Browsing by Author "Alabaça, Cláudia S."
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- A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencingPublication . Pereira-Leal, José B.; Abreu, Isabel A.; Alabaça, Cláudia S.; Almeida, Maria H.; Almeida, Paulo; Almeida, Tânia; Amorim, Maria I.; Araújo, Susana; Azevedo, Herlânder; Badia, Aleix; Batista, Dora; Bohn, Andreas; Capote, Tiago; Carrasquinho, Isabel; Chaves, Inês; Coelho, A. C.; Costa, Maria M. R.; Costa, Rita; Cravador, A.; Egas, Conceição; Faro, Carlos; Fortes, Ana M.; Fortunato, Ana S.; Gaspar, Maria J.; Gonçalves, Sónia; Graça, José; Horta, Marília; Inácio, Vera; Leitão, J. M.; Lino-Neto, Teresa; Marum, Liliana; Matos, José; Mendonça, Diogo; Miguel, Andreia; Miguel, Célia M.; Morais-Cecílio, Leonor; Neves, Isabel; Nóbrega, Filomena; Oliveira, Maria M.; Oliveira, Rute; Pais, Maria S.; Paiva, Jorge A.; Paulo, O. S.; Pinheiro, Miguel; Raimundo, João A. P.; Ramalho, J. C.; Ribeiro, Ana I.; Ribeiro, Teresa; Rocheta, Margarida; Rodrigues, Ana I.; Rodrigues, José C.; Saibo, Nelson J. M.; Santo, Tatiana; Santos, Ana M.; Sá-Pereira, Paula; Sebastiana, Mónica; Simões, Fernanda; Sobral, Rómulo S.; Tavares, Rui; Teixeira, Rita; Varela, Carolina; Veloso, Maria M.; Ricardo, Cândido P. P.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.
- Identificação de marcadores moleculares ligados ao gene de resistência ao míldio, PpALG1 em Brassica oleracea var tronchudaPublication . Alabaça, Cláudia S.; Leitão, José Manuel Peixoto TeixeiraO míldio das Crucíferas, causado pelo oomicete Hyaloperonospora Constant. parasitica (Pers. Ex Fr.) (Constantinescu e Fatehi, 2002), é uma doença que afecta a família Brassicaceae, sobretudo as espécies do género Brassica. Anteriormente, tinha sido identificada uma linha de Couve Algarvia (Brassica oleracea var tronchuda) resistente ao míldio na fase adulta cuja resistência se demonstrou ser controlada por um único gene dominante, designado PpALG1 (Monteiro et al., 2005). Este trabalho teve como objectivo a identificação de marcadores moleculares ligados ao gene PpALG1. Utilizando a estratégia de “Bulked Segregant Analysis” (BSA) para testar marcadores mapeados ao longo do mapa genético de B. oleracea concluiu-se que o gene PpALG1 se encontra ligado no mesmo grupo de ligamento (LG3) onde se encontra localizado o gene de resistência ao míldio, Pp523, identificado numa linha de brócolo. A estratégia de BSA foi novamente utilizada para testar marcadores seleccionados deste grupo, bem como para identificar novos marcadores RAPD ligados ao gene em estudo. Paralelamente foram testados marcadores STS provenientes de clones BAC de B. oleracea, pertencentes a um contig que abarca a região genómica do locus Pp523. No total foram analisados 14 marcadores moleculares polimórficos que aparentavam ligação ao gene PpALG1 nos 97 indivíduos que constituem a população de mapeamentoF2. A análise de segregação destes marcadores foi efectuada utilizando o software JoinMap3.0, da qual resultou um grupo de ligamento de seis marcadores ligados ao locus da resistência PpALG1. Actualmente, a interacção fenotipica hospedeiro-patogéneo está a ser reavaliada na população F3, avaliação a partir da qual serão constituídos novos “bulks” de DNA que permitam identificar marcadores DNA em estreita ligação ao gene PpALG1, condição essencial ao seu isolamento via “mapbased cloning”.
