Welcome to pandoraviruses at the 'Fourth TRUC’ club by Vikas eSharma, Vikas eSharma, Philippe eColson, Philippe eColson, Olivier eChabrol, Patrick eScheid, Pierre ePontarotti, Didier eRaoult, Didier eRaoult

“…Megaviruses have been previously described to comprise a fourth monophylogenetic TRUC (Things Resisting Uncompleted Classification) together with cellular domains in the universal tree of life. Recently described pandoraviruses have large (1.9-2.5 MB) and highly divergent genomes. …”
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Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities by Chistoserdov Andrei, Rodriguez-Mora Maria J, Amaral-Zettler Linda, Christen Richard, Behnke Anke, Stoeck Thorsten, Orsi William, Edgcomb Virginia P

“…</p> <p>Conclusion</p> <p>Our data highlight the magnitude of the under-sampled 'protistan gap' in the eukaryotic tree of life. This study illustrates that our current understanding of the ecological complexity of protist communities, and of the global species richness and genome diversity of protists, is severely limited. …”
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In Streptococcus thermophilus, Ammonia from Urea Hydrolysis Paradoxically Boosts Acidification and Reveals a New Regulatory Mechanism of Glycolysis by Stefania Arioli, Giulia Della Scala, Anđela Martinović, Leonardo Scaglioni, Stefania Mazzini, Federica Volonté, Martin Bastian Pedersen, Diego Mora

“…Apart from S. thermophilus, due to the high conservation of glycolytic enzymes in all branches of the tree of life and being aware of the role of ammonia as an effector of phosphofructokinase, we propose to reevaluate the physiological role of the ammonia production pathways in all organisms whose energy metabolism is supported by glycolysis.…”
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Cytokinin and Ethylene Cell Signaling Pathways from Prokaryotes to Eukaryotes by Baptiste Bidon, Samar Kabbara, Vincent Courdavault, Gaëlle Glévarec, Audrey Oudin, François Héricourt, Sabine Carpin, Lukáš Spíchal, Brad M. Binder, J. Mark Cock, Nicolas Papon

“…These considerations have now been called into question following the identification over recent years of genes encoding CK and ET receptor homologs in many other lineages within the tree of life. These advances shed new light on the dissemination and evolution of these hormones as both intra- and inter-specific communication molecules in prokaryotic and eukaryotic organisms.…”
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Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities by Kelly Gravuer, Anu Eskelinen, Anu Eskelinen, Anu Eskelinen, Anu Eskelinen

“…Estimated trait responses within several phyla were opposite to the community mean response, indicating that microbial responses, although largely consistent among soil types, were not uniform across the tree of life. Our results show that phylogenetic estimation of microbial traits can provide insight into how microbial ecological strategies interact with environmental changes. …”
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Cobamide Sharing Is Predicted in the Human Skin Microbiome by Mary Hannah Swaney, Shelby Sandstrom, Lindsay R. Kalan

“…Cobamides, the vitamin B12 class of cofactor, are essential for organisms across the tree of life. Because this vitamin is only produced by a limited fraction of prokaryotes, cobamide sharing is predicted to mediate community dynamics within microbial communities. …”
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Rapid Cis–Trans Coevolution Driven by a Novel Gene Retroposed from a Eukaryotic Conserved CCR4–NOT Component in <i>Drosophila</i> by Benjamin H. Krinsky, Robert K. Arthur, Shengqian Xia, Dylan Sosa, Deanna Arsala, Kevin P. White, Manyuan Long

“…Young, or newly evolved, genes arise ubiquitously across the tree of life, and they can rapidly acquire novel functions that influence a diverse array of biological processes. …”
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Exploration of the Germline Genome of the Ciliate <italic toggle="yes">Chilodonella uncinata</italic> through Single-Cell Omics (Transcriptomics and Genomics) by Xyrus X. Maurer-Alcalá, Rob Knight, Laura A. Katz

“…ABSTRACT Separate germline and somatic genomes are found in numerous lineages across the eukaryotic tree of life, often separated into distinct tissues (e.g., in plants, animals, and fungi) or distinct nuclei sharing a common cytoplasm (e.g., in ciliates and some foraminifera). …”
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Chloroplast genome sequencing analysis of <it>Heterosigma akashiwo </it>CCMP452 (West Atlantic) and NIES293 (West Pacific) strains by Lybrand Terry, Duplessis Melinda, Chang Jean, Zhou Yang, Jacobs Michael A, Cattolico Rose, McKay John, Ong Han, Sims Elizabeth, Rocap Gabrielle

“…<p>Abstract</p> <p>Background</p> <p>Heterokont algae form a monophyletic group within the stramenopile branch of the tree of life. These organisms display wide morphological diversity, ranging from minute unicells to massive, bladed forms. …”
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Lords of the biosphere: Plant winners and losers in the Anthropocene by W. John Kress, Gary A. Krupnick

