Shiitake (Lentinula edodes) is the most economically important cultivated mushroom, but yields are impacted by its competitor, Trichoderma spp. We previously found two unidentified Trichoderma species growing in bedlogs and sawdust shiitake media in Korea. Here, we identify and re-describe those two species based on molecular sequence data, morphology, and culture characteristics. Well-supported clades based on phylogenetic analyses of internal transcribed spacer, translation elongation factor 1-${\alpha}$, and RNA polymerase subunit II sequences grouped one of the unidentified Trichoderma spp. with Hypocrea pseudogelatinosa and the other with Hypocrea pseudostraminea, and their morphologies matched well with the original descriptions of the two Hypocrea species. This study reports the first phylogenetic analyses of H. pseudogelatinosa and Japanese strains of H. pseudostraminea. Based on the phylogenetic results, we redescribed these two species using modern taxonomic concepts in Hypocrea/Trichoderma.

Several species belonging to the Gibberella fujikuroi species (Gf ) complex are commonly associated with rice and corn, not only causing serious diseases, but also producing fumonisins, a group of mycotoxins harmful to animals and humans. To characterize the population structure of the putative fumonisin-producing Gf complex in Korea, we obtained 276 candidate isolates from rice and corn harvested in 2009 and 2010 by diagnostic polymerase chain reaction with several specific primer sets. Phylogenetic trees were constructed using multilocus sequences (combined RPB2 and EF1A, totaling 1.6 kb) from these isolates. Among the 135 isolates from rice, F. fujikuroi (teleomorph: G. fujikuroi; 59.3%) and F. proliferatum (G. intermedia; 13.3%) were predominant, followed by F. concentricum (5.9%). Additionally, twenty-five (18.5%) rice isolates belonged in a distinct subclade of F. commune, a non-member of the Gf complex. In contrast, F. verticillioides was the most predominant species (38.3%) among the 141 corn isolates, and followed by F. fujikuroi (27.7%), F. proliferatum (14.9%), F. subglutinans (7.1%), and F. concentricum (2.8%). A single mating type (MAT1-1) was found predominantly among the Gf complex isolates examined. Possible distinct subclades were detected within the populations of F. fujikuroi and F. proliferatum; however, this needs further confirmation. This is the first reported population-level characterization of putative fumonisin-producing Gf complex associated with rice and corn in Korea.

Xanthomonas oryzae pv. oryzae causing bacterial leaf blight disease in rice produces and secretes Hpa1 protein that belongs to harpin protein family. Previously it was reported that Hpa1 induced defense responses when it was produced in tobacco. In this study, we expressed hpa1 gene in rice and Arabidopsis to examine the effects of Hpa1 expression on disease resistance to both fungal and bacterial pathogens. Expression of hpa1 gene in rice enhanced disease resistance to both X. oryzae pv. oryzae and Magnaporthe grisea. Interestingly, individual transgenic rice plants could be divided into four groups, depending on responses to both pathogens. hpa1 expression in Arabidopsis also enhanced disease resistance to both Botrytis cineria and Xanthomonas campestris pv. campestris. To examine genes that are up-regulated in the transgenic rice plants after inoculation with X. oryzae pv. oryzae, known defense-related genes were assessed, and also microarray analysis with the Rice 5 K DNA chip was performed. Interestingly, expression of OsACS1 gene, which was found as the gene that showed the highest induction, was induced earlier and stronger than that in the wild type plant. These results indicate that hpa1 expression in the diverse plant species, including monocot and dicot, can enhance disease resistance to both fungal and bacterial plant pathogens.

