Genome evolution and evolutionary systems biology

Section edited by Maria Anisimova, Arndt von Haeseler and David Liberles

This section considers studies on genome evolution and systems biology approaches to determining evolutionary processes.

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  1. Research article

    Reconstruction of the evolution of microbial defense systems

    Evolution of bacterial and archaeal genomes is a highly dynamic process that involves intensive loss of genes as well as gene gain via horizontal transfer, with a lesser contribution from gene duplication. The...

    Pere Puigbò, Kira S. Makarova, David M. Kristensen, Yuri I. Wolf and Eugene V. Koonin

    BMC Evolutionary Biology 2017 17:94

    Published on: 4 April 2017

  2. Research article

    Evolutionary origin and function of NOX4-art, an arthropod specific NADPH oxidase

    NADPH oxidases (NOX) are ROS producing enzymes that perform essential roles in cell physiology, including cell signaling and antimicrobial defense. This gene family is present in most eukaryotes, suggesting a ...

    Ana Caroline Paiva Gandara, André Torres, Ana Cristina Bahia, Pedro L. Oliveira and Renata Schama

    BMC Evolutionary Biology 2017 17:92

    Published on: 29 March 2017

  3. Research article

    Surface layer proteins from virulent Clostridium difficile ribotypes exhibit signatures of positive selection with consequences for innate immune response

    Clostridium difficile is a nosocomial pathogen prevalent in hospitals worldwide and increasingly common in the community. Sequence differences have been shown to be present in the Surf...

    Mark Lynch, Thomas A. Walsh, Izabela Marszalowska, Andrew E. Webb, Micheál MacAogain, Thomas R. Rogers, Henry Windle, Dermot Kelleher, Mary J. O’Connell and Christine E. Loscher

    BMC Evolutionary Biology 2017 17:90

    Published on: 23 March 2017

    The Erratum to this article has been published in BMC Evolutionary Biology 2017 17:135

  4. Research article

    Evolution of group I introns in Porifera: new evidence for intron mobility and implications for DNA barcoding

    Mitochondrial introns intermit coding regions of genes and feature characteristic secondary structures and splicing mechanisms. In metazoans, mitochondrial introns have only been detected in sponges, cnidarian...

    Astrid Schuster, Jose V. Lopez, Leontine E. Becking, Michelle Kelly, Shirley A. Pomponi, Gert Wörheide, Dirk Erpenbeck and Paco Cárdenas

    BMC Evolutionary Biology 2017 17:82

    Published on: 20 March 2017

  5. Research Article

    Evolution of evolvability and phenotypic plasticity in virtual cells

    Changing environmental conditions pose a challenge for the survival of species. To meet this challenge organisms adapt their phenotype by physiological regulation (phenotypic plasticity) or by evolving. Regula...

    Thomas D. Cuypers, Jacob P. Rutten and Paulien Hogeweg

    BMC Evolutionary Biology 2017 17:60

    Published on: 28 February 2017

  6. Research article

    A genome-wide scan for genes under balancing selection in Drosophila melanogaster

    In the history of population genetics balancing selection has been considered as an important evolutionary force, yet until today little is known about its abundance and its effect on patterns of genetic diver...

    Myriam Croze, Andreas Wollstein, Vedran Božičević, Daniel Živković, Wolfgang Stephan and Stephan Hutter

    BMC Evolutionary Biology 2017 17:15

    Published on: 13 January 2017

  7. Research article

    Genome-wide analyses of chitin synthases identify horizontal gene transfers towards bacteria and allow a robust and unifying classification into fungi

    Chitin, the second most abundant biopolymer on earth after cellulose, is found in probably all fungi, many animals (mainly invertebrates), several protists and a few algae, playing an essential role in the dev...

    Isabelle R. Gonçalves, Sophie Brouillet, Marie-Christine Soulié, Simonetta Gribaldo, Catherine Sirven, Noémie Charron, Martine Boccara and Mathias Choquer

    BMC Evolutionary Biology 2016 16:252

    Published on: 24 November 2016

  8. Research article

    Structural differences and differential expression among rhabdomeric opsins reveal functional change after gene duplication in the bay scallop, Argopecten irradians (Pectinidae)

    Opsins are the only class of proteins used for light perception in image-forming eyes. Gene duplication and subsequent functional divergence of opsins have played an important role in expanding photoreceptive ...

    Anita J. Porath-Krause, Autum N. Pairett, Davide Faggionato, Bhagyashree S. Birla, Kannan Sankar and Jeanne M. Serb

    BMC Evolutionary Biology 2016 16:250

    Published on: 17 November 2016

  9. Research article

    Development of a toolbox to dissect host-endosymbiont interactions and protein trafficking in the trypanosomatid Angomonas deanei

    Bacterial endosymbionts are found across the eukaryotic kingdom and profoundly impacted eukaryote evolution. In many endosymbiotic associations with vertically inherited symbionts, highly complementary metabol...

    Jorge Morales, Sofia Kokkori, Diana Weidauer, Jarrod Chapman, Eugene Goltsman, Daniel Rokhsar, Arthur R. Grossman and Eva C. M. Nowack

    BMC Evolutionary Biology 2016 16:247

    Published on: 11 November 2016

  10. Research article

    Spatial pattern of genetic diversity and selection in the MHC class II DRB of three Neotropical bat species

    Although bats are natural reservoirs of many pathogens, few studies have been conducted on the genetic variation and detection of selection in major histocompatibility complex (MHC) genes. These genes are crit...

    Arielle Salmier, Benoit de Thoisy, Brigitte Crouau-Roy, Vincent Lacoste and Anne Lavergne

    BMC Evolutionary Biology 2016 16:229

    Published on: 26 October 2016

  11. Research article

    The evolutionally-conserved function of group B1 Sox family members confers the unique role of Sox2 in mouse ES cells

    In mouse ES cells, the function of Sox2 is essential for the maintenance of pluripotency. Since the Sox-family of transcription factors are well conserved in the animal kingdom, addressing the evolutionary ori...

    Hitoshi Niwa, Akira Nakamura, Makoto Urata, Maki Shirae-Kurabayashi, Shigehiro Kuraku, Steven Russell and Satoshi Ohtsuka

    BMC Evolutionary Biology 2016 16:173

    Published on: 31 August 2016

  12. Research Article

    First insights into the nature and evolution of antisense transcription in nematodes

    The development of multicellular organisms is coordinated by various gene regulatory mechanisms that ensure correct spatio-temporal patterns of gene expression. Recently, the role of antisense transcription in...

    Christian Rödelsperger, Kevin Menden, Vahan Serobyan, Hanh Witte and Praveen Baskaran

    BMC Evolutionary Biology 2016 16:165

    Published on: 22 August 2016

  13. Research article

    Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment

    Predicting adaptive trajectories is a major goal of evolutionary biology and useful for practical applications. Systems biology has enabled the development of genome-scale metabolic models. However, analysing ...

    Tobias Großkopf, Jessika Consuegra, Joël Gaffé, John C. Willison, Richard E. Lenski, Orkun S. Soyer and Dominique Schneider

    BMC Evolutionary Biology 2016 16:163

    Published on: 20 August 2016

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