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    1. Ecology
    2. Genetics and Genomics

    Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

    Simon Roux, Steven J Hallam ... Matthew B Sullivan
    From public microbial genomes, VirSorter revealed 12,498 viral genome sequences that expand the map of the global virosphere and whose analyses improve understanding of viral taxonomy, evolution and virus-host interactions.
    1. Evolutionary Biology
    2. Genetics and Genomics

    A timeline of bacterial and archaeal diversification in the ocean

    Carolina A Martinez-Gutierrez, Josef C Uyeda, Frank O Aylward
    Phylogenomics reveals the timeline over which marine bacteria and archaea colonized the oceans and shows the geological context of their diversification.
    1. Evolutionary Biology

    The evolutionary mechanism of non-carbapenemase carbapenem-resistant phenotypes in Klebsiella spp

    Natalia C Rosas, Jonathan Wilksch ... Trevor Lithgow
    Genetic, phenotypic, and evolutionary analysis of a clinical isolate provides an explanation of the intricate genetic factors behind non-carbapenemase carbapenem resistance and sheds light on the evolutionary mechanisms that influence the molecular basis of antibiotic resistance.
    1. Ecology

    Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment

    Jordan G Okie, Amisha T Poret-Peterson ... James J Elser
    Trait-based metagenomic analysis of an ecosystem fertilization experiment shows that genomic traits that affect the costs and rates of biochemical information-processing mediate community assembly.
    1. Chromosomes and Gene Expression
    2. Evolutionary Biology

    The emergence and evolution of gene expression in genome regions replete with regulatory motifs

    Timothy Fuqua, Yiqiao Sun, Andreas Wagner
    Mutagenizing sequences enriched with promoter motifs creates gene expression de novo, and helps to understand promoter logic, regulatory evolution, and the birth of de novo genes.
    1. Developmental Biology
    2. Evolutionary Biology

    Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals

    Alex de Mendoza, Hiroshi Suga ... Iñaki Ruiz-Trillo
    Functional genomics reveal complex genome regulation during the coenocytic development of the ichthyosporean Creolimax fragrantissima, a protist closely related to animals.
    1. Ecology
    2. Evolutionary Biology

    Does diversity beget diversity in microbiomes?

    Naïma Madi, Michiel Vos ... B Jesse Shapiro
    Microbiomediversity favors further diversity in a positive feedback that is strongest in lower-diversity biomes but which plateaus as niches are increasingly filled in higher-diversity biomes.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity

    Gurmeet Kaur, A Maxwell Burroughs ... L Aravind
    Multicellular and socially aggregating prokaryotes contain previously undescribed, chaperone-based systems predicted to mediate defensive biological conflicts, several components of which are thematically similar antecedents of eukaryotic apoptosis pathways.
    1. Structural Biology and Molecular Biophysics
    2. Computational and Systems Biology

    Prediction of enzymatic pathways by integrative pathway mapping

    Sara Calhoun, Magdalena Korczynska ... Andrej Sali
    A computational method identifies the functions of orphan enzymes by organizing them into metabolic pathways; the prediction of a new l-gulonate catabolic pathway is experimentally tested and confirmed.
    1. Cell Biology

    Endosymbiotic selective pressure at the origin of eukaryotic cell biology

    Parth K Raval, Sriram G Garg, Sven B Gould
    All the characteristic traits of the eukaryotic cell, the basic unit of all macroscopic life, commenced to originate in a prokaryote as means to serve an endosymbiont today known as mitochondria.