Identification of Prophages in Bacterial Genomes by Dinucleotide Relative Abundance Difference

BACKGROUND: Prophages are integrated viral forms in bacterial genomes that have been found to contribute to interstrain genetic variability. Many virulence-associated genes are reported to be prophage encoded. Present computational methods to detect prophages are either by identifying possible essential proteins such as integrases or by an extension of this technique, which involves identifying a region containing proteins similar to those occurring in prophages. These methods suffer due to the problem of low sequence similarity at the protein level, which suggests that a nucleotide based approach could be useful. METHODOLOGY: Earlier dinucleotide relative abundance (DRA) have been used to identify regions, which deviate from the neighborhood areas, in genomes. We have used the difference in the dinucleotide relative abundance (DRAD) between the bacterial and prophage DNA to aid location of DNA stretches that could be of prophage origin in bacterial genomes. Prophage sequences which deviate from bacterial regions in their dinucleotide frequencies are detected by scanning bacterial genome sequences. The method was validated using a subset of genomes with prophage data from literature reports. A web interface for prophage scan based on this method is available at http://bicmku.in:8082/prophagedb/dra.html. Two hundred bacterial genomes which do not have annotated prophages have been scanned for prophage regions using this method. CONCLUSIONS: The relative dinucleotide distribution difference helps detect prophage regions in genome sequences. The usefulness of this method is seen in the identification of 461 highly probable loci pertaining to prophages which have not been annotated so earlier. This work emphasizes the need to extend the efforts to detect and annotate prophage elements in genome sequences

Evolutionary genomics of a cold-adapted diatom: Fragilariopsis cylindrus

The Southern Ocean houses a diverse and productive community of organisms1, 2. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice3, 4, 5, 6, 7. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus8, 9, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO2. Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean

Comparative analysis of number of prophages identified by the approach reported here (DRAD), literature reports and another prophage detection method (phage_finder tool).

<p>Comparative analysis of number of prophages identified by the approach reported here (DRAD), literature reports and another prophage detection method (phage_finder tool).</p

Prophage loci, in pathogenic bacteria, identified by the method reported here (DRAD approach) indicated as * are PAIs reported by Yoon <i>et al</i> 2005 [22].

<p>Prophage loci, in pathogenic bacteria, identified by the method reported here (DRAD approach) indicated as * are PAIs reported by Yoon <i>et al</i> 2005 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001193#pone.0001193-Yoon1" target="_blank">[22]</a>.</p

Dinucleotide difference distribution for <i>Shigella sonnei:</i>

<p>pink-<i>Shigella sonnei</i> genome Vs <i>Shigella sonnei</i> genome, blue-<i>Shigella sonnei</i> genome Vs prophage dataset , yellow- their dinucleotide relative abundance difference (DRAD) value.</p

Variation of prophage number with bacterial genomes.

<p>– Indicated in green are prophages identified by the method reported here (DRAD), yellow and red represents prophage loci reported in literature <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001193#pone.0001193-Casjens1" target="_blank">[5]</a> , identified by phage_finder program <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001193#pone.0001193-Bose1" target="_blank">[35]</a> respectively.</p

Prophages identified using dinucleotide relative abundance difference method.

<p>Pathogenic organisms are indicated in * and organism surviving on varied ecological niche/having industrial significance are indicated in #. DRAD refers to the method reported here.</p

Sensitivity and Specificity across genomes.

<p>Comparision of prophage locus detected by DRAD against literature reported and evidence from annotation. DRAD refers to the method reported here.</p><p>TP–Probable True postivies, FN–false negatives , FP-False positives , Sn–Probable Senstivity, Sp-Probable Specificity</p

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.

The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO2. Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean