Alexander N. Ignatov

Reclassification of subspecies of Acidovorax avenae as A. Avenae (Manns 1905) emend., A. cattleyae (Pavarino, 1911) comb. nov., A. citrulli Schaad et al., 1978) comb. nov., and proposal of A. oryzae sp. nov.

The bacterium Acidovorax avenae causes disease in a wide range of economically important monocotyledonous and dicotyledonous plants, including corn, rice, watermelon, anthurium, and orchids. Genotypic and phenotypic relatedness among strains of phytopathogenic A. avenae subsp. avenae, A. avenae subsp. citrulli, A. avenae subsp. cattleyae and A. konjaci, as well as all other Acidovorax species, including A. facilis, the type strain of Acidovorax, was determined. The 16s rDNA sequencing confirmed previous studies showing the environmental species to be very distant from the phytopathogenic species. DNA/DNA reassociation assays on the different strains of A. avenae revealed four (A, B, C, and D) distinct genotypes. Taxon A included six A. avenae subsp. avenae strains from corn that had a mean reciprocal similarity of 81%; taxon B included six A. avenae subsp. avenae strains from rice that had a mean reciprocal similarity of 97%; taxon C contained 11 A. avenae subsp. citrulli strains from cucurbits (cantaloupe, watermelon, and pumpkin) that had a mean reciprocal similarity of 88%, and taxon D contained four A. avenae subsp. cattleyae strains from orchids that had a mean similarity of 98%. The mean reciprocal relatedness between taxa A, B, C, and D was less than 70%. Sequence analysis of 16S rDNA and the 16S-23S rDNA internally transcribed spacer region, as well as AFLP analysis, revealed the same four taxa. All four were easily differentiated phenotypically from each other and from all other recognized Acidovorax species. Strains of A. avenae did not contain 3-hydroxyoctanoic acid, which was found in all other species. On the basis of these and previous genetic and phenotypic results, we propose an emendation of the species A. avenae. A. avenae subsp. citrulli (C strains) and A. avenae subsp. cattleyae (D strains) should be elevated to species rank as A. citrulli and A. cattleyae, respectively. We further propose a new taxon for the B strains, A. oryzae sp. nov. with FC-143T = ICPB 30003T = ICMP 3960T = ATCC 19882T as the type strain.

The 203 kbp mitochondrial genome of the phytopathogenic fungus Sclerotinia borealis reveals multiple invasions of introns and genomic duplications.

Here we report the complete sequence of the mitochondrial (mt) genome of the necrotrophic phytopathogenic fungus Sclerotinia borealis, a member of the order Helotiales of Ascomycetes. The 203,051 bp long mtDNA of S. borealis represents one of the largest sequenced fungal mt genomes. The large size is mostly determined by the presence of mobile genetic elements, which include 61 introns. Introns contain a total of 125,394 bp, are scattered throughout the genome, and are found in 12 protein-coding genes and in the ribosomal RNA genes. Most introns contain complete or truncated ORFs that are related to homing endonucleases of the LAGLIDADG and GIY-YIG families. Integrations of mobile elements are also evidenced by the presence of two regions similar to fragments of inverton-like plasmids. Although duplications of some short genome regions, resulting in the appearance of truncated extra copies of genes, did occur, we found no evidences of extensive accumulation of repeat sequences accounting for mitochondrial genome size expansion in some other fungi. Comparisons of mtDNA of S. borealis with other members of the order Helotiales reveal considerable gene order conservation and a dynamic pattern of intron acquisition and loss during evolution. Our data are consistent with the hypothesis that horizontal DNA transfer has played a significant role in the evolution and size expansion of the S. borealis mt genome.

Genetic Diversity in Populations of Xanthomonas campestris pv. campestris in Cruciferous Weeds in Central Coastal California

ABSTRACT Xanthomonas campestris pv. campestris (X. campestris) infects a large number of cruciferous plants, including weeds. California has one of the largest and most diverse populations of wild cruciferous plants in the world. Although considerable information is available on the genetic diversity of X. campestris in commercial crop plants, nothing is known about the diversity in strains infecting weeds. To assess the genetic diversity among strains of X. campestris in weeds in noncultivated and cultivated areas, strains of the pathogen were isolated from populations of cruciferous weeds growing in coastal valley crop-production sites and from remote nonproduction sites along the California central coast. Results of fingerprinting over 68 strains using amplified fragment length polymorphism along with representative strains by sequence analysis showed the presence of seven genotypes. Genotypes A and B were limited to coastal sites; genotypes C, D, and E were from inland cultivated sites; and genotypes F and G were present in both coastal noncultivated and inland cultivated sites. Crop strains were grouped outside any weed strain group and were separated from the weed strains and other pathovars of X. campestris. These results revealed, for the first time, that strains of X. campestris present in noncultivated coastal weed populations generally were unique to a site and genetically distinct from strains present in populations of weeds in crop-production areas located nearby.