Burkholderia pyrrocinia CH-67 is a biocontrol bacterium with strong antifungal activity against several plant pathogenic fungi. Transposon mutagenesis was performed to identify the genes responsible for the antifungal activity of B. pyrrocinia CH-67. Of the 2,500 mutants tested using the Fulvia fulva spore screening method, a mutant deficient in antifungal activity, M208, was selected. DNA sequence analysis of the transposon-inserted region revealed that a gene encoding an adenylate kinase-related kinase was disrupted in M208. Antifungal activity was restored in M208 when a full-length adenylate kinase gene with its promoter was introduced in trans. The deduced amino acid sequence of adenylate kinase from CH-67 was 80% identical to that of B. cenocepacia MCO-3. Adenosine diphosphate supplementation or high levels of adenosine triphosphate and adenosine monophosphate together restored antifungal activity in M208, suggesting that adenylate kinase of B. pyrrocinia CH-67 is involved in antifungal activity expression.

Molecular characterization of Cucumber mosaic virus (CMV) was done by using samples from tomato and cucurbitaceous plants collected from different locations in the northwest region of Iran. After screening by enzyme-linked immunosorbent assay, 91 CMV-infected samples were identified. Biological properties of eight representative isolates were compared with each other revealing two distinct phenotypes on squash and tomato plants. Phylogenetic analyses based on nucleotide sequences of the coat protein (CP), movement protein (MP) and 2b of the new isolates, together with that of previously reported isolates, led to the placement of the Iranian isolates in subgroups IA and IB according to CP and MP genes, but in subgroup IA according to the 2b gene. These data suggest that reassortment may have been a major event in the evolution of CMV in Iran, and that the Iranian isolates are derived from a common recent ancestor that had passed through a bottleneck event.

Eight potato-producing provinces of Iran were surveyed during the growing seasons of 2004-2006 to detect the presence of Tomato yellow fruit ring virus (TYFRV), a tentative species in the genus Tospovirus. A total of 1,957 potato leaf samples were collected from plants with tospovirus-like symptoms of chlorotic or necrotic spots, chlorosis and necrosis. The samples were tested by enzyme-linked immunosorbent assay using TYFRV-specific antibodies. Among those tested, 498 samples (25.4%) were found to be infected with the virus. The virus was detected in 72.4% of the potato fields in all provinces surveyed. Thirteen potato isolates of TYFRV were selected for further biological and molecular studies. Based on their reactions on Nicotiana tabacum plants, the isolates were separated into two groups, namely L (local infection) and N (systemic infection). The nucleotide sequences of the nucleoprotein (N) genes of the isolates were determined and compared with the homologous sequences in Genbank. No recombination evidence was found in the isolates using different recombination-detecting programs. In the phylogenetic tree, the potato isolates fell into two major groups: IRN-1 and IRN-2 corresponding to the two biologically separated groups. This study shows for the first time the biological and phylogenetic relationships of geographically distant TYFRV isolates from potatoes in the mid-Eurasian country of Iran.

Initial subcellular responses in susceptible (PI 274420) and resistant (cv. Hartwig) soybeans infected with the soybean cyst nematode (SCN) were examined 2 and 4 days after inoculation (DAI). Subcellular features common to both soybeans at 2 DAI included hypertrophied initial syncytial cells (ISCs) and syncytium-component cells (SCs) with a dense cytoplasm containing proliferated rough and smooth endoplasmic reticulum (RER and SER), a hypertrophied nucleolus, and reduced vacuoles, suggesting that the nematode-infected cells were dedifferentiated. In the resistant soybean, a striking initial subcellular difference from the susceptible soybean was the dilation of the RER, indicating ER dysfunction and leading to cell death. This disturbed nematode feeding, as evidenced by disrupted feeding tubes. In PI 274420, the ISC cytoplasm was depleted, with the exception of ER membranes, at 4 DAI, while the SC cytoplasm was dense with proliferation of starch-containing plastids around multiple nuclei that might be derived from the congregation of nuclei in the neighboring SCs and in part by nuclear division without cytokinesis. In cv. Hartwig, syncytia were necrotized with secondary cell wall thickening outside the plasma membrane and an extremely dense cytoplasm containing a nucleus with an electron-lucent nucleolus, accompanied by the proliferation of closely stacked parallel RER and ribosomes. These results suggest that syncytia develop continuously in PI 274420 to produce and store nutritional substances in SCs, providing for the nematode through ISC until maturation, but in cv. Hartwig, syncytia degenerate early due to excessive metabolism, blocking nematode feeding and cytoplasmic connections with adjacent intact cells.

