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Complete genome sequence of Deinococcus swuensis, a bacterium resistant to radiation toxicity

Deinococcus swuensis DY59T is a Grampositive, coccus-shaped bacterium. Most members of the genus Deinococcus are able to grow in the presence of high levels of chronic radiation toxicity and desiccation because they can protect enzymes from reactive oxygen species generated during ionizing radiation. The mechanisms behind the resistance to radiation toxicity and the genomic features of resistance could be useful to exploit Deinococcus swuensis in the biotechnological applications such as detoxification of xenobiotic contaminated with radioactive wastes. Strain DY59T showed resistance to gamma radiation with a D10 value (i.e. the dose required to reduce the bacterial population by 10-fold) in excess of 5 kGy. However, the genus Deinococcus is slightly characterized at the genome level, despite its potential importance. Thus, the present study determined the features of Deinococcus swuensis DY59T, as well as its genome sequence and annotation. The genome comprised of 3,531,443 bp with a G + C content of 67.4%, which included 3,305 protein-coding genes and 58 RNA genes. Based on the genome annotation, the strain DY59T undergoes prokaryotic type nucleotide excision repair pathway, restores the damaged gene, and resists the ionizing radiation toxicity.

Biological Characterization of Marssonina coronaria Associated with Apple Blotch Disease

Abstract Marssonina coronaria associated with apple blotch disease causes severe premature defoliation, and is widely distributed in Korea. Thirteen isolates were collected from orchards located in Gyeongbuk Province from 2005~2007. All isolates displayed over 99.6% and 99.2% sequence similarity to each other in internal transcribed spacer regions and partial sequences of 28S rDNA, respectively. The isolates were phylogenetically closely related to Chinese isolates. Selected isolates did not differ in their pathogenicity. The optimum conditions for fungal growth were 20°C and pH 6 on peptone potato dextrose agar (PPDA). Peptone and mannose were the best nitrogen and carbon source, respectively. Fungal growth was better on PPDA than on common potato dextrose agar. This study provides valuable information for integrated disease management program and facilitates the routine culturing of M. coronaria.

Cobweb disease on Agaricus bisporus caused by Cladobotryum mycophilum in Korea

This report is the first of cobweb disease on Agaricus bisporus in Korea. Cobweb on both fruit bodies and casing soils were observed on several mushroom farms in Gyeongbuk Province, Korea. Classical and molecular characterization indicated that the causal agent is Cladobotryummycophilum. The isolated fungus was used to inoculate fruiting bodies of A. bisporus and caused the same symptoms.

First report of Candidatus Phytoplasma asteris associated with yellowing and rosetting of Japanese spurge in Korea

Phytoplasma-induced leaf yellowing, stunting and rosetting were observed on Japanese spurge (Pachysandra terminalis) in Jung-gu of Daegu city, Korea. Molecular analyses based on PCR–RFLP and 16S rDNA sequences indicated that the phytoplasma associated with Japanese spurge yellows disease is a new strain of Candidatus Phytoplasma asteris. This report is the first on the occurrence of phytoplasma disease on Japanese spurge in Korea.

Draft Genome Sequence of Chryseobacterium sp. Strain P1-3, a Keratinolytic Bacterium Isolated from Poultry Waste

ABSTRACT Chryseobacterium sp. strain P1-3, harboring keratin degrading activity, has recently been isolated from poultry waste. Here, we report the 4.6-Mbp draft genome sequence of the keratinolytic bacterium with a G+C content of 37.0% and 4,087 protein-coding genes.

Microflora of phytopathogen-transferring Bradysia agrestis: a step toward finding ideal candidates for paratransgenesis

Owing to the effect of symbiotic gut bacteria on the proliferation of infectious disease-transferring insects and their potential as paratransgenic tools, their identification or securing their use in controlling insect vectors is urgently needed. Bradysia agrestis is one of the major plant epidemic vectors in East Asia; however, its normal microbiota remains unstudied. This research was primarily designed to secure promising candidates for use in a paratransgenic approach to phytopathogen control, as well as to provide a picture of the gut microbiota of wild-caught B. agrestis from a blight field. A total of 180 larvae from three different regions in South Korea were analyzed for their gut microfloral composition. Diverse bacterial strains were purely isolated based on morphological differences in microbiological media. We found a total of 64 bacterial strains in the B. agrestis midgut and analyzed their 16S rRNA gene sequences for molecular identification and phylogenetic characterization. Furthermore, the microbial diversity of each normal microbiota group was analyzed with various diversity indices. Bacterial biota including species diversity, richness or species distribution, species constituents, and dominance varied by each regional vector group. The most widely distributed species was Bacillus aryabhattai, and the most common genera were Bacillus and Microbacterium. These saprophytic bacteria were isolated from all regional groups and their potential as paratransgenic candidates for controlling B. agrestis-mediated plant disease is discussed.

Biological Characterization of Marssonina coronaria Infecting Apple Trees in Korea

Apple blotch is a major apple disease and recently it causes critical economic losses in apple orchards in Korea. In this review, we described the history of apple blotch researches, ecology and life cycle of Marssonina coronaria, cultural and molecular characteristics and simple isolation method as well. Furthermore, characteristic of apple blotch like symptoms, its cause still unknown, occurs frequently in cv. “Fuji” was described in detail.

Outbreak of Rust Caused by Coleosporium asterum on Solidago virgaurea var. gigantea in Ulleung-do.

