Occurrence of Chrysanthemum chlorotic mottle viroid in Japan

Chrysanthemum chlorotic mottle viroid (CChMVd) was detected in Akita Prefecture, Japan, from chrysanthemums (Dendranthema grandiflorum) with distinct yellow leaf mottling and necrosis. The four clones are 398–399 nucleotides long and are thought to be the symptomatic type based on their UUUC sequence at positions 82–85 in the CChMVd tetraloop.The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under accession numbers AB181857–AB181860     

Isolation and characterization of a novel potyvirus tentatively named Ornithogalum virus 2

A novel potyvirus, tentatively named Ornithogalum virus 2 (OV-2) because only its nucleotide sequence of the coat protein gene has been revealed, was isolated for the first time from Ornithogalum thyrsoides. OV-2 had a flexuous particle (700–740 nm in length) and was sap and aphid transmissible. The virus had a narrow host range; of 36 test plants in 12 families, only O. thyrsoides and O. dubium were infected. Because the virus caused characteristic stripe mosaic on O. thyrsoides, we propose Ornithogalum stripe mosaic virus (OrSMV), instead of OV-2 for the proper name of the virus. The nucleotide sequence data reported is available in the DDBJ/EMBL/GenBank databases under accession number AB271783.     

First report of <Emphasis Type="Italic">Bean common mosaic virus</Emphasis> in yam bean [<Emphasis Type="Italic">Pachyrhizus erosus</Emphasis> (L.) Urban] in Indonesia

Severe mosaic with leaf malformation and green vein banding was observed on yam bean in West and Central Java, Indonesia. Virions of the causal virus were flexuous filaments, about 700 nm in length, with a coat protein of 30 kDa. The virus was transmitted by mechanical inoculation and by aphids in a nonpersistent manner. The nucleotide sequence of the coat protein gene had the highest identity with that of Bean common mosaic virus (BCMV, genus Potyvirus) isolate VN/BB2-5. Based on demarcation criteria, including the genome sequence and host range, we tentatively designate this isolate as BCMV-IYbn (Indonesian yam bean). The nucleotide sequence reported is available in the DDBJ/EMBL/GenBank databases under accession number AB289438.     

Cycas necrotic stunt virus isolated from gladiolus plants in Japan

An undescribed spherical virus ca. 30 nm in diameter was isolated from gladiolus (Gladiolus spp.) plants in Japan. The virus had a moderate host range within eight families. Purified virus preparations contained two large RNA components and one coat protein with mobility similar to Cycas necrotic stunt virus (CNSV) from cycas (Cycas revolute). The virus was serologically closely related to CNSV. Its nucleotide sequence of the coat protein gene had 89% common identity with that of CNSV. These results indicated that the virus isolated from gladiolus is a new strain of CNSV. The nucleotide sequence data reported are available in the DDBJ/EMBL/Gen Bank databases under the accession number AB237656.     

Occurrence of rocket larkspur witches’ broom caused by “<Emphasis Type="Italic">Candidatus</Emphasis> Phytoplasma asteris” in Japan

In October 2001, a disease of rocket larkspur (Cosolida ambigua (L.) P. W. Ball et Heyw), characterized by witches’ broom, yellows and virescence of flowers, was found in Yakage Town in Okayama Prefecture. Electron microscopy revealed the presence of phytoplasma-like bodies in the phloem of diseased plants. The causal phytoplasma was identified as “Candidatus Phytoplasma asteris” based on 16S rDNA sequence analysis, and demonstrated to be acquired by the leafhopper Macrosteles striifrons. The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession number AB258330.     

Occurrence of chrysanthemum virescence caused by “<Emphasis Type="Italic">Candidatus</Emphasis> Phytoplasma aurantifolia” in Okinawa

In 1999, a disease of chrysanthemum [Dendranthema grandiflorum (Ramat.) Kitamura], characterized by virescence of flowers, occurred in Okinawa Prefecture. The causal agent was identified as “Candidatus Phytoplasma aurantifolia” based on 16S rDNA sequencing. The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under accession number AB247462.     

