiple acquisitions of genes from fungi.
Journal ArticleDOI
TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach.
TL;DR: An accurate multi-class taxonomic classifier was developed for environmental genomic fragments TACOA, which can predict with high reliability the taxonomic origin of genomic fragments as short as 800 bp.
Journal ArticleDOI
Endosymbiotic associations within protists.
TL;DR: Endosymbiosis seems to represent a general evolutionary strategy of protists to acquire novel biochemical functions and is thus an important source of genetic innovation.
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.