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Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution


e-ISSN: 1759-6653

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An ABC Method for Estimating the Rate and Distribution of Effects of Beneficial Mutations

Jorge A. Moura de Sousa, Paulo R.A. Campos and Isabel Gordo.

in Genome Biology and Evolution

January 2013; p ublished online March 2013 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Evolutionary Biology; Genetics and Genomics. 7289 words.

Determining the distribution of adaptive mutations available to natural selection is a difficult task. These are rare events and most of them are lost by chance. Some theoretical works...

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Abundant Degenerate Miniature Inverted-Repeat Transposable Elements in Genomes of Epichloid Fungal Endophytes of Grasses

Damien J. Fleetwood, Anar K. Khan, Richard D. Johnson, Carolyn A. Young, Shipra Mittal, Ruth E. Wrenn, Uljana Hesse, Simon J. Foster, Christopher L. Schardl and Barry Scott.

in Genome Biology and Evolution

January 2011; p ublished online September 2011 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Evolutionary Biology; Genetics and Genomics. 7668 words.

Miniature inverted-repeat transposable elements (MITEs) are abundant repeat elements in plant and animal genomes; however, there are few analyses of these elements in fungal genomes....

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Abundant Gene-by-Environment Interactions in Gene Expression Reaction Norms to Copper within <i>Saccharomyces cerevisiae</i>

Andrea Hodgins-Davis, Aleksandra B. Adomas, Jonas Warringer and Jeffrey P. Townsend.

in Genome Biology and Evolution

January 2012; p ublished online September 2012 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Evolutionary Biology; Genetics and Genomics. 11569 words.

Genetic variation for plastic phenotypes potentially contributes phenotypic variation to populations that can be selected during adaptation to novel ecological contexts. However, the basis...

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Abundant Gene-by-Environment Interactions in Gene Expression Reaction Norms to Copper within Saccharomyces cerevisiae

Andrea Hodgins-Davis, Aleksandra B. Adomas, Jonas Warringer and Jeffrey P. Townsend.

in Genome Biology and Evolution

January 2012; p ublished online November 2012 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Evolutionary Biology; Genetics and Genomics. 103 words.

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Abundant Indispensable Redundancies in Cellular Metabolic Networks

Zhi Wang and Jianzhi Zhang.

in Genome Biology and Evolution

January 2009; p ublished online April 2009 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Evolutionary Biology; Genetics and Genomics. 8442 words.

Cellular life is a highly redundant complex system; yet, the evolutionary maintenance of the redundancy remains unexplained. Using a systems biology approach, we infer that 37–47% of...

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Accelerated Evolution of Schistosome Genes Coding for Proteins Located at the Host–Parasite Interface

Gisele S. Philippsen, R. Alan Wilson and Ricardo DeMarco.

in Genome Biology and Evolution

P ublished online January 2015 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Evolutionary Biology; Genetics and Genomics. 8554 words.

Study of proteins located at the host–parasite interface in schistosomes might provide clues about the mechanisms utilized by the parasite to escape the host immune system attack....

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Accumulation and Rapid Decay of Non-LTR Retrotransposons in the Genome of the Three-Spine Stickleback

Eryn Blass, Michael Bell and Stéphane Boissinot.

in Genome Biology and Evolution

January 2012; p ublished online April 2012 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Evolutionary Biology; Genetics and Genomics. 6708 words.

The diversity and abundance of non–long terminal repeat (LTR) retrotransposons (nLTR-RT) differ drastically among vertebrate genomes. At one extreme, the genome of placental mammals is...

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The Accumulation of Gene Regulation Through Time

Maria Warnefors and Adam Eyre-Walker.

in Genome Biology and Evolution

January 2011; p ublished online March 2011 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Evolutionary Biology; Genetics and Genomics. 3086 words.

Gene expression is governed by an intricate combination of transcription factors (TFs), microRNAs (miRNAs), splicing factors, and other regulators. Genes cannot support infinitely complex...

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Accurate Transposable Element Annotation Is Vital When Analyzing New Genome Assemblies

Roy N. Platt, Laura Blanco-Berdugo and David A. Ray.

in Genome Biology and Evolution

P ublished online January 2016 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Evolutionary Biology; Genetics and Genomics. 5034 words.

Transposable elements (TEs) are mobile genetic elements with the ability to replicate themselves throughout the host genome. In some taxa TEs reach copy numbers in hundreds of thousands and...

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Acetic Acid Bacteria Genomes Reveal Functional Traits for Adaptation to Life in Insect Guts

Bessem Chouaia, Stefano Gaiarsa, Elena Crotti, Francesco Comandatore, Mauro Degli Esposti, Irene Ricci, Alberto Alma, Guido Favia, Claudio Bandi and Daniele Daffonchio.

in Genome Biology and Evolution

P ublished online March 2014 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Evolutionary Biology; Genetics and Genomics. 3514 words.

Acetic acid bacteria (AAB) live in sugar rich environments, including food matrices, plant tissues, and the gut of sugar-feeding insects. By comparing the newly sequenced genomes of Asaia...

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Adaptation to Low Salinity Promotes Genomic Divergence in Atlantic Cod (<i>Gadus morhua</i> L.)

