Comparison of the complete genome sequence of two closely related isolates of 'Candidatus Phytoplasma australiense' reveals genome plasticity.

BACKGROUND: 'Candidatus Phytoplasma australiense' is associated with at least nine diseases in Australia and New Zealand. The impact of this phytoplasma is considerable, both economically and environmentally. The genome of a NZ isolate was sequenced in an effort to understand its pathogenicity and ecology. Comparison with a closely related Australian isolate enabled us to examine mechanisms of genomic rearrangement. RESULTS: The complete genome sequence of a strawberry lethal yellows (SLY) isolate of 'Candidatus Phytoplasma australiense' was determined. It is a circular genome of 959,779 base pairs with 1126 predicted open reading frames. Despite being 80 kbp larger than another 'Ca. Phytoplasma australiense' isolate PAa, the variation between housekeeping genes was generally less than 1% at a nucleotide level. The difference in size between the two isolates was largely due to the number and size of potential mobile units (PMUs), which contributed to some changes in gene order. Comparison of the genomes of the two isolates revealed that the highly conserved 5' UTR of a putative DNA-directed RNA polymerase seems to be associated with insertion and rearrangement events. Two types of PMUs have been identified on the basis of the order of three to four conserved genes, with both PMUs appearing to have been present in the last common ancestor of 'Ca. Phytoplasma asteris' and 'Ca. Phytoplasma australiense'. Comparison with other phytoplasma genomes showed that modification methylases were, in general, species-specific. A putative methylase (xorIIM) found in 'Ca. Phytoplasma australiense' appeared to have no analogue in any other firmicute, and we believe has been introduced by way of lateral gene transfer. A putative retrostransposon (ltrA) analogous to that found in OY-M was present in both isolates, although all examples in PAa appear to be fragments. Comparative analysis identified highly conserved 5' and 3' UTR regions of ltrA, which may indicate how the gene is excised and inserted. CONCLUSIONS: Comparison of two assembled 'Ca. Phytoplasma australiense' genomes has shown they possess a high level of plasticity. This comparative analysis has yielded clues as to how rearrangements occur, and the identification of sets of genes that appear to be associated with these events.

Large-scale genomic 2D visualization reveals extensive CG-AT skew correlation in bird genomes.

BACKGROUND: Bird genomes have very different compositional structure compared with other warm-blooded animals. The variation in the base skew rules in the vertebrate genomes remains puzzling, but it must relate somehow to large-scale genome evolution. Current research is inclined to relate base skew with mutations and their fixation. Here we wish to explore base skew correlations in bird genomes, to develop methods for displaying and quantifying such correlations at different scales, and to discuss possible explanations for the peculiarities of the bird genomes in skew correlation. RESULTS: We have developed a method called Base Skew Double Triangle (BSDT) for exhibiting the genome-scale change of AT/CG skew as a two-dimensional square picture, showing base skews at many scales simultaneously in a single image. By this method we found that most chicken chromosomes have high AT/CG skew correlation (symmetry in 2D picture), except for some microchromosomes. No other organisms studied (18 species) show such high skew correlations. This visualized high correlation was validated by three kinds of quantitative calculations with overlapping and non-overlapping windows, all indicating that chicken and birds in general have a special genome structure. Similar features were also found in some of the mammal genomes, but clearly much weaker than in chickens. We presume that the skew correlation feature evolved near the time that birds separated from other vertebrate lineages. When we eliminated the repeat sequences from the genomes, the AT and CG skews correlation increased for some mammal genomes, but were still clearly lower than in chickens. CONCLUSION: Our results suggest that BSDT is an expressive visualization method for AT and CG skew and enabled the discovery of the very high skew correlation in bird genomes; this peculiarity is worth further study. Computational analysis indicated that this correlation might be a compositional characteristic, present not only in chickens, but also remained or developed in some mammals during evolution. Special aspects of bird metabolism related to e.g. flight may be the reason why birds evolved or retained the skew correlation. Our analysis also indicated that repetitive DNA sequence elements need to be taken into account in studying the evolution of the correlation between AT and CG skews.

On the reliable identification of plant sequences containing a polyadenylation site.

It is a challenging task to predict with high reliability whether plant genomic sequences contain a polyadenylation (polyA) site or not. In this paper, we solve the task by means of a systematic machine-learning procedure applied on a dataset of 1000 Arabidopsis thaliana sequences flanking polyA sites. Our procedure consists of three steps. In the first step, we extract informative features from the sequences using the highly informative k-mer windows approach. Experiments with five classifiers show that the best performance is approximately 83%. In the second step, we improve performance to 95% by reducing the number of features using linear discriminant analysis, followed by applying the linear discriminant classifier. In the third step, we apply the transductive confidence machines approach and the receiver operating characteristic isometrics approach. The resulting two classifiers enable presetting any desired performance by dealing carefully with sequences for which it is unclear whether they contain polyA sites or not. For example, in our case study, we obtain 99% performance by leaving 26% of the sequences unclassified, and 100% performance by leaving 40% of the sequences unclassified. This is clearly useful for experimental verification of putative polyA sites in the laboratory. The novel methods in our machine-learning procedure should find applications in several areas of bioinformatics.