Occurrence of strawberry marginal chlorosis caused by “Candidatus Phlomobacter fragariae” in Japan

In February 2004, a disease of strawberry (Fragaria × ananassa Duch.), causing little-leaf, proliferation, malformation of fruits, and marginal chlorosis of leaves, occurred in Ehime Prefecture, Japan. The causal pathogen was identified as a phloem-restricted bacterium-like organism, “Candidatus Phlomobacter fragariae,” based on polymerase chain reaction (PCR) detection, electron microscopy, and sequence analysis of PCR products. This is the first report of strawberry marginal chlorosis in Asia. The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession number AB246669.     

Characterization of a novel potyvirus tentatively named <Emphasis Type="Italic">Ornithogalum</Emphasis> virus 3, successfully isolated from <Emphasis Type="Italic">O. thyrsoides</Emphasis> co-infected with two other potyviruses by single-aphid inoculation

A potyvirus tentatively named Ornithogalum virus 3 (OV-3) was successfully isolated by single-aphid transmissions from O. thyrsoides mix-infected with OV-3, Ornithogalum mosaic virus (OrMV) and Ornithogalum stripe mosaic virus (OrSMV). OV-3, a flexuous, rod-shaped particle of ca. 690 nm, was sap and aphid transmissible. The virus had a narrow host range and caused necrotic mosaic on O. thyrsoides under cold conditions. We therefore propose the name Ornithogalum necrotic mosaic virus (OrNMV) for OV-3. A synergistic increase in symptom severity was apparent on O. thyrsoides mix-infected with OrSMV/OrNMV, but not with either OrMV/OrNMV or OrMV/OrSMV. The nucleotide sequence data reported is available in the DDBJ/EMBL/GenBank databases under accession number AB282754.     

Phylogenetic analysis of elongation factor Tu gene of phytoplasmas from Japan

The elongation factor Tu (tuf) gene from nine Japan phytoplasma isolates was amplified with the polymerase chain reaction, and the DNA sequences of the tuf gene were determined. The tuf gene from 14 phytoplasma isolates, including reference isolates and other bacteria, were phylogenetically analyzed. A nucleotide sequence of the tuf gene among seven aster yellows group (16Sr I-B and I-D) phytoplasmas had 97%–100% similarity, and the tuf gene of two phytoplasmas of the X-disease group (16Sr III-B) had 99% similarity. The tuf genes had lower homology than did the 16S rRNA gene in the phytoplasma groups. A phylogenetic tree of amino acid sequences of the tuf gene was nearly equal to that of the 16S rRNA gene but differed somewhat from the tree based on the 16S rRNA gene in that paulownia witches broom (PaW: 16Sr I-D) and American aster yellows (AAY: 16Sr I-B) were in a subclade.The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession numbers AB095495, AB095667, AB095668, AB095669, AB095670, AB095671, AB095672, AB095673 and AB095674     

Occurrence of bacterial rot of onion bulbs caused by Burkholderia cepacia in Japan

In 2001, a bacterial rot of onion (Allium cepa L.) bulbs was observed in Japan. The causal agent was identified as Bukholderia cepacia (Palleroni & Holmes 1981 ex Burhkolder 1950) Yabuuchi, Kosako, Oyaizu, Yano, Hotta, Ezaki, and Arakawa 1993. The identified bacteria were divided into two groups (Y and W) based on colony colors, and several phenotypic and genetic characteristics. Based on recA polymerase chain reaction assays, the strains of the Y and W groups belong to genomovar I (B. cepacia sensu stricto) and genomovar III (B. cenocepacia), respectively.The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession numbers AB162427 and AB162428     

Eremothecium ashbyi causes soybean yeast-spot and is associated with stink bug, Riptortus clavatus

Many fusiform ascospores observed on soybean seeds with yeast spot disease symptoms differed significantly from those of Eremothecium coryli, the known causal agent of yeast spot disease in soybean. On the basis of morphological and physiological characteristics and sequence data of the internal transcribed spacer regions including the 5.8S rDNA and D1/D2 regions of 26S rDNA, this fungus was identified as E. ashbyi. Pathogenicity of E. ashbyi was confirmed by reinoculation test. This report is the report on E. ashbyi causing soybean yeast spot disease. In addition, this study showed that E. ashbyi was transmitted by the stink bug, Riptortus clavatus, as was E. coryli, the two Eremothecium yeasts may have been acquired when the stink bug fed on infected soybeans and overwintered in this insect species. The nucleotide sequence data reported are available in the GeneBank/EMBL/DDBJ database as accessions AB294407 to AB294412 for E. ashbyi EA1, EA7 and EA11.     

<Emphasis Type="Italic">Eremothecium coryli</Emphasis> and <Emphasis Type="Italic">E.</Emphasis><Emphasis Type="Italic">ashbyi</Emphasis> cause yeast spot of azuki bean

Yeast-like fungi were isolated from lesions on azuki bean (cv. Shin-Kyotodainagon) seeds that had been sucked by bean bugs in Kyoto Prefecture, Japan. On the basis of morphological and physiological characteristics and sequence data of the internal transcribed spacer (ITS) regions including the 5.8S rDNA, these yeasts were identified as Eremothecium coryli and E. ashbyi. Pathogenicity of those yeasts was confirmed by a reinoculation test. To our knowledge, this is the first report of the occurrence of yeast spot in azuki bean in Japan. The nucleotide sequence data reported are available in the GeneBank/EMBL/DDBJ database as accessions AB478291–AB478309 for E. coryli AZC1–19 and AB478310–AB478317 for E. ashbyi AZA1–8.     

Evidence of a new Tomato yellow leaf curl virus in Japan and its detection using PCR

A new isolate of Tomato yellow leaf curl virus (TYLCV) has been identified from tomato plants in Kochi Prefecture in Japan and designated TYLCV-[Tosa]. The complete nucleotide sequence of the isolate was determined and found to consist of 2781 nt. In phylogenetic analyses of entire nucleotide sequences, TYLCV-[Tosa] was delineated as a single branch and was more closely related to TYLCV-[Almeria] than TYLCV isolates Ng, Sz, or Ai reported in Japan, which had spread since 1996. Isolate TYLCV-[Tosa] is suggested to be a newly introduced, novel isolate of TYLCV that dispersed into Kochi Prefecture. In addition, a rapid method using the polymerase chain reaction to separate TYLCV isolates into four genetic groups was established. This method would be useful for reliable diagnosis based on genetic differences among isolates of TYLCV.The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under accession numbers AB192965 and AB192966     

DNA sequence analysis of ribosomal ITS region 1 of Phytophthora vignae f. sp. adzukicola, the pathogen that causes stem rot of adzuki bean

Sequences of the internal transcribed spacer (ITS) region 1 were used to examine the phylogenetic relationships among races of 19 isolates of Phytophthora vignae f. sp. adzukicola and between this forma specialis and three isolates of the closely related P. vignae f. sp. vignae. The ITS 1 sequences were highly conserved (> 98.7% similarity) among representatives of both formae speciales groups. The results of this study indicate that P. vignae is a monophyletic group. The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession nos. AB120062–AB120080 and AB120122     

The hrpZ and hrpA genes are variable, and useful for grouping Pseudomonas syringae bacteria

The hrpS to hrpB regions from strains of Pseudomonas syringae were amplified by polymerase chain reaction (PCR) and the DNA sequence determined. The order of hrpS, hrpA, hrpZ, and hrpB was consistent among P. syringae strains. The sequence of hrpS was highly conserved. In a cluster analysis with the hrpS sequence, P. syringae strains were divided into four groups (I, II, III, and IV) and one undetermined strain, in agreement with previous studies. In contrast, the hrpZ sequences contained insertions, deletions, and base substitutions followed by changes in amino acids. Based on cluster analysis of hrpA, hrpZ, and hrpB, P. syringae strains could be divided into five groups. One of the four groups (group I) in the cluster analysis of hrpS could be further divided into two subgroups (groups IA and IB). Groups II, III, and IV were the same in the two analyses. Group-specific primers were designed, based on the DNA sequences of hrpZ, that could differentiate the groups of P. syringae strains. The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession numbers AB112552 to AB112581     

<Emphasis Type="Italic">Turnip yellow mosaic virus</Emphasis> isolated from Chinese cabbage in Japan

A virus that caused a distinct yellow mosaic was isolated in Okayama, Japan from Chinese cabbage (Brassica rapa L., Pekinensis group). The virus, with spherical particles ca. 28 nm in diameter, was mechanically transmissible only to cruciferous species. From the host range, characteristic morphology of virus particles, serology and sequence analysis of coat protein gene, the causal virus was identified as Turnip yellow mosaic virus (TYMV). Seed transmission of TYMV at 0–2.2% in Chinese cabbage was confirmed. This report is the first of TYMV from Chinese cabbage and in Japan. The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases as accessions AB358971 and AB358972.     

Phylogeny of five predominant pospiviroid species in Belgium

In Belgium pospiviroids are routinely detected in various hosts. The most frequently found pospiviroids are: Citrus exocortis viroid (CEVd), Chrysanthemum stunt viroid (CSVd), Potato spindle tuber viroid (PSTVd), Tomato apical stunt viroid (TASVd) and Tomato chlorotic dwarf viroid (TCDVd). Apart from the high incidence of pospiviroids in latently-infected ornamentals, viroids have also been found in plants where they cause disease: PSTVd and TCDVd in tomatoes and CSVd in chrysanthemum. In order to gain more epidemiological data on these infections, this study has conducted phylogenetic analyses of Belgian isolates for each of these five pospiviroid species. PSTVd and CEVd-isolates show a clustering depending on host plant identity. This was not observed for TCDVd and TASVd. A very high degree of sequence similarity was noticeable for CSVd-isolates from various hosts. During the past decade, PSTVd and CSVd-infected mother plants have been systematically eradicated in Belgium after positive detection results, also when found in symptomless plants, leading to a decreased trend of these quarantine pests in the past few years. However, other non-quarantine pospiviroid species are still ubiquitously present in many ornamentals. Since these pospiviroids can be equally harmful to crops as the two quarantine pests PSTVd and CSVd, there is still a risk that transmission occurs from symptomless-infected ornamental plants to economically important crops in Belgium such as tomato, pepper and chrysanthemum.     

Cloning of the pathogenicity-related gene <Emphasis Type="Italic">FPD1</Emphasis> in <Emphasis Type="Italic">Fusarium oxysporum</Emphasis> f. sp. <Emphasis Type="Italic">lycopersici</Emphasis>

We selected a reduced-pathogenicity mutant of Fusarium oxysporum f. sp. lycopersici, a tomato wilt pathogen, from the transformants generated by restriction enzyme-mediated integration (REMI) transformation. The gene tagged with the plasmid in the mutant was predicted to encode a protein of 321 amino acids and was designated FPD1. Homology search showed its partial similarity to a chloride conductance regulatory protein of Xenopus, suggesting that FPD1 is a transmembrane protein. Although the function of FPD1 has not been identified, it does participate in the pathogenicity of F. oxysporum f. sp. lycopersici because FPD1-deficient mutants reproduced the reduced pathogenicity on tomato.The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession number AB110097     

Sclerotinia rot of blueberry caused by <Emphasis Type="Italic">Sclerotinia sclerotiorum</Emphasis>

In 2002, rotted flower clusters and blighted shoot tips and leaves were observed on highbush blueberry (Vaccinium corymbosum L.) and rabbiteye blueberry (V. ashei Reade) plants in Chiba, Japan. The causal fungus isolated from the diseased plants was morphologically identified as Sclerotinia sclerotiorum (Libert) de Bary. The fungus reproduced natural symptoms after inoculation, then reisolated from the symptomatic parts. This is the first report of blueberry sclerotinia rot caused by S. sclerotiorum. The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under accession numbers AB269903#(020501) and AB233346 (020505).