Rice blast fungus sequenced

This article does not have an abstract

CastorDB: a comprehensive knowledge base for Ricinus communis

<p>Abstract</p> <p>Background</p> <p><it>Ricinus communis </it>is an industrially important non-edible oil seed crop, native to tropical and subtropical regions of the world. Although, <it>R. communis </it>genome was assembled in 4X draft by JCVI, and is predicted to contain 31,221 proteins, the function of most of the genes remains to be elucidated. A large amount of information of different aspects of the biology of <it>R. communis </it>is available, but most of the data are scattered one not easily accessible. Therefore a comprehensive resource on Castor, Castor DB, is required to facilitate research on this important plant.</p> <p>Findings</p> <p>CastorDB is a specialized and comprehensive database for the oil seed plant <it>R. communis</it>, integrating information from several diverse resources. CastorDB contains information on gene and protein sequences, gene expression and gene ontology annotation of protein sequences obtained from a variety of repositories, as primary data. In addition, computational analysis was used to predict cellular localization, domains, pathways, protein-protein interactions, sumoylation sites and biochemical properties and has been included as derived data. This database has an intuitive user interface that prompts the user to explore various possible information resources available on a given gene or a protein.</p> <p>Conclusion</p> <p>CastorDB provides a user friendly comprehensive resource on castor with particular emphasis on its genome, transcriptome, and proteome and on protein domains, pathways, protein localization, presence of sumoylation sites, expression data and protein interacting partners.</p

Functional analysis of a novel ABC transporter ABC4 from Magnaporthe grisea

The ATP-binding cassette (ABC) superfamily of membrane transporters has been implicated to play a role in pathogenesis in various phytopathogenic fungi. In an insertional mutagenesis screen for pathogenicity mutants of Magnaporthe grisea obtained via Agrobacterium tumefaciens-mediated transformation (ATMT), a novel gene belonging to the ABC transporter family was identified. The gene ABC4 was predicted to be 5045 bp in length coding for a protein of 1654 amino acids. The mutant did not form functional appressoria and was nonpathogenic. When compared with wild type, the mutant showed increased sensitivity to certain antifungal compounds and phytoalexins, implying the role of ABC4 in multidrug resistance (MDR) as well as establishment in the host. Reverse transcriptase PCR showed the expression of ABC4 in wild-type strain while it was absent in the mutant abc4. In real-time PCR, the expression of ABC4 was seen to be enhanced in the presence of various drugs tested. The data suggests that ABC4 is required for the pathogenicity of M. grisea, helping the fungus to cope with the cytotoxic environment during infection

Expression of a plant defensin in rice confers resistance to fungal phytopathogens

Transgenic rice (Oryza sativa L. cv. Pusa basmati 1), overexpressing the Rs-AFP2 defensin gene from the Raphanus sativus was generated by Agrobacterium tumefaciens-mediated transformation. Expression levels of Rs-AFP2 ranged from 0.45 to 0.53% of total soluble protein in transgenic plants. It was observed that constitutive expression of Rs-AFP2 suppresses the growth of Magnaporthe oryzae and Rhizoctonia solani by 77 and 45%, respectively. No effect on plant morphology was observed in the Rs-AFP2 expressing rice lines. The inhibitory activity of protein extracts prepared from leaves of Rs-AFP2 plants on the in vitro growth of M. oryzae indicated that the Rs-AFP2 protein produced by transgenic rice plants was biologically active. Transgene expression of Rs-AFP2 was not accompanied by an induction of pathogenesis-related (PR) gene expression, suggesting that the expression of Rs-AFP2 directly inhibits the pathogens. Here, we demonstrate that transgenic rice plants expressing the Rs-AFP2 gene show enhanced resistance to M. oryzae and R. solani, two of the most important pathogens of rice

Bacterial population structure of the jute-retting environment

Jute is one of the most versatile bast fibers obtained through the process of retting, which is a result of decomposition of stalks by the indigenous microflora. However, bacterial communities associated with the retting of jute are not well characterized. To investigate the presence of microorganisms during the process of jute retting, full-cycle rRNA approach was followed, and two 16S rRNA gene libraries, from jute-retting locations of Krishnanagar and Barrackpore, were constructed. Phylotypes affiliating to seven bacterial divisions were identified in both libraries. The bulk of clones came from Proteobacteria (~37, 41%) and a comparatively smaller proportion of clones from the divisions-Firmicutes (~11, 12%), Cytophaga-Flexibacter-Bacteroidetes group (CFB; ~9, 7%), Verrucomicrobia (~6, 5%), Acidobacteria (~4, 5%), Chlorobiales (~5, 5%), and Actinobacteria (~4, 2%) were identified. Percent coverage value and diversity estimations of phylotype richness, Shannon-Weiner index, and evenness confirmed the diverse nature of both the libraries. Evaluation of the retting waters by whole cell rRNA-targeted flourescent in situ hybridization, as detected by domain- and group-specific probes, we observed a considerable dominance of the β-Proteobacteria (25.9%) along with the CFB group (24.4%). In addition, 32 bacterial species were isolated on culture media from the two retting environments and identified by 16S rDNA analysis, confirming the presence of phyla, Proteobacteria (~47%), Firmicutes (~22%), CFB group (~19%), and Actinobacteria (~13%) in the retting niche. Thus, our study presents the first quantification of the dominant and diverse bacterial phylotypes in the retting ponds, which will further help in improving the retting efficiency, and hence the fiber quality

