Quantifying intrachromosomal GC heterogeneity in prokaryotic genomes

Bernaola‐Galván, Pedro; Oliver, José Luis Tejera; Carpena, Pedro; Clay, Oliver; Bernardi, Giorgio

doi:10.1016/j.gene.2004.02.042

Cited by 28 publications

(24 citation statements)

References 59 publications

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“…Indeed, the GC-content distribution of the reads indicated that the three datasets were biased towards GC-rich members of the community (Figure 2). In previous works it has been shown that if a bacterial genome is split into equally size non-overlapping sequences, the distribution of the GC-content of the sequences (especially for short ones) will be similar to a normal distribution centered on GC-content of the genome [28,29]. Consequently, the GC-content of reads sequenced from a single bacterium is expected to roughly follow a normal distribution and the GC-content of a metagenome could be approximately modeled by means of a mixture of normal distributions.…”

Section: Resultsmentioning

confidence: 99%

Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes

et al. 2013

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BackgroundSequencing technologies have different biases, in single-genome sequencing and metagenomic sequencing; these can significantly affect ORFs recovery and the population distribution of a metagenome. In this paper we investigate how well different technologies represent information related to a considered organism of interest in a metagenome, and whether it is beneficial to combine information obtained using different technologies. We analyze comparatively three metagenomic datasets acquired from a sample containing the anammox bacterium Candidatus ’Brocadia fulgida’ (B. fulgida). These datasets were obtained using Roche 454 FLX and Sanger sequencing with two different libraries (shotgun and fosmid).ResultsIn each dataset, the abundance of the reads annotated to B. fulgida was much lower than the abundance expected from available cell count information. This was due to the overrepresentation of GC-richer organisms, as shown by GC-content distribution of the reads. Nevertheless, by considering the union of B. fulgida reads over the three datasets, the number of B. fulgida ORFs recovered for at least 80% of their length was twice the amount recovered by the best technology. Indeed, while taxonomic distributions of reads in the three datasets were similar, the respective sets of B. fulgida ORFs recovered for a large part of their length were highly different, and depth of coverage patterns of 454 and Sanger were dissimilar.ConclusionsPrecautions should be sought in order to prevent the overrepresentation of GC-rich microbes in the datasets. This overrepresentation and the consistency of the taxonomic distributions of reads obtained with different sequencing technologies suggests that, in general, abundance biases might be mainly due to other steps of the sequencing protocols. Results show that biases against organisms of interest could be compensated combining different sequencing technologies, due to the differences of their genome-level sequencing biases even if the species was present in not very different abundances in the metagenomes.

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Section: Resultsmentioning

confidence: 99%

Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes

et al. 2013

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“…CpG rich regions (isochores) are rich in genes and induce lower scale clustering [42][43][44][45][46].…”

Section: Exit and Recurrence Distance Distributionsmentioning

confidence: 99%

DNA viewed as an out-of-equilibrium structure

Provata

Nicolis

2014

Phys. Rev. E

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The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory and information theory. The use of chi-square tests shows that DNA cannot be described as a low order Markov chain of order up to r = 6. Although detailed balance seems to hold at the level of purine-pyrimidine notation it fails when all four basepairs are considered, suggesting spatial asymmetry and irreversibility. Furthermore, the block entropy does not increase linearly with the block size, reflecting the long range nature of the correlations in the human genomic sequences. To probe locally the spatial structure of the chain we study the exit distances from a specific symbol, the distribution of recurrence distances and the Hurst exponent, all of which show power law tails and long range characteristics. These results suggest that human DNA can be viewed as a non-equilibrium structure maintained in its state through interactions with a constantly changing environment. Based solely on the exit distance distribution accounting for the nonequilibrium statistics and using the Monte Carlo rejection sampling method we construct a model DNA sequence. This method allows to keep all long range and short range statistical characteristics of the original sequence. The model sequence presents the same characteristic exponents as the natural DNA but fails to capture point-to-point details. *

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“…Compositional heterogeneity is widespread in evolution (Cammarano et al, 2009), even in prokaryotes (Bernaola-Galván et al 2004; Bohlin et al 2010). But to the best of our knowledge, most of the physiological features associated with the compositional heterogeneity had almost exclusively been found in mammals.…”

Section: Introductionmentioning

confidence: 99%

An Isochore-Like Structure in the Genome of the FlatwormSchistosoma mansoni

et al. 2016

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Eukaryotic genomes are compositionally heterogeneous, that is, composed by regions that differ in guanine–cytosine (GC) content (isochores). The most well documented case is that of vertebrates (mainly mammals) although it has been also noted among unicellular eukaryotes and invertebrates. In the human genome, regarded as a typical mammal, this heterogeneity is associated with several features. Specifically, genes located in GC-richest regions are the GC3-richest, display CpG islands and have shorter introns. Furthermore, these genes are more heavily expressed and tend to be located at the extremes of the chromosomes. Although the compositional heterogeneity seems to be widespread among eukaryotes, the associated properties noted in the human genome and other mammals have not been investigated in depth in other taxa. Here we provide evidence that the genome of the parasitic flatworm Schistosoma mansoni is compositionally heterogeneous and exhibits an isochore-like structure, displaying some features associated, until now, only with the human and other vertebrate genomes, with the exception of gene concentration.

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Quantifying intrachromosomal GC heterogeneity in prokaryotic genomes

Cited by 28 publications

References 59 publications

Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes

Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes

DNA viewed as an out-of-equilibrium structure

An Isochore-Like Structure in the Genome of the FlatwormSchistosoma mansoni

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