RESUMEN
To understand newly sequenced genomes of closely related species, comprehensively curated reference genome databases are becoming increasingly important. We have extended CyanoBase (http://genome.microbedb.jp/cyanobase), a genome database for cyanobacteria, and newly developed RhizoBase (http://genome.microbedb.jp/rhizobase), a genome database for rhizobia, nitrogen-fixing bacteria associated with leguminous plants. Both databases focus on the representation and reusability of reference genome annotations, which are continuously updated by manual curation. Domain experts have extracted names, products and functions of each gene reported in the literature. To ensure effectiveness of this procedure, we developed the TogoAnnotation system offering a web-based user interface and a uniform storage of annotations for the curators of the CyanoBase and RhizoBase databases. The number of references investigated for CyanoBase increased from 2260 in our previous report to 5285, and for RhizoBase, we perused 1216 references. The results of these intensive annotations are displayed on the GeneView pages of each database. Advanced users can also retrieve this information through the representational state transfer-based web application programming interface in an automated manner.
Asunto(s)
Alphaproteobacteria/genética , Cianobacterias/genética , Bases de Datos Genéticas , Genoma Bacteriano , Bradyrhizobium/genética , Genes Bacterianos , Internet , Mesorhizobium/genética , Anotación de Secuencia Molecular , Rhizobium/genética , Sinorhizobium/genéticaRESUMEN
Aiming at herbicide-assisted cultivation of Botryococcus braunii for prevention of algal contamination, herbicide-tolerant mutant lines of B. braunii were established for two widely used herbicides, methyl viologen and glufosinate. Some established mutant lines exhibited vigorous oil production and growth in herbicide-containing media. Because the two herbicides were effective in controlling the growth of the algal competitors of B. braunii, these mutants can be directly used in industrial attempts for cost-effective oil production in herbicide-assisted non-axenic systems. This is the first report of mutagenesis of B. braunii.
Asunto(s)
Chlorophyta/efectos de los fármacos , Chlorophyta/genética , Resistencia a los Herbicidas/genética , Herbicidas/toxicidad , Mutación/genética , Chlorophyta/crecimiento & desarrollo , Mutagénesis/efectos de los fármacosRESUMEN
Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere.
Asunto(s)
Bradyrhizobium/genética , ADN Bacteriano/química , ADN Bacteriano/genética , Genoma Bacteriano , Análisis de Secuencia de ADN , Proteínas Bacterianas/genética , Composición de Base , Bradyrhizobium/aislamiento & purificación , Bradyrhizobium/fisiología , Redes y Vías Metabólicas/genética , Datos de Secuencia Molecular , Sistemas de Lectura Abierta , ARN no Traducido/genética , Microbiología del Suelo , Simbiosis , SinteníaRESUMEN
Because of the increasing use of maize hybrids with genetically modified (GM) stacked events, the established and commonly used bulk sample methods for PCR quantification of GM maize in non-GM maize are prone to overestimate the GM organism (GMO) content, compared to the actual weight/weight percentage of GM maize in the grain sample. As an alternative method, we designed and assessed a group testing strategy in which the GMO content is statistically evaluated based on qualitative analyses of multiple small pools, consisting of 20 maize kernels each. This approach enables the GMO content evaluation on a weight/weight basis, irrespective of the presence of stacked-event kernels. To enhance the method's user-friendliness in routine application, we devised an easy-to-use PCR-based qualitative analytical method comprising a sample preparation step in which 20 maize kernels are ground in a lysis buffer and a subsequent PCR assay in which the lysate is directly used as a DNA template. This method was validated in a multilaboratory collaborative trial.
Asunto(s)
ADN de Plantas/análisis , Plantas Modificadas Genéticamente/genética , Reacción en Cadena de la Polimerasa/métodos , Semillas/genética , Zea mays/genética , Reproducibilidad de los Resultados , Zea mays/clasificaciónRESUMEN
The Bt11 maize-specific qualitative detection method based on polymerase chain reaction (PCR) in the JAS analytical test handbook has been widely used for administrative monitoring of GM crops and quality control of commercially distributed grains. In the present investigation, some apparently false-positive detections were observed in assays using the Bt11 maize-specific method, and these erroneous results were proved to have been caused by non-specific DNA amplification. We improved the detection method to reduce non-specific amplification by decreasing the concentration of magnesium ions in the PCR mixture. The subsequent evaluation of analytical performance demonstrated no marked difference between the currently used and the improved methods, except for the reduced non-specific amplification. We conclude that the currently used standard method should be replaced with the improved method for the reliable detection of Bt11 maize.