Paul R. Berg, Sissel Jentoft, Bastiaan Star, Kristoffer H. Ring, Halvor Knutsen, Sigbjørn Lien, Kjetill S. Jakobsen and Carl André.

in Genome Biology and Evolution

P ublished online May 2015 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Evolutionary Biology; Genetics and Genomics. 13148 words.

How genomic selection enables species to adapt to divergent environments is a fundamental question in ecology and evolution. We investigated the genomic signatures of local adaptation in...

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An Advanced System of the Mitochondrial Processing Peptidase and Core Protein Family in <i>Trypanosoma brucei</i> and Multiple Origins of the Core I Subunit in Eukaryotes

Jan Mach, Pavel Poliak, Anna Matušková, Vojtěch Žárský, Jiří Janata, Julius Lukeš and Jan Tachezy.

in Genome Biology and Evolution

January 2013; p ublished online April 2013 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Evolutionary Biology; Genetics and Genomics. 8660 words.

Mitochondrial processing peptidase (MPP) consists of α and β subunits that catalyze the cleavage of N-terminal mitochondrial-targeting sequences (N-MTSs) and deliver preproteins to the...

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Alarmingly High Segregation Frequencies of Quinolone Resistance Alleles within Human and Animal Microbiomes Are Not Explained by Direct Clinical Antibiotic Exposure

Wesley Field and Ruth Hershberg.

in Genome Biology and Evolution

P ublished online May 2015 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Evolutionary Biology; Genetics and Genomics. 8704 words.

Antibiotic resistance poses a major threat to human health. It is therefore important to characterize the frequency of resistance within natural bacterial environments. Many studies have...

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Albuminoid Genes: Evolving at the Interface of Dispensability and Selection

Alessandra Mozzi, Diego Forni, Rachele Cagliani, Uberto Pozzoli, Jacopo Vertemara, Nereo Bresolin and Manuela Sironi.

in Genome Biology and Evolution

P ublished online October 2014 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Evolutionary Biology; Genetics and Genomics. 8771 words.

The albuminoid gene family comprises vitamin D-binding protein (GC), alpha-fetoprotein (AFP), afamin (AFM), and albumin (ALB). Albumin is the most abundant human serum protein, and, as the...

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Algae Sense Exact Temperatures: Small Heat Shock Proteins Are Expressed at the Survival Threshold Temperature in <i>Cyanidioschyzon merolae</i> and <i>Chlamydomonas reinhardtii</i>

Yusuke Kobayashi, Naomi Harada, Yoshiki Nishimura, Takafumi Saito, Mami Nakamura, Takayuki Fujiwara, Tsuneyoshi Kuroiwa and Osami Misumi.

in Genome Biology and Evolution

P ublished online September 2014 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Evolutionary Biology; Genetics and Genomics. 5428 words.

The primitive red alga Cyanidioschyzon merolae inhabits acidic hot springs and shows robust resistance to heat shock treatments up to 63 °C. Microarray analysis was performed to identify...

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Alternative Processing as Evolutionary Mechanism for the Origin of Novel Nonprotein Coding RNAs

Dingding Mo, Carsten A. Raabe, Richard Reinhardt, Juergen Brosius and Timofey S. Rozhdestvensky.

in Genome Biology and Evolution

January 2013; p ublished online October 2013 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Evolutionary Biology; Genetics and Genomics. 6919 words.

The evolution of new genes can ensue through either gene duplication and the neofunctionalization of one of the copies or the formation of a de novo gene from hitherto nonfunctional,...

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Analyses of Charophyte Chloroplast Genomes Help Characterize the Ancestral Chloroplast Genome of Land Plants

Peter Civáň, Peter G. Foster, Martin T. Embley, Ana Séneca and Cymon J. Cox.

in Genome Biology and Evolution

P ublished online March 2014 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Evolutionary Biology; Genetics and Genomics. 8703 words.

Despite the significance of the relationships between embryophytes and their charophyte algal ancestors in deciphering the origin and evolutionary success of land plants, few chloroplast...

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Analyses of Corallimorpharian Transcriptomes Provide New Perspectives on the Evolution of Calcification in the Scleractinia (Corals)

Mei-Fang Lin, Aurelie Moya, Hua Ying, Chaolun Allen Chen, Ira Cooke, Eldon E. Ball, Sylvain Forêt and David J. Miller.

in Genome Biology and Evolution

P ublished online January 2017 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Evolutionary Biology; Genetics and Genomics. 5682 words.

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Analyses of Nuclearly Encoded Mitochondrial Genes Suggest Gene Duplication as a Mechanism for Resolving Intralocus Sexually Antagonistic Conflict in Drosophila

Miguel Gallach, Chitra Chandrasekaran and Esther Betrán.

in Genome Biology and Evolution

January 2010; p ublished online October 2010 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Evolutionary Biology; Genetics and Genomics. 10104 words.

Gene duplication is probably the most important mechanism for generating new gene functions. However, gene duplication has been overlooked as a potentially effective way to resolve genetic...

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Analysis of Coevolving Gene Families Using Mutually Exclusive Orthologous Modules

Xiuwei Zhang, Martin Kupiec, Uri Gophna and Tamir Tuller.

in Genome Biology and Evolution

January 2011; p ublished online April 2011 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Evolutionary Biology; Genetics and Genomics. 6152 words.

Coevolutionary networks can encapsulate information about the dynamics of presence and absence of gene families in organisms. Analysis of such networks should reveal fundamental principles...

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