We identified two novel expansin (EXP) genes in the expressed sequence tag database of Bursaphelenchus xylophilus, designated as Bx-EXPB2 and -EXPB3. Novel Bx-EXPBs encoded 150 amino acids and their similarities in coding sequence were 70.7-84.0% to the previously reported EXPB1 of B. xylophilus. Bx-EXPB2 and Bx-EXPB3 were clustered with Bx-EXPB1 and Bm-EXPB1, respectively, forming the independent phylogeny with other nematode EXPs. All identified Bx-EXPBs contained the signal peptide and were only expressed during the propagative stage, suggesting that they are secreted to facilitate nematode migration through hosts by loosening cell walls during infection. Quantitative real-time PCR analysis showed that the relative accumulation of Bx-EXPB3 mRNAs was the highest among the three Bx-EXPs examined and the order of mRNA accumulation was as follows: Bx-EXPB3 > Bx-EXPB2 >> Bx-EXPB1. Homology modeling of Bx-EXPBs showed that the structurally optimum template was EXLX1 protein of Bacillus subtilis, whichshared residues essential for catalytic activity with Bx-EXPB1 and Bx-EXPB2 except for Bx-EXPB3. Taken together, Bx-EXPB1 and Bx-EXPB2 may be involved migration through plant tissues and play a role in pathogenesis.

Eleven hot pepper accessions collected in Vietnam showed stable resistance to bacterial wilt as well-known resistance sources, MC4 and MC5, in repeated inoculation tests with different Ralstonia solanacearum isolates conducted from 2004 to 2010. Seven of these accessions (specifically KC981, KC1006, KC1021, KC1027, KC1045, KC1050, and KC1055) resulted in stable male sterile F1 plants in the crosses with a cytoplasmically male sterile (CMS) Chilseong (CMS-A, Srfrf ), and therefore, they were maintainers (CMS-B) with a genotype of Nrfrf. The rest (KC980, KC995, KC999, and KC1009) produced stable male fertile F1 plants in the crosses, and therefore, were restorers (CMS-C) with a genotype of N(S)RfRf. Therefore, the maintainer and restorer sources of resistance may be used in preference in breeding maternal (CMS and their maintainers) and paternal parents (restorers) for resistance to bacterial wilt, respectively, in the hybrid breeding system utilizing cytoplasmic male sterility.

Pseudomonas syringae pv. actinidiae strains, the causal agents of bacterial canker on kiwifruit, were isolated from Korea and Italy in 2011. Among 87 isolates, a total of six representative strains, three from Korea and three from Italy, were identified on the basis of biochemical and physiological tests. Identities were confirmed by PCR using P. syringae pv. actinidiae-specific primers PsaF1/R2, which amplified a 280-bp DNA fragment. The strains isolated from Korea in this study displayed BOX-PCR patterns similar to those isolated from Italy but different from those isolated previously in Korea or the pathotype P. syringae pv. actinidiae strain. The effector hopA1 and hopH1 genes, which are known to be present in strains isolated recently from France and Italy, were also present in P. syringae pv. actinidiae strains, SYS1, SYS2 and SYS4, isolated from Korea in this work. However, no amplicons of the expected size were obtained from strains previously isolated from Korea and Japan. In addition, the Korean strains isolated in this work belonged to haplotype I for the cts gene identical to those strains isolated from recent outbreaks in Italy. These results suggest that P. syringae pv. actinidiae strains isolated from Korea and examined in this work are a new type of strain similar to those found from recent outbreaks in Italy. This is the first report on the occurrence of cts haplotype I strains of P. syringae pv. actinidiae affecting kiwifruit plants in Korea.