A novel gene MGA1 is required for appressorium formation in Magnaporthe grisea

Insertional mutagenesis is an effective way to study the infection mechanism of fungal pathogens. In an attempt to identify the genes involved in appressorium formation from Magnaporthe grisea, we carried out Agrobacterium tumefaciens mediated transformation (ATMT) of the fungus. Analysis of the region flanking the T-DNA integration site in one of the appressorium mutants showed insertion in a gene coding a 78 amino acid protein (MGA1), showing no significant homology to any of the known proteins. The mutant mga1 caused neither foliar nor root infection. Complementation of the mutated gene with the full length wild type gene restored appressorium formation as well as rice infection demonstrating the involvement of this gene in pathogenicity of M. grisea. In an indirect immunolocalisation assay, the MGA1 expression was seen predominantly in germ tube and appressoria. The mutant was impaired in glycogen and lipid mobilization required for appressorium formation. The glycerol content in the mycelia of the mutant under hyperosmotic stress conditions was less as compared to wild type and was thus unable to tolerate the hyperosmotic stress induced by sorbitol. We hypothesize that MGA1 plays a crucial role in signal transduction leading to the metabolism of glycogen and lipids, which is a part of appressorium differentiation process

Leucothecium emdenii: a novel Larvicidal fungus against mosquito Larvae

This article does not have an abstract

Development of a sequence characterized amplified region (SCAR) based indirect selection method for a dominant blast-resistance gene in rice

Two randomly amplified polymorphic DNA (RAPD) markers, OPF6<SUB>2700</SUB> and OPH18<SUB>2400</SUB>, tightly linked to Pi-10, a dominant blast-resistance gene conferring complete resistance to isolate 106 (international race IB46) of the blast fungus were identified. To derive sequence characterized amplified regions (SCARs) from OPF6<SUB>2700</SUB> and OPH18<SUB>2400</SUB>, these amplified RAPD products were cloned and sequenced. Nucleotide sequence information, obtained for each end of the two linked RAPD markers, was used to design 24-mer oligonucleotide primers for PCR amplification of the respective SCARs. Polymorphisms appearing as differences in the length of the SCAR's alternate alleles were considered for the indirect selection of Pi-10. Such polymorphisms converted the linked dominant RAPD loci into codominant SCAR markers and also facilitated the indirect scoring of the blast-resistant and blast-susceptible genotypes. The development of length variant codominant SCAR markers linked to a major gene for blast resistance in rice is described. The codominant SCARs will facilitate marker-assisted selection of the Pi-10 locus in rice breeding programs and will also be useful as genetic markers for high resolution mapping of the Pi-10 region

Cloning and growth-regulated expression of the gene encoding the hepatitis B virus middle surface antigen in Yarrowia lipolytica

Expression of the gene encoding the hepatitis B virus middle surface antigen (pre-HBsAg) in the yeast Yarrowia lipolytica has been studied. The preS2-HBsAg gene was expressed from the alkaline extracellular protease-encoding gene (XPR2) promoter. In the fusion construct, the membrane-spanning 'a' domain of preS2-HBsAg has been replaced by the leader peptide and the prol region of the alkaline protease, thus eliminating the epitope responsible for the immune escape mechanism. Expression has been found to be growth-stage dependent with the highest protein accumulation during the stationary phase, accounting for around 2.35% of the total soluble intracellular proteins. The produced protein was assembled into Dane particles and was immunogenic in mice. The expression vector was found to be stable for at least 100 generations under non-selective conditions

A simple protocol for isolation of fungal DNA

Genomic DNA was isolated from as little as 2 mg dry biomass of Magnaporthe grisea by microwave treatment within 30 s. The quantity of DNA was good enough for PCR analysis and Dot blot hybridization. This technique can be used for various studies, such as DNA fingerprinting to study the population structure of the phytopathogen in different regions, and for a quick screening of M. grisea transformants