Genome Biology

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The gain and loss of genes during 600 million years of vertebrate evolution

Tine Blomme, Klaas Vandepoele, Stefanie De Bodt, Cedric Simillion, Steven Maere and Yves Van de Peer*

Genome Biology 2006, 7:R43 doi:10.1186/gb-2006-7-5-r43

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Research article   Open Access

A synthetic rainbow trout linkage map provides new insights into the salmonid whole genome duplication and the conservation of synteny among teleosts

Rene Guyomard, Mekki Boussaha, Francine Krieg, Caroline Hervet, Edwige Quillet BMC Genetics 2012, 13:15 (16 March 2012)

Research article   Open Access

The odds of duplicate gene persistence after polyploidization

Frédéric JJ Chain, Jonathan Dushoff, Ben J Evans BMC Genomics 2011, 12:599 (12 December 2011)

Research   Open Access Highly Accessed

RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.)

Caroline Pont, Florent Murat, Carole Confolent, Sandrine Balzergue, Jérôme Salse Genome Biology 2011, 12:R119 (2 December 2011)

Transcriptomics reveals the evolutionary trajectory of polyploidization, with insights into gene networks and genome organization

Proceedings   Open Access

Evolution of orthologous tandemly arrayed gene clusters

Olivier Tremblay Savard, Denis Bertrand, Nadia El-Mabrouk BMC Bioinformatics 2011, 12(Suppl 9):S2 (5 October 2011)

Research article   Open Access

The Potential for pathogenicity was present in the ancestor of the Ascomycete subphylum Pezizomycotina

Aminael Sánchez-Rodríguez, Cindy Martens, Kristof Engelen, Yves Van de Peer, Kathleen Marchal BMC Evolutionary Biology 2010, 10:318 (21 October 2010)

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Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants

Xiaofan Zhou, Zhenguo Lin, Hong Ma Genome Biology 2010, 11:R38 (6 April 2010)

A phylogentic analysis reveals that many gene duplications occurred prior to the split in animals, fungi and plants.

Research   Open Access Highly Accessed

2× genomes - depth does matter

Michel C Milinkovitch, Raphaël Helaers, Eric Depiereux, Athanasia C Tzika, Toni Gabaldón Genome Biology 2010, 11:R16 (9 February 2010)

The use of low coverage genomes in comparative evolutionary analyses skews estimates of gene gains and losses.

Software   Open Access Highly Accessed

PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees

Philippe Gouret, Julie D Thompson, Pierre Pontarotti BMC Bioinformatics 2009, 10:298 (19 September 2009)

Research   Open Access

Variation in gene duplicates with low synonymous divergence in Saccharomyces cerevisiae relative to Caenorhabditis elegans

Vaishali Katju, James C Farslow, Ulfar Bergthorsson Genome Biology 2009, 10:R75 (13 July 2009)

Differences between yeast and worm duplicates result from differences in mechanisms of duplication and effective population size.

Research article   Open Access

Comparative genomics and evolution of conserved noncoding elements (CNE) in rainbow trout

Hooman K Moghadam, Moira M Ferguson, Roy G Danzmann BMC Genomics 2009, 10:278 (23 June 2009)

Research article   Open Access

Temporal pattern of loss/persistence of duplicate genes involved in signal transduction and metabolic pathways after teleost-specific genome duplication

Yukuto Sato, Yasuyuki Hashiguchi, Mutsumi Nishida BMC Evolutionary Biology 2009, 9:127 (5 June 2009)

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Phylogeny and evolution of Rab7 and Rab9 proteins

Paweł Mackiewicz, Elżbieta Wyroba BMC Evolutionary Biology 2009, 9:101 (14 May 2009)

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The apoptotic machinery as a biological complex system: analysis of its omics and evolution, identification of candidate genes for fourteen major types of cancer, and experimental validation in CML and neuroblastoma

Cinzia Di Pietro, Marco Ragusa, Davide Barbagallo, Laura R Duro, Maria R Guglielmino, Alessandra Majorana, Rosario Angelica, Marina Scalia, Luisa Statello, Loredana Salito, Luisa Tomasello, Salvo Pernagallo, Salvo Valenti, Vito D'Agostino, Patrizio Triberio, Igor Tandurella, Giuseppe A Palumbo, Piera La Cava, Viviana Cafiso, Taschia Bertuccio, Maria Santagati, Giovanni Li Destri, Salvatore Lanzafame, Francesco Di Raimondo, Stefania Stefani, Bud Mishra, Michele Purrello BMC Medical Genomics 2009, 2:20 (30 April 2009)

Research article   Open Access

Expression profiles of urbilaterian genes uniquely shared between honey bee and vertebrates

Toshiaki Matsui, Toshiyuki Yamamoto, Stefan Wyder, Evgeny M Zdobnov, Tatsuhiko Kadowaki BMC Genomics 2009, 10:17 (12 January 2009)

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Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions

Tomas A Larsson, Frida Olsson, Gorel Sundstrom, Lars-Gustav Lundin, Sydney Brenner, Byrappa Venkatesh, Dan Larhammar BMC Evolutionary Biology 2008, 8:184 (25 June 2008)

Further evidence for two early vertebrate tetraploidization events is revealed by comparative analysis of neuropeptide Y receptor gene regions of pufferfish with those in Drosophila, mouse and humans pointing to gene family expansion via chromosome duplication.