We determined the complete genome sequence of a Vietnamese isolate of Southern rice black-streaked dwarf virus (SRBSDV). Whole genome comparisons and phylogenetic analysis showed that the genome of the Vietnamese isolate shared high nucleotide sequence identities of over 97.5% with those of the reported Chinese isolates, confirming a common origin of them. Moreover, the greatest divergence between different SRBSDV isolates was found in the segments S1, S3, S4 and S6, which differs from the sequence alignment results between SRBSDV and Rice black streaked dwarf virus (RBSDV), implying that SRBSDV evolved in a unique way independent of RBSDV. This is the first report of a complete nucleotide sequence of SRBSDV from Vietnam and our data provides new clues for further understanding of molecular variation and epidemiology of SRBSDV in Southeast Asia.

Dinoflagellates are considered one of the most abundant and diverse groups of marine microplankton and viruses are recognized as one of the significant factors affecting the plankton dynamics. Here, we report basic characteristics of a new dinoflagellate-infecting virus, Heterocapsa pygmaea DNA virus (HpygDNAV) which infects a toxic dinoflagellate, H. pygmaea. HpygDNAV is a polyhedral large virus (ca. 160-170 nm in diameter) propagating in its host's cytoplasm. Because of the virion size, appearance in thin sections, and propagation characteristics, HpygDNAV is assumed to harbor a large double-stranded DNA genome; i.e., HpygDNAV is most likely a nucleocytoplasmic large DNA virus (NCLDV) belonging to the family Phycodnaviridae. Its infectivity is strain-specific, rather than species-specific, as is the case for other algal viruses. The burst size and latent period are estimated to be roughly 100-250 infectious units $cell^{-1}$ and < 96 h, respectively.

The chitinase producing Lysobacter enzymogenes C-3 has previously been shown to suppress plant pathogens in vitro and in the field, but little is known of the regulation of chitinase production, or its role in antimicrobial activity and biocontrol. In this study, we isolated and characterized chitinase-defective mutants by screening the transposon mutants of L. enzymogenes C-3. These mutations disrupted genes involved in diverse functions: glucose-galactose transpoter (gluP), disulfide bond formation protein B (dsbB), Clp protease (clp), and polyamine synthase (speD). The chitinase production of the SpeD mutant was restored by the addition of exogenous spermidine or spermine to the bacterial cultures. The speD and clp mutants lost in vitro antifungal activities against plant fungal pathogens. However, the gluP and dsbB mutants showed similar antifungal activities to that of the wild-type. The growth of the mutants in nutrient rich conditions containing chitin was similar with that of the wild-type. However, growth of the speD and gluP mutants was defective in chitin minimal medium, but was observed no growth retardation in the clp and dsbB mutant on chitin minimal medium. In this study, we identified the four genes might be involved and play different role in the production of extracellular chitinase and antifungal activity in L. enzymogenes C-3.

The effect of heavy metals on seedling growth and pigment levels was studied in Arabidopsis using essential (Cu, Mn, and Zn) and non-essential metals (Pb and Hg). Generally increasing the concentrations of the metals resulted in a gradual decrease in root and shoot lengths, a decrease in chlorophylls, an increase in anthocyanins and a fluctuation in carotenoid content depending on the metal types. The toxicity of the metals decreased in the following order: Cu > Hg > Pb > Zn > Mn. Among the five metals, Cu was exceptionally toxic and the most potent inducer of anthocyanins. Pb induced the smallest quantity of anthocyanins but it was the strongest inducer of carotenoids. It suggests that the Cu-stressed Arabidopsis may use anthocyanins as its main antioxidants while the Pb-stressed Arabidopsis use carotenoids as its main protectants. All of the five metals induced an accumulation of anthocyanins. The consistent increase in anthocyanin content in the metal-stressed Arabidpsis indicates that anthocyanins play a major role in the protection against metal stresses.