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Approximately 90% of Arabidopsis' unique gene content is found in syntenic blocks that were formed during the most recent whole-genome duplication. Within these blocks, 28.6% of the genes have a retained pair; the remaining genes have been lost from one of the homeologs. We create a minimized genome by condensing local duplications to one gene, removing(More)
Recovery of ribosomal small subunit genes by assembly of short read community DNA sequence data generally fails, making taxonomic characterization difficult. Here, we solve this problem with a novel iterative method, based on the expectation maximization algorithm, that reconstructs full-length small subunit gene sequences and provides estimates of relative(More)
Gamma-Ray Bursts (GRBs) directed at Earth from within a few kpc may have damaged the biosphere, primarily though changes in atmospheric chemistry which admit greatly increased Solar UV. However, GRBs are highly variable in spectrum and duration. Recent observations indicate that short (~0.1 s) burst GRBs, which have harder spectra, may be sufficiently(More)
BACKGROUND Sediments are massive reservoirs of carbon compounds and host a large fraction of microbial life. Microorganisms within terrestrial aquifer sediments control buried organic carbon turnover, degrade organic contaminants, and impact drinking water quality. Recent 16S rRNA gene profiling indicates that members of the bacterial phylum Chloroflexi are(More)
BACKGROUND Analyses of DNA sequences from cultivated microorganisms have revealed genome-wide, taxa-specific nucleotide compositional characteristics, referred to as genome signatures. These signatures have far-reaching implications for understanding genome evolution and potential application in classification of metagenomic sequence fragments. However,(More)
BD1-5, OP11, and OD1 bacteria have been widely detected in anaerobic environments, but their metabolisms remain unclear owing to lack of cultivated representatives and minimal genomic sampling. We uncovered metabolic characteristics for members of these phyla, and a new lineage, PER, via cultivation-independent recovery of 49 partial to near-complete(More)
BACKGROUND Archaea represent a significant fraction of Earth's biodiversity, yet they remain much less well understood than Bacteria. Gene surveys, a few metagenomic studies, and some single-cell sequencing projects have revealed numerous little-studied archaeal phyla. Certain lineages appear to branch deeply and may be part of a major phylum radiation. The(More)
Gamma-ray bursts (hereafter GRB) produce a flux of radiation detectable across the observable Universe. A GRB within our own galaxy could do considerable damage to the Earth's biosphere; rate estimates suggest that a dangerously near GRB should occur on average two or more times per billion years. At least five times in the history of life, the Earth(More)
Gamma-Ray Bursts (GRBs) are likely to have made a number of significant impacts on the Earth during the last billion years. The gamma radiation from a burst within a few kpc would quickly deplete much of the Earth's protective ozone layer, allowing an increase in solar UVB radiation reaching the surface. This radiation is harmful to life, damaging DNA and(More)
Abstrac.t-Based on the intensity and rates of various kinds of intense ionizing radiation events such as supernovae and gamma-ray bursts, it is likely that the Earth has been subjected to one or more events of potential mass extinction level intensity during the Phanerozoic. These induce changes in atmospheric chemistry so that the level of Solar(More)