Draft Genome Sequence of Xanthomonas arboricola Strain 3004, a Causal Agent of Bacterial Disease on Barley

ABSTRACT 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.

Theory of hysteresis during electron heating of electromagnetic wave scattering by self-organized dust structures in complex plasmas

Dust structuring is a natural and universal process in complex plasmas. The scattering of electromagnetic waves by dust structures is governed by the factor of coherency, i.e., the total number of coherent electrons in a single structure. In the present paper, we consider how the factor of coherency changes due to additional pulse electron heating and show that it obeys a hysteresis. After the end of the pulse heating, the scattering intensity differs substantially from that before heating. There are three necessary conditions for scattering hysteresis: first, the radiation wavelength should be larger than the pattern (structure) size; second, the total number of coherent electrons confined by the structure should be large; and third, the heating pulse duration should be shorter than the characteristic time of dust structure formation. We present the results of numerical calculations using existing models of self-consistent dust structures with either positively or negatively charged dust grains. It is sh...

Draft Genome Sequence of Sclerotinia borealis, a Psychrophilic Plant Pathogenic Fungus.

ABSTRACT Sclerotinia borealis is a necrotrophic phytopathogenic fungus notable for its wide host range and environmental persistence. It grows at low temperatures, causing snow mold disease of crop plants. To understand the molecular mechanisms of its pathogenesis and adaptation to the psychrophilic lifestyle, we determined the 39.3-Mb draft genome sequence of S. borealis F-4128.

Coherent scattering of electromagnetic waves by self-organized dust structures: Degree of coherence

It is demonstrated explicitly that the scattering of electromagnetic waves by dust structures can be strongly enhanced as compared to incoherent scattering by random electrons. If the size of the dust structure is much less than the wavelength of the incident radiation, the scattering is coherent. In this case, the scattering is proportional to the square of the total number of electrons in the structure. In the opposite limit, the scattering is incoherent being proportional to the total number of electrons in the structure. The factor describing the degree of coherency is calculated numerically for several models of self-organized structures. It is demonstrated in general way that for sudden heating of electrons, the factor of coherency in scattering by structures can decrease by several orders of magnitude with subsequent increase after the heating is switched off. In laboratory dusty plasmas, the coherent scattering is proposed for diagnostics of universal structuring instability and as a probe for determining the properties typical for self-organized nature of structures that are observed in recent experiments.

Genetic diversity of turnip mosaic virus and the mechanism of its transmission by Brassica seeds.

I8, and I10) characteristic of viruses isolated from 87 samples of cultivated plants of the genus Brassica that had the symptoms of turnip mosaic in Moscow region were classified by the signs of lesion of host plants, response of indicator plants, and results of ELISA. For all the isolates, three taxonomically informative genes P1, Nib, and CP were partly sequenced. Phylogenetic analysis showed that they belonged to two phylogee netic groups with cDNA similarity of 95%. According to preliminary information, one group of virus isolates was brought to Russia with the seed collection of Brass sica rapa L. varieties. It was demonstrated that the TuMV I2 isolate is transmitted by seeds of TuMVVsuss ceptible and TuMVVtolerant plants of the genus Brass sica at a frequency of up to 40%, and the mechanism of the virus transmission through infection of the embryo was shown. The analysis of the obtained genomic cDNA sequence of the TuMV isolate I2 showed that its ability to be transmitted by seeds may be associated with amino acid substitutions in the P1 gene sequence. Turnip mosaic virus (TuMV) infects a wide range of cultivated, wild, and weedy species of 156 genera belonging to 43 families of plants, including all cultii vated species of the family Brassicaceae [1] and causes significant economic losses during the cultivation of crops of the species Brassica [2]. This is the only memm ber of the genus Potyvirus infecting plants of the family Brassicaceae [3]. Two TuMV isolates from Russia were included by foreign researchers for comparison of the virus genetic polymorphism; however, the diversity of the Russian population of the virus has to be investigated. The group of potiviruses includes 179 species, of which less than 10% are transmitted with seeds at a frequency of 1 to 80%. Only one case of TuMV detection in Raphaa nus raphanistrum seeds with a frequency of 4% was described in the literature [4]. However, the authors [4] have not demonstrated the fact of infection of the new generation of plants; for this reason, the absence of transmission of this virus with plant seeds is acknowledged. It is believe that this virus is transmitt ted only by insect vectors, primarily aphids of the genn era Macrosiphum or Myzus [1]. This study was performed on plant samples with the symptoms of TuMV infection, which were collected in different areas of Moscow region. To identify and conn firm …