A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing

Background: Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management. Results: We generated in excess of 7 million sequence reads, by pyrosequencing 21 normalized cDNA libraries derived from multiple Q. suber tissues and organs, developmental stages and physiological conditions. We deployed a stringent sequence processing and assembly pipeline that resulted in the identification of ~159,000 unigenes. These were annotated according to their similarity to known plant genes, to known Interpro domains, GO classes and E.C. numbers. The phylogenetic extent of this ESTs set was investigated, and we found that cork oak revealed a significant new gene space that is not covered by other model species or EST sequencing projects. The raw data, as well as the full annotated assembly, are now available to the community in a dedicated web portal at http://www.corkoakdb.org. Conclusions: This genomic resource represents the first trancriptome study in a cork producing species. It can be explored to develop new tools and approaches to understand stress responses and developmental processes in forest trees, as well as the molecular cascades underlying cork differentiation and disease response.Peer Reviewe

The complete genome sequence of Chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability

Chromobacterium violaceum is one of millions of species of free-living microorganisms that populate the soil and water in the extant areas of tropical biodiversity around the world. Its complete genome sequence reveals (i) extensive alternative pathways for energy generation, (ii) ≈500 ORFs for transport-related proteins, (iii) complex and extensive systems for stress adaptation and motility, and (iv) wide-spread utilization of quorum sensing for control of inducible systems, all of which underpin the versatility and adaptability of the organism. The genome also contains extensive but incomplete arrays of ORFs coding for proteins associated with mammalian pathogenicity, possibly involved in the occasional but often fatal cases of human C. violaceum infection. There is, in addition, a series of previously unknown but important enzymes and secondary metabolites including paraquat-inducible proteins, drug and heavy-metal-resistance proteins, multiple chitinases, and proteins for the detoxification of xenobiotics that may have biotechnological applications

Rotavirus G and P types in children from Belém, northern Brazil, as determined by RT-PCR: occurrence of mixed P type infections

Ministério da Saúde. Fundação Nacional de Saúde. Instituto Evandro Chagas. Belém, PA, Brasil.Laboratório de Biologia Molecular. Florianópolis, SC, Brasil.Laboratório de Biologia Molecular. Florianópolis, SC, Brasil.Ministério da Saúde. Fundação Nacional de Saúde. Instituto Evandro Chagas. Belém, PA, Brasil.Laboratório de Biologia Molecular. Florianópolis, SC, Brasil.Ministério da Saúde. Fundação Nacional de Saúde. Instituto Evandro Chagas. Belém, PA, Brasil.Fifty-four group A rotavirus-positive stool samples, obtained from children aged less than three years during a longitudinal (December 1982 to March 1986) study in Belém, Brazil, were re-examined. The samples were tested by reverse-transcription and polymerase chain reaction to determine their G-type and P-type specificity. Only 17 (32 percent)of these rotavirus strains could be successfully G- and P-genotyped. While 10 (59 percent) of the 17 strains showed single G- and P-type specificity, the remaining belonged to single G- and mixed P-genotypes. Rotavirus strains P[8], G1 and P[4], G1 predominated, accounting for 29 percent and 18 percent of the typed strains respectively. Mixed P-type infections caused by rotaviruses classified as P[8]+P[4], G1 were identified in 23 percent. All but 3 of the 54 rotavirus strains displayed long genomic profiles, as demonstrated by the analysis of RNA by polyacrylamide gel electrophoresis. Most (70 percent ) rotavirus strains with single G- and P-type specificity were detected during the first year of life, whereas 5 (71 percent) of the seven mixed P-type infections occurred throughout the second or third year of age. Reinfections were noted in two children, both of them being infected with P[8]+P[4], G1 rotavirus strains when aged 20 months. The high proportion of untypeable rotavirus strains suggests that unusual types may be circulating in Belém. In addition, the occurrence of mixed P-type infections in our region indicates the potential for reassortment between different rotavirus genogroups. Monitoring of these rotavirus strains may have important implication in the context of future strategies of rotavirus vaccination in Brazi