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Loss of genes implicated in gastric function during platypus evolution

Gonzalo R Ordoñez, LaDeana W Hillier, Wesley C Warren, Frank Grützner, Carlos López-Otín, Xose S Puente Genome Biology 2008, 9:R81 (15 May 2008)

Several genes implicated in food digestion have been deleted or inactivated in platypus. This loss perhaps explains the anatomical and physiological differences in the gastrointestinal tract between monotremes and other vertebrates and provides insights into platypus genome evolution.

Research article   Open Access

Expansion of signaling genes for adaptive immune system evolution in early vertebrates

Kinya Okada, Kiyoshi Asai BMC Genomics 2008, 9:218 (14 May 2008)

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Consistent and contrasting properties of lineage-specific genes in the apicomplexan parasites Plasmodium and Theileria

Chih-Horng Kuo, Jessica C Kissinger BMC Evolutionary Biology 2008, 8:108 (11 April 2008)

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Selection of housekeeping genes for gene expression studies in larvae from flatfish using real-time PCR

Carlos Infante, Makoto P Matsuoka, Esther Asensio, José Cañavate, Michael Reith, Manuel Manchado BMC Molecular Biology 2008, 9:28 (6 March 2008)

Research article   Open Access

Evolutionary consequences of a large duplication event in Trypanosoma brucei: Chromosomes 4 and 8 are partial duplicons

Andrew P Jackson BMC Genomics 2007, 8:432 (23 November 2007)

Research   Open Access

Quantification of ortholog losses in insects and vertebrates

Stefan Wyder, Evgenia V Kriventseva, Reinhard Schröder, Tatsuhiko Kadowaki, Evgeny M Zdobnov Genome Biology 2007, 8:R242 (16 November 2007)

Comparison of the gene repertoires of 5 vertebrates and 5 insects showed that the rate of losses correlates well with the species' rates of molecular evolution and radiation times and suggests that the Urbilateria genome contained more than 7,000 genes.

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The limits of subfunctionalization

Thomas MacCarthy, Aviv Bergman BMC Evolutionary Biology 2007, 7:213 (7 November 2007)

Research article   Open Access

Molecular characterization, gene expression and dependence on thyroid hormones of two type I keratin genes (sseKer1 and sseKer2) in the flatfish Senegalese sole (Solea senegalensis Kaup)

Carlos Infante, Manuel Manchado, Esther Asensio, José Cañavate BMC Developmental Biology 2007, 7:118 (23 October 2007)

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Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni

Simone Hoegg, Jeffrey L Boore, Jennifer V Kuehl, Axel Meyer BMC Genomics 2007, 8:317 (10 September 2007)

Comparing Hox gene clusters in Cichlid fish to known Hox genes in other teleosts reveals a surprising level of variation between species and an ongoing process of gene loss.

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Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications

Nicol Siegel, Simone Hoegg, Walter Salzburger, Ingo Braasch, Axel Meyer BMC Genomics 2007, 8:312 (6 September 2007)

Research article   Open Access

Ancient intron insertion sites and palindromic genomic duplication evolutionally shapes an elementally functioning membrane protein family

Motoko Tanaka-Kunishima, Yoshihiro Ishida, Kunitaro Takahashi, Motoo Honda, Takashi Oonuma BMC Evolutionary Biology 2007, 7:143 (20 August 2007)

Research   Open Access

Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution

Matthew W Hahn Genome Biology 2007, 8:R141 (16 July 2007)

A consistent bias in tree reconciliation methods is described that occurs when the inferred gene tree is not correct, casting doubt on previous conclusions about ancient duplications and losses in vertebrate genome history.

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The human phylome

Jaime Huerta-Cepas, Hernán Dopazo, Joaquín Dopazo, Toni Gabaldón Genome Biology 2007, 8:R109 (13 June 2007)

The human phylome, which includes evolutionary relationships of all human proteins and their homologs among thirty-nine fully sequenced eukaryotes, is reconstructed.

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Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia

Timothy Hughes, Diana Ekman, Himanshu Ardawatia, Arne Elofsson, David A Liberles Genome Biology 2007, 8:213 (22 May 2007)

Can dosage compensation completely explain gene retention after whole-genome duplication?

Research article   Open Access

The evolution of the vertebrate metzincins; insights from Ciona intestinalis and Danio rerio

Julie Huxley-Jones, Toni-Kim Clarke, Christine Beck, George Toubaris, David L Robertson, Raymond P Boot-Handford BMC Evolutionary Biology 2007, 7:63 (17 April 2007)