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A new view of the tree of life
New genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, are used to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included. Expand
Unusual biology across a group comprising more than 15% of domain Bacteria
This work reconstructed 8 complete and 789 draft genomes from bacteria representing >35 phyla and documented features that consistently distinguish these organisms from other bacteria, infer that this group, which may comprise >15% of the bacterial domain, has shared evolutionary history, and describe it as the candidate phyla radiation (CPR). Expand
Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes.
It is found that islands of retention contain "connected genes," those genes predicted-by the gene balance hypothesis-to be resistant to removal because the products they encode interact with other products in a dose-sensitive manner, creating a web of dependency. Expand
Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling
This study sequenced DNA from complex sediment and planktonic consortia from an aquifer adjacent to the Colorado River and reconstructed the first complete genomes for Archaea using cultivation-independent methods, which dramatically expand genomic sampling of the domain Archaea and clarify taxonomic designations within a major superphylum. Expand
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
A novel iterative method is proposed, based on the expectation maximization algorithm, that reconstructs full-length small subunit gene sequences and provides estimates of relative taxon abundances in microbial communities. Expand
Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla
Bacterial PERegrinations Many branches of the bacterial domain of life are only known from sequences that turn up in metagenomic analyses and are still only named by acronym—for example, theExpand
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
Terabase-scale cultivation-independent metagenomics is applied to aquifer sediments and groundwater and 2,540 draft-quality, near-complete and complete strain-resolved genomes are reconstructed, finding that few organisms within the community can conduct multiple sequential redox transformations. Expand
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy
A tool that enables a flexible set of existing binning algorithms to be combined, resulting in improved binning accuracy and the recovery of more near-complete genomes from metagenomes compared to standalone methods is presented. Expand
Diverse uncultivated ultra-small bacterial cells in groundwater.
The hypothesis that bacteria from phyla lacking cultivated representatives are small and thus might be enriched by filtration for coupled genomic and ultrastructural characterization is tested. Expand
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria
Cyanobacteria were responsible for the oxygenation of the ancient atmosphere; however, the evolution of this phylum is enigmatic, as relatives have not been characterized. Here we use whole genomeExpand