- Physical mapping in a triplicated genome: mapping the downy mildew resistance locus Pp523 in Brassica oleracea L.Publication . Carlier, Jorge; Alabaça, Cláudia S.; Sousa, N. H.; Coelho, P. S.; Monteiro, A. A.; Paterson, A. H.; Leitão, J. M.We describe the construction of a BAC contig and identification of a minimal tiling path that encompass the dominant and monogenically inherited downy mildew resistance locus Pp523 of Brassica oleracea L. The selection of BAC clones for construction of the physical map was carried out by screening gridded BAC libraries with DNA overgo probes derived from both genetically mapped DNA markers flanking the locus of interest and BAC-end sequences that align to Arabidopsis thaliana sequences within the previously identified syntenic region. The selected BAC clones consistently mapped to three different genomic regions of B. oleracea. Although 83 BAC clones were accurately mapped within a similar to 4.6 cM region surrounding the downy mildew resistance locus Pp523, a subset of 33 BAC clones mapped to another region on chromosome C8 that was similar to 60 cM away from the resistance gene, and a subset of 63 BAC clones mapped to chromosome C5. These results reflect the triplication of the Brassica genomes since their divergence from a common ancestor shared with A. thaliana, and they are consonant with recent analyses of the C genome of Brassica napus. The assembly of a minimal tiling path constituted by 13 (BoT01) BAC clones that span the Pp523 locus sets the stage for map-based cloning of this resistance gene.
- The downy mildew resistance locus Pp523 is located on chromosome C8 of Brassica oleracea L.Publication . Carlier, Jorge; Alabaça, Cláudia S.; Coelho, P. S.; Monteiro, A. A.; Leitão, J. M.We have previously constructed a genetic map of Brassica oleracea L. containing the Pp523 locus that confers downy mildew resistance to adult plants. In this work, 44 SSR markers of reference for the Brassica C genome chromosomes were added to the map, allowing the nine major linkage groups to be assigned to the nine chromosomes of B. oleracea. Locus Pp523 was located on chromosome C8, and a locus determining flower colour was mapped to chromosome C3. In comparison with the first version of the map, the new map is denser and more compact. The available genomic information on B. oleracea was enriched with the chromosome location of two phenotypic traits and 421 DNA markers (RAPD, ISSR, AFLP, SCAR, BAC-end derived STS, SSR and other PCR markers). Conversely, the genomic information on B. oleracea chromosome C8 is being used as an additional tool for the map-based cloning of Pp523, the first gene for adult plant resistance to downy mildew precisely located to a specific chromosome of this crop species.
- The ENU-induced powdery mildew resistant mutant pea (Pisum sativum L.) lines S(er1mut1) and F(er1mut2) harbour early stop codons in the PsMLO1 genePublication . Santo, Tatiana; Rashkova, M.; Alabaça, Cláudia S.; Leitão, J. M.Two pea (Pisum sativum L.) powdery mildew-resistant mutant lines, S(er1mut1) and F(er1mut2), were previously obtained by experimental chemical mutagenesis with ethylnitrosourea. Identification and subsequent analysis of the genomic sequence of the PsMLO1 gene revealed one single nucleotide mutation in each mutant line that leads to either a transversion or a transition, respectively, resulting in premature stop codons that drastically truncate the protein product of this gene in these two mutant lines. These results confirm the previous findings that PsMLO1 is the powdery mildew resistance gene er1. Only one additional mutation (transition) was observed in the S(er1mut1), downstream of the protein-truncating stop codon. Mutations were not identified in the intron regions of the gene. Specific molecular markers (cleaved amplified polymorphic sequences and sequence-tagged sites) were generated for the protein-truncating mutations, and these provide breeders with very efficient tools for marker-assisted selection when either of the two mutated lines are used in plant breeding programmes.