The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

Reddy, T. B. K.; Thomas, Alex D.; Stamatis, Dimitri; Bertsch, Jon; Isbandi, Michelle; Jansson, Jakob; Mallajosyula, Jyothi; Pagani, Ioanna; Lobos, Elizabeth A.; Kyrpides, Nikos C.

doi:10.1093/nar/gku950

Cited by 303 publications

(251 citation statements)

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“…The fixation probability F can be approximated by FðxÞ ≈ sðxÞ 1 − e −NesðxÞ , [2] where N e is the effective population size (16). The effective population size is estimated for each prokaryotic group from the dN/dS ratio (Methods).…”

Section: Resultsmentioning

confidence: 99%

“…The tight spacing of protein-coding genes likely results from a combination of the deletion bias and purifying selection that efficiently eliminates nonfunctional, noncoding sequences. T he majority of bacterial and archaeal genomes are small, at least compared with the genomes of multicellular and many unicellular eukaryotes (1,2). Also, with the exception of deteriorating genomes of some parasitic bacteria, the prokaryotic genomes are highly compact, with densely packed protein-coding genes and a low fraction of noncoding sequences (3).…”

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confidence: 99%

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Theory of prokaryotic genome evolution

Sela

Wolf

Koonin

2016

Proc. Natl. Acad. Sci. U.S.A.

137

168

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Bacteria and archaea typically possess small genomes that are tightly packed with protein-coding genes. The compactness of prokaryotic genomes is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. Here, by fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. These results suggest that the number of genes in prokaryotic genomes reflects the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias (i.e., the rate of deletion of genetic material being slightly greater than the rate of acquisition). Thus, new genes acquired by microbial genomes, on average, appear to be adaptive. The tight spacing of protein-coding genes likely results from a combination of the deletion bias and purifying selection that efficiently eliminates nonfunctional, noncoding sequences. T he majority of bacterial and archaeal genomes are small, at least compared with the genomes of multicellular and many unicellular eukaryotes (1, 2). Also, with the exception of deteriorating genomes of some parasitic bacteria, the prokaryotic genomes are highly compact, with densely packed protein-coding genes and a low fraction of noncoding sequences (3). The small genome size is thought to be selected for fast replication, whereas the high gene density additionally facilitates coregulation of gene expression via the operon organization (4, 5). Across the full range of cellular life forms, a significant positive correlation has been shown to exist between genome size and N e u, where N e is the effective population size, and u is the mutation rate per nucleotide (6-9). Accordingly, a simple and appealing population genetic theory has been developed, under which selection strength controls genome size and complexity (6, 9). Prokaryotes, with the exception of some parasites, have large effective population sizes on the order of 10 9 or even higher, which implies strong selection enabling prokaryotes to maintain compact genomes (10). Under this strong selection regime, even short nonfunctional sequences incur cost that is "visible" to selection, conceivably through a combination of increasing energy expenditure and reducing the replication rate, and are efficiently weeded out (11). In eukaryotes, at least the multicellular forms, the effective population ...

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Theory of prokaryotic genome evolution

Sela

Wolf

Koonin

2016

Proc. Natl. Acad. Sci. U.S.A.

137

168

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“…6 Large-scale genome sequencing projects are now providing significant insights into the sizes and metabolic functions of the genomes of a wide variety of pure cultures of microorganisms , JimenezInfante, Ngugi et al 2014, Reddy, Thomas et al 2015, Salipante, Roach et al 2015. The outcome of size analysis of sequenced prokaryotic genomes revealed that there is high variability in genome size between and within species.…”

Section: Accepted Manuscriptmentioning

confidence: 99%

Contemporary molecular tools in microbial ecology and their application to advancing biotechnology

Rashid

Stingl

2015

Biotechnology Advances

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“…The Genomes OnLine Database (GOLD) that monitors sequencing projects worldwide has grown from just 1575 sequencing projects in 2005 to over 70,000 in 2015 (Reddy et al 2015). This is partly caused by a rapid drop in the price of high-throughput sequencing (Hayden 2014), but also an increase of free user-friendly bioinformatical tools such as MG-RAST (Meyer et al 2008), MEGAN (Huson et al 2016) and user fora such as seqanswers.com, biostars.org etc.…”

Section: Introductionmentioning

confidence: 99%