“…Societal Impact Statement The impact of humans on Earth's biodiversity varies across the Tree of Life. The extirpation and extinction of species is often determined by compatibility with human activities. …”
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Range expansion promotes cooperation in an experimental microbial metapopulation by Datta, Manoshi Sen, Korolev, Kirill Sergeevich, Dudley, Carmel R., Gore, Jeff, Cvijovic, Ivana

“…Natural populations throughout the tree of life undergo range expansions in response to changes in the environment. …”
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Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss by Bansal, Mukul S., Alm, Eric J., Kellis, Manolis

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Social interactions in bacteria mediated by bacteriocins and horizontal gene transfer by Thomas, JL

“…In my thesis, I aim to expand our understanding of bacterial sociality in natural populations and further across the bacterial tree of life. I do this using two different approaches. …”

Impact of Rearing Conditions on the Ambrosia Beetle’s Microbiome by Luis Arturo Ibarra-Juarez, Damaris Desgarennes, Mirna Vázquez-Rosas-Landa, Emanuel Villafan, Alexandro Alonso-Sánchez, Ofelia Ferrera-Rodríguez, Andrés Moya, Daniel Carrillo, Luisa Cruz, Gloria Carrión, Abel López-Buenfil, Clemente García-Avila, Enrique Ibarra-Laclette, Araceli Lamelas

“…Ambrosia beetles, along with termites and leafcutter ants, are the only fungus-farming lineages within the tree of life. Bacteria harbored by ambrosia beetles may play an essential role in the nutritional symbiotic interactions with their associated fungi; however, little is known about the impact of rearing conditions on the microbiota of ambrosia beetles. …”
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Single-Cell Transcriptomics Reveal a Correlation between Genome Architecture and Gene Family Evolution in Ciliates by Ying Yan, Xyrus X. Maurer-Alcalá, Rob Knight, Sergei L. Kosakovsky Pond, Laura A. Katz

“…We combine single-cell transcriptomics with bioinformatic tools, focusing on understudied and uncultivable lineages selected from across the ciliate tree of life. Our analyses show that genome architecture correlates with patterns of protein evolution as lineages with more canonical somatic genomes, such as the class Karyorelictea, have more conserved patterns of molecular evolution compared to other classes. …”
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The genome sequence of the eastern grey squirrel, Sciurus carolinensis Gmelin, 1788 [version 1; peer review: 2 approved] by Dan Mead, Kathryn Fingland, Rachel Cripps, Roberto Portela Miguez, Michelle Smith, Craig Corton, Karen Oliver, Jason Skelton, Emma Betteridge, Jale Doulcan, Michael A. Quail, Shane A. McCarthy, Kerstin Howe, Ying Sims, James Torrance, Alan Tracey, Richard Challis, Richard Durbin, Mark Blaxter

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A sampling strategy for genome sequencing the British terrestrial arthropod fauna [version 1; peer review: 2 approved] by Craig R. Macadam, Ian Barnes, Heather Allen, Christopher Fletcher, Gavin R. Broad, Inez Januszczak, Peter W.H. Holland, Peter O. Mulhair, Owen T. Lewis, Benjamin W. Price, Lyndall Pereira da Conceicoa, Laura Sivess, Chris Raper, Liam Crowley, Olga Sivell, Mara Lawniczak, Douglas Boyes

“…The Darwin Tree of Life (DToL) project aims to sequence and assemble high-quality genomes from all eukaryote species in Britain and Ireland, with the first phase of the project concentrating on family-level coverage plus species of particular ecological, biomedical or evolutionary interest. …”
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The Parameter-Fitness Landscape of <italic toggle="yes">lexA</italic> Autoregulation in <named-content content-type="genus-species">Escherichia coli</named-content> by Beverley C. Kozuch, Marla G. Shaffer, Matthew J. Culyba

“…NAR is common across the tree of life, enabling rapid homeostatic control of gene expression. …”
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Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae) by Kevin Debray, Jordan Marie-Magdelaine, Tom Ruttink, Jérémy Clotault, Fabrice Foucher, Valéry Malécot

“…Abstract Background With an ever-growing number of published genomes, many low levels of the Tree of Life now contain several species with enough molecular data to perform shallow-scale phylogenomic studies. …”
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Visualization of Lokiarchaeia and Heimdallarchaeia (Asgardarchaeota) by Fluorescence <italic toggle="yes">In Situ</italic> Hybridization and Catalyzed Reporter Deposition (CARD-FIS... by Michaela M. Salcher, Adrian-Ştefan Andrei, Paul-Adrian Bulzu, Zsolt G. Keresztes, Horia L. Banciu, Rohit Ghai

“…Despite their singular phylogenetic position at the base of the eukaryotic tree of life, the morphology of these bewildering organisms remains a mystery, except for the report of an unusual morphology with long, branching protrusions of the cultivated Lokiarchaeion strain “Candidatus Prometheoarchaeum syntrophicum” MK-D1. …”
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