Shin-ichi Fuji

Complete nucleotide sequence of the genomic RNA of Aconitum latent virus (genus Carlavirus) isolated from Delphinium sp.

Summary. We determined the complete nucleotide sequence of Aconitum latent virus (AcLV-D) isolated from Delphinium sp. The genomic RNA of AcLV-D is 8,657 nucleotides in length, excluding the poly (A) tail. Based on computer analysis, six open reading frames (ORFs) were identified as for other carlaviruses. Although each ORF differs from those of previously reported carlaviruses, the coat protein of AcLV and Potato virus M (PVM) shows a high level of identity. The results suggest that AcLV is a distinct carlavirus species but closely related to PVM.

Comparisons among isolates of Sweet potato feathery mottle virus using complete genomic RNA sequences

We determined the complete or partial nucleotide sequences of eight Sweet potato feathery mottle virus (SPFMV) isolates and compared them with 12 other partial SPFMV sequences. The genome organization of the isolate Bungo (strain group C) was very different from those of isolates in the russet crack, ordinary (O), and east Africa groups. 10-O appeared to be a recombinant of isolates S and O, with a recombination site within the P1 gene. This study will help to provide a better understanding of the taxonomy and biology of SPFMV and how these features relate to virulence.

Complete nucleotide sequence of the new potexvirus Alstroemeria virus X

Summary.A flexuous virus was isolated in Japan from an alstroemeria plant showing mosaic symptoms. The virus had a broad host range but had systemically latent infectivity in alstroemeria. The virus was assigned to the genus Potexvirus based on morphology and physical properties and on an analysis of the complete nucleotide sequence. The genomic RNA of the virus was 7,009 nucleotides in length, excluding the 3′-terminal poly (A) tail. It contained five open reading frames (ORFs), which was consistent with other members of the genus Potexvirus. Although nucleotide sequences of the ORFs differ from previously reported potexviruses, a phylogenetic analysis placed it phylogenetically close to Narcissus mosaic virus and Scallion virus X. Therefore, we propose that this virus should be designated as Alstroemeria virus X (AlsVX).

Nucleotide sequence of coat protein gene of yam mild mosaic virus, isolated in Papua New Guinea.

SummaryWe determined the 3′-termimus 1353 nucleotides (nts) in length excluding the poly (A) tail of yam mild mosaic potyvirus (YMMV) RNA. The sequence starts within a long open reading frame (ORF) 1209 nts and is followed by untranslated region (3′-UTR) of 144 nts. The coat protein (CP) contains 266 amino acids (aa) with molecular ratio (Mr) of approximately 30 kDa. The CP of YMMV differs substantially from yam mosaic virus (YMV), Japanese yam mosaic virus (JYMV) (57 and 61% of amino acid sequence identity) and other potyvirus species. This result suggests that YMMV should be classified as a new yam potyvirus.

Isolation of novel types of Arabidopsis mutants with altered reactions to cadmium: cadmium-gradient agar plates are an effective screen for the heavy metal-related mutants

We are interested in elucidating the molecular mechanisms underlying plant reactions to the toxic heavy metal cadmium (Cd). To this end, we devised a new screening strategy using agar plates with a gradient of Cd concentrations, termed Cd-gradient agar plates (CGAPs), to isolate Arabidopsis mutants that displayed altered reactions to the metal. Arabidopsis M2 seeds, derived from ethyl methanesulfonate (EMS) treated seeds, were germinated on the CGAPs such that the primary root of each seedling elongated against increasing concentrations of Cd on the surface of the plate. Under these conditions, the lengths of the primary roots reliably demonstrated the degree of Cd tolerance of individual seedlings. The use of CGAPs also allowed close observation of the root reaction of each seedling to Cd without causing lethal damage. The screen identified three mutant lines, MRC-32, MRC-22 and MRC-26, which showed distinctly different characteristics. MRC-32 plants exhibited enhanced tolerance to Cd and contained Cd at higher concentrations than wild-type (WT) plants treated with the heavy metal. The whole root system of MRC-22 plants showed a Cd-phobic response. MRC-26 plants accumulated less Cd in their aboveground tissues than WT plants, suggesting that they were defective in transporting the heavy metal from roots to aboveground tissues. We also determined the likely chromosomal location of each mutation.

Broad bean wilt virus 2 in yams

We identified Broad bean wilt virus 2 (BBWV-2) in yams based on particle morphology, test plant symptoms, protein features, aphid transmission, and molecular classification using nucleotide sequences of coat protein genes.

Nucleotide sequence of the coat protein genes of alstroemeria mosaic virus and amazon lily mosaic virus, a tentative species of genus potyvirus.

Summary.The nucleotide sequences of the 3′ terminal region of the genomes of Alstroemeria mosaic virus (AlsMV) and the Amazon lily mosaic virus (ALiMV) have been determined. These sequences contain the complete coding region of the viral coat protein (CP) gene followed by a 3′-untranslated region (3′-UTR). AlsMV and ALiMV share 74.9% identity in the amino acid sequence of the CP, and 55.6% identity in the nucleotide sequence of the 3′-UTR. Phylogenetic analysis of these CP genes and 3′-UTRs in relation to those of 79 potyvirus species revealed that AlsMV and ALiMV should be assigned to the Potato virus Y (PVY) subgroup. AlsMV and ALiMV were concluded to have arisen independently within the PVY subgroup.

Nucleotide sequences of the coat protein gene of potyviruses infecting Ornithogalum thyrsoides

Summary. Species of three viral genera infecting Ornithogalum thyrsoides plants showing mosaic symptoms were identified using RT-PCR and degenerate universal primers for each viral genus. The DNA fragments obtained encoded the coat protein (CP) gene and were sequenced. The plants were found to be infected with one or other of three potyvirus species, one of them was Ornithogalum mosaic virus (OrMV). The other two viruses were previously unrecorded and were named Ornithogalum virus 2 (OV-2) and 3 (OV-3). Direct comparison and phylogenetic analysis with published OrMV isolates revealed that the CP of the three OrMV-like clones were more similar to Pterostylis virus Y (PtVY) than to OrMV. No carlavirus or potexvirus was isolated.

Modeling Infection of Spring Onion by Puccinia allii in Response to Temperature and Leaf Wetness

The influence of temperature and leaf wetness duration on infection of spring onion (Japanese bunching onion) leaves by Puccinia allii was examined in controlled-environment experiments. Leaves of potted spring onion plants (Allium fistulosum cv. Yoshikura) were inoculated with urediniospores and exposed to 6.5, 10, 15, 22, or 27 h of wetness at 5, 10, 15, 20, or 25 degrees C. The lesion that developed increased in density with increasing wetness duration. Relative infection was modeled as a function of both temperature and wetness duration using the modified version of Weibulls cumulative distribution function (R(2) = 0.9369). Infection occurred between 6.5 and 27 h of leaf wetness duration at 10, 15, 20, and 25 degrees C and between 10 and 27 h at 5 degrees C, and increased rapidly between 6.5 and 15 h of wetness at 10, 15, and 20 degrees C. At 25 degrees C, few uredinia developed regardless of the wetness duration. Parameter H, one of eight parameters used in the equation and which controls the asymmetry in the response curve, varied markedly according to the temperature, so that the model could be improved by representing H as a function of wetness duration (R(2) = 0.9501).

Deleterious effects of fungi isolated from paddy soils on seminal root of rice

Soil samples were collected from rice paddies at 22 locations in northeastern Honshu, Japan. In 20 of the samples, seedling growth of rice was improved by soil pasteurization (aerated steaming at 60°C for 30 min), although no typical disease symptoms were observed in the seedlings grown in the untreated soil samples. In most locations, rice seedlings grew better in a potting medium containing root material from plants grown in the pasteurized portion of a soil sample than in a medium with root material from plants grown in the unpasteurized portion of the same sample. The results suggest that microorganisms that restrained rice seedling growth may be common in the soils of rice paddies. Approximately 800 isolates were obtained from seedling roots grown in unpasteurized soils and grouped by cultural and microscopic morphologies. The deleterious effects of 79 isolates from 21 major groups, most of which were soil-dwelling taxa, were examined after direct inoculation of the seminal roots. Isolates of Curvularia sp., Cirrenalia sp., Eppicoccum nigrum, Fusarium graminearum, F. oxysporum, Gliocladium virens, Humicola sp., Penicillium sp., Rhizoctonia oryzae-sativae, Sclerotium hydrophilum, Trichoderma aureoviride, and T. harzianum inhibited root growth, suggesting that deleterious root-infecting fungi were more common in paddy soil than previously thought. These fungi may be involved in the restraint of rice seedling growth.