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Reunião dos grupos de Bioinformática COEC no BioCant

Biocant, 8 Junho 2010 – 14h30

Com o objectivo de debater a pipeline de análise de dados.

 

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Sobre nós

O montado de sobro (Quercus suber) constitui um recurso nacional único e emblemático, devido ao seu significado ecológico e sócio-económico e ao valor comercial da cortiça de que Portugal é o principal produtor (ca 1/3 da produção mundial).
O conhecimento actual sobre a diversidade do germoplasma de Q. suber, a sua plasticidade ao stress e a formação da cortiça, entre outros aspectos é escasso, apesar da investigação recente nas áreas de ecofisiologia e da selecção/melhoramento.
Os carvalhos Mediterrânicos de folha perene (sobreiro e azinheira) estão ameaçados por políticas desastrosas do uso do solo, mudanças climáticas, stresses bióticos e incêndios. Para proteger a riqueza destes ecossistemas em Portugal e no sul da Europa, urge fazer mais investigação nestas espécies. As respostas aos stresses biótico e abiótico e aos processos de desenvolvimento−vegetativo e reprodutivo, produção de sementes − e os mecanismos de formação de cortiça são temas prioritários de investigação.
A investigação em carvalhos, especificamente no sobreiro, beneficiaria com a construção dum “chip” de genes para estudos de transcriptómica. A transcriptómica estabelece uma ligação dinâmica entre o genoma, o proteoma e o fenótipo celular, e permite a avaliação da expressão diferencial de genes durante o desenvolvimento ou em resposta a condições ambientais variadas. A obtenção e a sequenciação de sequências expressas (ESTs), visando a construção de um “chip” de genes, dará suporte a tais estudos e fornecerá ainda informação útil ao projecto de sequenciação do genoma de sobreiro.
Um Consórcio Português estabelecido no âmbito da Plataforma de Genómica Funcional propõe-se através de um esforço concertado contribuir com ESTs para a construção do “chip”. Dentre a tecnologia de “microarrays” disponível, foi escolhida a empresa Affymetrix para o produzir. Graças a esta iniciativa concertada serão estabelecidas novas competências a nível nacional, ao mesmo tempo que será estimulada a cooperação e assim permitida a implementação do número de grupos dedicados a investigar este valioso recurso nacional. Além disso, a organização dos grupos em Consórcio será uma garantia duma subsequente utilização do “chip”.
O Consórcio organizou 12 projectos envolvendo diferentes parceiros a fim de contemplar o maior número de condições, e garantir a detecção da expressão dum número máximo de genes de Q. suber a usar no “chip de genes”. Cada projecto inclui investigadores com experiência específica para o seu tema. O RNA total será extraído a partir de material vegetal específico. Os cDNAs serão preparados e normalizados a partir do RNA num laboratório com competência para este serviço (Evrogen) a fim de reduzir as perdas de transcritos pouco abundantes. O cDNA normalizado será sequenciado pela tecnologia 454 (centralizada na empresa BIOCANT Technological Park), com rendimentos teóricos de 106 bases, 500 Mbp/amostra, 400 pb/sequência.
O agrupamento de “contíguos” de ESTs e as anotações preliminares serão efectuados por BIOCANT. Uma equipa especializada de bioinformáticos implementará bases de dados e canais de informação para organizar e analisar o grande volume de informação gerada e a disponibilizar à comunidade científica. A plataforma pública criada, CorkOakDB, servirá como importante ferramenta de investigação e de apresentação deste primeiro projecto genómico Português em larga escala.
Os 12 projectos que integram o Consócio, identificados por SOBREIRO/##/2009, são: 14 (Stress Biótico: resposta radicular à infecção por Phytophthora cinnamomi); 17 (Produção de cortiça); 19 (Desenvolvimento dos gametófitos masculinos e femininos); 25 (Germinação da bolota); 29 (Desenvolvimento do fruto e do embrião); 30 (Plataforma Bioinformática); 33 (Stress abiótico: stresses hídrico, salino e oxidativo); 34 (Simbiose micorrízica); 35 (Stress abiótico: calor e frio); 36 (Detecção e validação de polimorfismos); 38 (Qualidade da cortiça); 39 (Abrolhamento e desenvolvimento foliar).

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