Abstract From June to October 2012, severe outbreaks of rust disease on Solidago virgaurea var. gigantea were observed in 5 different regions of Ulleung-do, Korea. Typical rust symptoms appeared as yellow spots, uredinia on leaves, and massive urediniospores covering the entire plant. Severely infected plants became discolored and died. On the basis of its morphological and molecular characteristics, the causal agent was identified as Coleosporium asterum. This pathogen has been reported as rust disease on S. virgaurea in the Canada and United States. In Korea, rust disease on S. virgaurea var. gigantea was reported as Uromyces rudbeckia in 1992. To the best of our knowledge, C. asterum is a novel rust pathogen on S. virgaurea var. gigantea in Korea.

Reclassification of aster yellows group phytoplasmas in Korea

Aster yellows group phytoplasmas were reclassified by analysis of the 16S rRNA gene sequence, their phylogeny and the presence of interoperon heterogeneity. Nine phytoplasmas were classified into subgroups 16SrI-B and 16SrI-D using the 16S rRNA gene sequence. Then, based on the presence of interoperon heterogeneity, subgroup 16SrI-B phytoplasmas were differentiated into three subunits as 16SrI-B(a): mulberry dwarf, sumac witches’ broom and porcelain vine witches’ broom; 16SrI-B(b): angustata ash witches’ broom and Japanese spurge yellows; and 16SrI-B(c): onion yellow dwarf, water dropwort witches’ broom and hare’s ear yellow dwarf phytoplasma.

Multiplex PCR Assay for Simultaneous Detection of Korean Quarantine Phytoplasmas

Animal, Plant and Fisheries Quarantine and Inspection Agency, Anyang 430-757, Korea(Received on August 23, 2011; Revised on October 16, 2011; Accepted on October 17, 2011)Multiplex PCR assays were developed for the simul-taneous detection of ten important Korean quarantinephytoplasmas. The species-specific primers were design-ed based on ribosomal protein, putative preproteintranslocase Y, immunodominant protein, elongationfactor TU, chaperonin protein and the 16S rRNA genesof ‘Candidatus (Ca.) Phytoplasma’ species. Three mainprimer sets were prepared from ten designed primerpairs to limit nonspecific amplification as much aspossible. The multiplex PCR assay using the threeprimer sets successfully amplified the correct conservedgenes for each ‘Ca. Phytoplasma’ species. In addition,ten important ‘Ca. Phytoplasma’ species could be easilydetermined by recognizing band patterns specific foreach phytoplasma species from three primer sets.Moreover, a high sensitivity of multiplex PCR for eachprimer set was observed for samples containing a lowDNA concentration (10 ng/µl). This study provides theuseful multiplex PCR assay as a convenient method todetect the presence of ten important quarantinephytoplasmas in Korea.Keywords : ‘Candidatus Phytoplasma’ species, Detection,Multiplex PCR, QuarantinePhytoplasma associated plant diseases occur in many cropsworldwide and more than 300 distinct plant diseases havebeen attributed to phytoplasmas, affecting hundreds of plantgenera (Hoshi et al., 2007). Phytoplasmas severely affectherbaceous and woody plants and are the primary limitingfactors for many important crops all over the world. Manyof the most important diseases from an economic stand-point are those affecting woody plants, including coconutlethal yellowing, peach X-disease, grapevine yellows andapple proliferation, and those affecting herbaceous plants,including vegetable crops, ornamental plants and legumes(Bertaccini and Duduk, 2009). Because of these diseases,the movement of the affected plant species should beinternationally restricted through quarantine regulations(Lee et al., 2000). In Korea, phytoplasma related diseases have been report-ed in about 50 different plant species and the phytoplasmaswere found to be associated with 6 ‘Candidatus (Ca.)Phytoplasma (P.)’ species including ‘Ca. P. asteris’, ‘Ca. P.pruni’, ‘Ca. P. trifolii’, ‘Ca. P. solani’, ‘Ca. P. castaneae’and ‘Ca. P. ziziphi’. Among them, ‘Candidatus Phyto-plasma asteris’ associated plant diseases were found toaffect the widest range of plants (Lee et al., 2004). TheKorea National Plant Quarantine Services (NPQS) listed 20phytoplasma diseases that should be prohibited and re-gulated including apple proliferation, strawberry witches’broom, walnut witches’ broom, etc. Those diseases wereassociated with 10 important ‘Ca. Phytoplasma’ speciesand among them; ‘Ca. P. asteris’ associated plant diseaseswere reported to be present in 54 plant families of 350 plantspecies (http://www.nqps.go.kr). Nowadays, molecularbased identification has been widely used to quickly detectpathogens. Nested PCR following PCR primed by phyto-plasma-universal primers are commonly used in phyto-plasma detection in Korea. Generally, identification of anunknown phytoplasma species from one disease requires asignificant amount of time. After PCR analyses, sequencingor restriction fragment length polymorphism analyses areneeded to further differentiate pathogen at the phytoplasmaspecies level. Thus, quick and efficient detection methodsfor ten important phytoplasma species are needed inregards to quarantine services. Simultaneous detection oftwo or more DNA targets can be achieved by duplex ormultiplex PCR in a single reaction by adding severalspecific primers into the PCR cocktail. Lopez et al. (2006)demonstrated that the multiplex PCR is a valuable tool fordetection and identification purposes in plant pathologybecause more than one pathogen frequently infect a singlecrop or host. Therefore, in this study, we developed amultiplex PCR assay by designing phytoplasma species-specific primer pairs based on various conserved genesincluding 16S rRNA, ribosomal protein gene operon (rp),