Gene projects: a genome web tool for ongoing mining and annotation applied to CitEST

Genome projects, both genomic DNA and ESTs (cDNA), generate a large amount of information, demanding time and a well-structured bioinformatics laboratory to manage these data. These genome projects use information available in heterogeneous formats from different sources. The amount and heterogeneity of this information, as well as the absence of a world consensus pattern, make the integration of these data a difficult task. At the same time, sub-tasks, such as microarray analyses of these projects, are very complex. This creates a demand for the development of creative solutions for ongoing annotation, thematic projects, microarray experiments, etc. This paper presents Gene Projects, a system developed to integrate all kinds of solutions.10301036Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom Disease of cacao

<p>Abstract</p> <p>Background</p> <p>The basidiomycete fungus <it>Moniliophthora perniciosa </it>is the causal agent of Witches' Broom Disease (WBD) in cacao (<it>Theobroma cacao</it>). It is a hemibiotrophic pathogen that colonizes the apoplast of cacao's meristematic tissues as a biotrophic pathogen, switching to a saprotrophic lifestyle during later stages of infection. <it>M. perniciosa</it>, together with the related species <it>M. roreri</it>, are pathogens of aerial parts of the plant, an uncommon characteristic in the order Agaricales. A genome survey (1.9× coverage) of <it>M. perniciosa </it>was analyzed to evaluate the overall gene content of this phytopathogen.</p> <p>Results</p> <p>Genes encoding proteins involved in retrotransposition, reactive oxygen species (ROS) resistance, drug efflux transport and cell wall degradation were identified. The great number of genes encoding cytochrome P450 monooxygenases (1.15% of gene models) indicates that <it>M. perniciosa </it>has a great potential for detoxification, production of toxins and hormones; which may confer a high adaptive ability to the fungus. We have also discovered new genes encoding putative secreted polypeptides rich in cysteine, as well as genes related to methylotrophy and plant hormone biosynthesis (gibberellin and auxin). Analysis of gene families indicated that <it>M. perniciosa </it>have similar amounts of carboxylesterases and repertoires of plant cell wall degrading enzymes as other hemibiotrophic fungi. In addition, an approach for normalization of gene family data using incomplete genome data was developed and applied in <it>M. perniciosa </it>genome survey.</p> <p>Conclusion</p> <p>This genome survey gives an overview of the <it>M. perniciosa </it>genome, and reveals that a significant portion is involved in stress adaptation and plant necrosis, two necessary characteristics for a hemibiotrophic fungus to fulfill its infection cycle. Our analysis provides new evidence revealing potential adaptive traits that may play major roles in the mechanisms of pathogenicity in the <it>M. perniciosa</it>/cacao pathosystem.</p

American oil palm from Brazil: genetic diversity, population structure, and core collection.

The American oil palm [Elaeis oleifera (Knuth) Cortés] has pronounced importance in oil palm breeding programs. Here, a germplasm bank (GB) of E. oleifera plants collected in the Amazon rainforest in Brazil was submitted to single nucleotide polymorphism (SNP) marker identification, selection, and use, aiming to characterize genetic diversity and population structure and to design a core collection (CC). Five hundred and fifty-three plants from 206 subsamples, collected at 19 localities spread throughout six geographic regions, were submitted to genotyping-by-sequencing analysis. A set of 1,827 high-quality SNP markers was then selected and used to run the genetic diversity and population structure analysis. The genetic diversity found is of moderate degree, and probably only a small portion of the species diversity is represented in the collection. The possible reason for that is the collecting strategy used, which collected subsamples only around the most prominent watercourses in the region. The average degree of genetic differentiation among subsamples is very high, indicating the presence of high interpopulation differentiation. The collection showed a low level of endogamy. The low average gene flow found indicates that genetic isolation caused by drift is occurring, and there is a need to review the conservation strategy. A set of 245 SNPs distributed throughout all 16 chromosomes was used to design CC based on maximizing the strategy of diversity. The optimal adjustment of the validated parameters, maintained while taking fewest subsamples, led to the choice of a model containing 20% of the entire collection as the ideal to form the CC

Physiological and comparative genomic analysis of new isolated yeasts Spathaspora sp. JA1 and Meyerozyma caribbica JA9 reveal insights into xylitol production.

Xylitol is a five-carbon polyol of economic interest that can be produced by microbial xylose reduction from renewable resources. The current study sought to investigate the potential of two yeast strains, isolated from Brazilian Cerrado biome, in the production of xylitol as well as the genomic characteristics that may impact this process. Xylose conversion capacity by the new isolates Spathaspora sp. JA1 and Meyerozyma caribbica JA9 was evaluated and compared with control strains on xylose and sugarcane biomass hydrolysate. Among the evaluated strains, Spathaspora sp. JA1 was the strongest xylitol producer, reaching product yield and productivity as high as 0.74 g/g and 0.20 g/(L.h) on xylose, and 0.58 g/g and 0.44 g/(L.h) on non-detoxified hydrolysate. Genome sequences of Spathaspora sp. JA1 and M. caribbica JA9 were obtained and annotated. Comparative genomic analysis revealed that the predicted xylose metabolic pathway is conserved among the xylitol-producing yeasts Spathaspora sp. JA1, M. caribbica JA9 and Meyerozyma guilliermondii, but not in Spathaspora passalidarum, an efficient ethanol-producing yeast. Xylitol-producing yeasts showed strictly NADPH-dependent xylose reductase and NAD+-dependent xylitol-dehydrogenase activities. This imbalance of cofactors favors the high xylitol yield shown by Spathaspora sp. JA1, which is similar to the most efficient xylitol producers described so far

Gene projects: a genome web tool for ongoing mining and annotation applied to CitEST

Genome projects, both genomic DNA and ESTs (cDNA), generate a large amount of information, demanding time and a well-structured bioinformatics laboratory to manage these data. These genome projects use information available in heterogeneous formats from different sources. The amount and heterogeneity of this information, as well as the absence of a world consensus pattern, make the integration of these data a difficult task. At the same time, sub-tasks, such as microarray analyses of these projects, are very complex. This creates a demand for the development of creative solutions for ongoing annotation, thematic projects, microarray experiments, etc. This paper presents Gene Projects, a system developed to integrate all kinds of solutions