Genomic GC content prediction in prokaryotes from a sample of genes

Zavala, Alejandro; Naya, Hugo; Romero, Héctor; Sabbía, V.; Piovani, Rosina; Musto, Héctor

doi:10.1016/j.gene.2005.06.030

Cited by 13 publications

(6 citation statements)

References 11 publications

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“…However, Anaeromyxobacter dehalogenans is an outlier with lower coverage than would be predicted by the model (actual coverage = 0.406, predicted coverage = 0.563, 99.9% predicted interval: 0.412-0.713). In addition, we confirmed the significant association between log genome size and GC content such that organisms with smaller genomes have lower GC content ( Figure 2, linear regression p < 0.001) [16].…”

Section: Sequence Space Coveragesupporting

confidence: 72%

Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples

2008

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Section: Sequence Space Coveragesupporting

confidence: 72%

Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples

2008

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“…An additional concern is that GϩC content can vary locally within a genome, such that the GϩC content of individual DNA fragments can vary from the mean genome GϩC content. Thus, as a genome is cut into smaller and smaller fragments, the variation between the GϩC contents of the individual fragments and the GϩC content of the genome will tend to increase (44). The anticipated result would be that the range of densities occupied by DNA from a given genome (i.e., the width of the band in the gradient) would increase as the molecular weight of DNA fragments decreases.…”

Section: Whilementioning

confidence: 99%

“…The anticipated result would be that the range of densities occupied by DNA from a given genome (i.e., the width of the band in the gradient) would increase as the molecular weight of DNA fragments decreases. Thus, the GϩC content of DNA fragments that are smaller than 5 kbp can vary by as much as 13% for a single genome (44). These effects may help to explain why low but detectable amounts of nucleic acids can be recovered throughout density gradients (8,16,19,25,37).…”

Section: Whilementioning

confidence: 99%

Stable Isotope Probing with ¹⁵ N Achieved by Disentangling the Effects of Genome G+C Content and Isotope Enrichment on DNA Density

Buckley

Huangyutitham

Hsu

et al. 2007

Appl Environ Microbiol

135

129

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Stable isotope probing (SIP) of nucleic acids is a powerful tool that can identify the functional capabilities of noncultivated microorganisms as they occur in microbial communities. While it has been suggested previously that nucleic acid SIP can be performed with 15 N, nearly all applications of this technique to date have used 13 C. Successful application of SIP using 15 N-DNA ( 15 N-DNA-SIP) has been limited, because the maximum shift in buoyant density that can be achieved in CsCl gradients is approximately 0.016 g ml ؊1 for 15 N-labeled DNA, relative to 0.036 g ml ؊1 for 13 C-labeled DNA. In contrast, variation in genome G؉C content between microorganisms can result in DNA samples that vary in buoyant density by as much as 0.05 g ml ؊1 . Thus, natural variation in genome G؉C content in complex communities prevents the effective separation of 15

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“…bulgaricus ATCC 11842 was performed by the analysis of G+C content for the 16S-ITS-23S, rpoB , rpoC , pheS and rpoA gene sequences (Table S3). This approach of assessing and predicting genomic G+C content based on the comparison of G+C content of individual housekeeping genes compared to the results of DNA G+C content determined experimentally by the HPLC (high performance liquid chromatography) technique, has been successfully demonstrated and published for multiple bacterial species (Fournier et al , 2006; Kuhnert & Korczak, 2006; Lorén et al , 2010; Zavala et al , 2005). Previously published data demonstrated minimal differences (±3–5 %) between genomic G+C content predicted from analysis of individual housekeeping genes and the results of G+C content estimated using HPLC.…”

mentioning

confidence: 99%

Lactobacillus brantae sp. nov., isolated from faeces of Canada geese (Branta canadensis)

Volokhov

Amselle

Beck

et al. 2012

International Journal of Systematic and Evolutionary Microbiology

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Three strains of lactic acid bacteria (LAB) were isolated from the faeces of apparently healthy wild Canada geese (Branta canadensis) in 2010 by cultivating faecal LAB on Rogosa SL agar under aerobic conditions. These three isolates were found to share 99.9 % gene sequence similarity of their 16S rRNA, their 16S-23S intergenic transcribed spacer region (ITS), partial 23S rRNA, rpoB, rpoC, rpoA and pheS gene sequences. However, the three strains exhibited lower levels of sequence similarity of these genetic targets to all known LAB, and the phylogenetically closest species to the geese strains were Lactobacillus casei, Lactobacillus paracasei, Lactobacillus rhamnosus and Lactobacillus saniviri. In comparison to L. casei ATCC 393 T , L. paracasei ATCC 25302 T , L. rhamnosus ATCC 7469 T and L. saniviri DSM 24301 T , the novel isolates reacted uniquely in tests for cellobiose, galactose, mannitol, citric acid, aesculin and dextrin, and gave negative results in tests for L-proline arylamidase and L-pyrrolydonyl-arylamidase, and in the Voges-Proskauer test. Biochemical tests for cellobiose, aesculin, galactose, gentiobiose, mannitol, melezitose, ribose, salicin, sucrose, trehalose, raffinose, turanose, amygdalin and arbutin could be used for differentiation between L. saniviri and the novel strains. On the basis of phenotypic and genotypic characteristics, and phylogenetic data, the three isolates represent a novel species of the genus Lactobacillus, for which the name Lactobacillus brantae sp. nov. is proposed. The type strain is SL1108 T (5ATCC BAA-2142 T 5LMG 26001 T 5DSM 23927 T ) and two additional strains are SL1170 and SL60106.

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Genomic GC content prediction in prokaryotes from a sample of genes

Cited by 13 publications

References 11 publications

Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples

Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples

Stable Isotope Probing with ¹⁵ N Achieved by Disentangling the Effects of Genome G+C Content and Isotope Enrichment on DNA Density

Lactobacillus brantae sp. nov., isolated from faeces of Canada geese (Branta canadensis)

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Genomic GC content prediction in prokaryotes from a sample of genes

Cited by 13 publications

References 11 publications

Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples

Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples

Stable Isotope Probing with 15 N Achieved by Disentangling the Effects of Genome G+C Content and Isotope Enrichment on DNA Density

Lactobacillus brantae sp. nov., isolated from faeces of Canada geese (Branta canadensis)

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Stable Isotope Probing with ¹⁵ N Achieved by Disentangling the Effects of Genome G+C Content and Isotope Enrichment on DNA Density