We report here the annotated genome sequence of Xanthomonas arboricola strain 3004, isolated from barley leaves with symptoms of streak and capable of infecting other plant species. We sequenced the genome of X. arboricola strain 3004 to improve the understanding of molecular mechanisms of the pathogenesis and evolution of the genus Xanthomonas.

Identification of promoter sequences in the eukaryotic genome, by computer methods, is an important task of bioinformatics. However, this problem has not been solved since the best algorithms have a false positive probability of 10−3–10−4 per nucleotide. As a result of full genome analysis, there may be more false positives than annotated gene promoters. The probability of a false positive should be reduced to 10−6–10−8 to reduce the number of false positives and increase the reliability of the prediction. The method for multi alignment of the promoter sequences was developed. Then, mathematical methods were developed for calculation of the statistically important classes of the promoter sequences. Five promoter classes, from the rice genome, were created. We developed promoter classes to search for potential promoter sequences in the rice genome with a false positive number less than 10−8 per nucleotide. Five classes of promoter sequences contain 1740, 222, 199, 167 and 130 promoters, respectively. A total of 145,277 potential promoter sequences (PPSs) were identified. Of these, 18,563 are promoters of known genes, 87,233 PPSs intersect with transposable elements, and 37,390 PPSs were found in previously unannotated sequences. The number of false positives for a randomly mixed rice genome is less than 10−8 per nucleotide. The method developed for detecting PPSs was compared with some previously used approaches. The developed mathematical method can be used to search for genes, transposable elements, and transcript start sites in eukaryotic genomes.

The yielding capacity of grapevine growth and the quality of the resulting product heavily depend on the health of the cultivated plants. The phytopathogens affecting the vineyards can cause a significant reduction in the yield and quality of the product. For this reason, it is extremely important to use diagnostic methods that make it possible to identify the pathogens, and to choose the correct method of plant protection. This review considers the main viral grapevine pathogens, and the existing methods of their diagnosis. The limitations of conventional diagnostic methods that are based either on the visual assessment of symptoms, or on bio-testing, are analyzed. A major focus is placed on two intensively developed approaches of diagnosis, molecular genetic and immunochemical methods. Applications of amplification techniques and DNA chips are presented, as well as opportunities for next-generation sequencing. A reduction of assay duration and labor intensity in combination with the assay shifts from specialized laboratories toward the places of sampling are considered as the main factors influencing the development of immunodiagnostic techniques. The potential place of diagnostic tests in vine-growing practices, and the requirements for their most efficient applications for early disease diagnosis is also discussed.

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