<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Pereira-Leal, José B</style></author><author><style face="normal" font="default" size="100%">Abreu, Isabel a</style></author><author><style face="normal" font="default" size="100%">Alabaça, Cláudia S</style></author><author><style face="normal" font="default" size="100%">Almeida, Maria Helena</style></author><author><style face="normal" font="default" size="100%">Almeida, Paulo</style></author><author><style face="normal" font="default" size="100%">Almeida, Tânia</style></author><author><style face="normal" font="default" size="100%">Amorim, Maria Isabel</style></author><author><style face="normal" font="default" size="100%">Araújo, Susana</style></author><author><style face="normal" font="default" size="100%">Azevedo, Herlânder</style></author><author><style face="normal" font="default" size="100%">Badia, Aleix</style></author><author><style face="normal" font="default" size="100%">Batista, Dora</style></author><author><style face="normal" font="default" size="100%">Bohn, Andreas</style></author><author><style face="normal" font="default" size="100%">Capote, Tiago</style></author><author><style face="normal" font="default" size="100%">Carrasquinho, Isabel</style></author><author><style face="normal" font="default" size="100%">Chaves, Inês</style></author><author><style face="normal" font="default" size="100%">Coelho, Ana Cristina</style></author><author><style face="normal" font="default" size="100%">Costa, Maria Manuela Ribeiro</style></author><author><style face="normal" font="default" size="100%">Costa, Rita</style></author><author><style face="normal" font="default" size="100%">Cravador, Alfredo</style></author><author><style face="normal" font="default" size="100%">Egas, Conceição</style></author><author><style face="normal" font="default" size="100%">Faro, Carlos</style></author><author><style face="normal" font="default" size="100%">Fortes, Ana M</style></author><author><style face="normal" font="default" size="100%">Fortunato, Ana S</style></author><author><style face="normal" font="default" size="100%">Gaspar, Maria João</style></author><author><style face="normal" font="default" size="100%">Gonçalves, Sónia</style></author><author><style face="normal" font="default" size="100%">Graça, José</style></author><author><style face="normal" font="default" size="100%">Horta, Marília</style></author><author><style face="normal" font="default" size="100%">Inácio, Vera</style></author><author><style face="normal" font="default" size="100%">Leitão, José M</style></author><author><style face="normal" font="default" size="100%">Lino-Neto, Teresa</style></author><author><style face="normal" font="default" size="100%">Marum, Liliana</style></author><author><style face="normal" font="default" size="100%">Matos, José</style></author><author><style face="normal" font="default" size="100%">Mendonça, Diogo</style></author><author><style face="normal" font="default" size="100%">Miguel, Andreia</style></author><author><style face="normal" font="default" size="100%">Miguel, Célia M</style></author><author><style face="normal" font="default" size="100%">Morais-Cecílio, Leonor</style></author><author><style face="normal" font="default" size="100%">Neves, Isabel</style></author><author><style face="normal" font="default" size="100%">Nóbrega, Filomena</style></author><author><style face="normal" font="default" size="100%">Oliveira, Maria Margarida</style></author><author><style face="normal" font="default" size="100%">Oliveira, Rute</style></author><author><style face="normal" font="default" size="100%">Pais, Maria Salomé</style></author><author><style face="normal" font="default" size="100%">Paiva, Jorge a</style></author><author><style face="normal" font="default" size="100%">Paulo, Octávio S</style></author><author><style face="normal" font="default" size="100%">Pinheiro, Miguel</style></author><author><style face="normal" font="default" size="100%">Raimundo, João Ap</style></author><author><style face="normal" font="default" size="100%">Ramalho, José C</style></author><author><style face="normal" font="default" size="100%">Ribeiro, Ana I</style></author><author><style face="normal" font="default" size="100%">Ribeiro, Teresa</style></author><author><style face="normal" font="default" size="100%">Rocheta, Margarida</style></author><author><style face="normal" font="default" size="100%">Rodrigues, Ana Isabel</style></author><author><style face="normal" font="default" size="100%">Rodrigues, José C</style></author><author><style face="normal" font="default" size="100%">Saibo, Nelson Jm</style></author><author><style face="normal" font="default" size="100%">Santo, Tatiana E</style></author><author><style face="normal" font="default" size="100%">Santos, Ana Margarida</style></author><author><style face="normal" font="default" size="100%">Sá-Pereira, Paula</style></author><author><style face="normal" font="default" size="100%">Sebastiana, Mónica</style></author><author><style face="normal" font="default" size="100%">Simões, Fernanda</style></author><author><style face="normal" font="default" size="100%">Sobral, Rómulo S</style></author><author><style face="normal" font="default" size="100%">Tavares, Rui</style></author><author><style face="normal" font="default" size="100%">Teixeira, Rita</style></author><author><style face="normal" font="default" size="100%">Varela, Carolina</style></author><author><style face="normal" font="default" size="100%">Veloso, Maria Manuela</style></author><author><style face="normal" font="default" size="100%">Ricardo, Cândido Pp</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC genomics</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Cork oak</style></keyword><keyword><style  face="normal" font="default" size="100%">EST sequencing</style></keyword><keyword><style  face="normal" font="default" size="100%">Quercus suber</style></keyword><keyword><style  face="normal" font="default" size="100%">transcriptome</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2014</style></year></dates><volume><style face="normal" font="default" size="100%">15</style></volume><pages><style face="normal" font="default" size="100%">371</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">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.</style></abstract><accession-num><style face="normal" font="default" size="100%">24885229</style></accession-num><notes><style face="normal" font="default" size="100%">APS</style></notes><research-notes><style face="normal" font="default" size="100%">APS</style></research-notes></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sebastiana, Mónica</style></author><author><style face="normal" font="default" size="100%">Figueiredo, Andreia</style></author><author><style face="normal" font="default" size="100%">Monteiro, Filipa</style></author><author><style face="normal" font="default" size="100%">Martins, Joana</style></author><author><style face="normal" font="default" size="100%">Franco, Catarina</style></author><author><style face="normal" font="default" size="100%">Coelho, Ana Varela</style></author><author><style face="normal" font="default" size="100%">Vaz, Fátima</style></author><author><style face="normal" font="default" size="100%">Simões, Tânia</style></author><author><style face="normal" font="default" size="100%">Penque, Deborah</style></author><author><style face="normal" font="default" size="100%">Pais, Maria Salomé</style></author><author><style face="normal" font="default" size="100%">Ferreira, Sílvia</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A possible approach for gel-based proteomic studies in recalcitrant woody plants.</style></title><secondary-title><style face="normal" font="default" size="100%">SpringerPlus</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">2-de</style></keyword><keyword><style  face="normal" font="default" size="100%">ectomycorrhizal roots</style></keyword><keyword><style  face="normal" font="default" size="100%">grapevine</style></keyword><keyword><style  face="normal" font="default" size="100%">Mass spectrometry</style></keyword><keyword><style  face="normal" font="default" size="100%">oak</style></keyword><keyword><style  face="normal" font="default" size="100%">pine</style></keyword><keyword><style  face="normal" font="default" size="100%">protein extraction</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year></dates><volume><style face="normal" font="default" size="100%">2</style></volume><pages><style face="normal" font="default" size="100%">210</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Woody plants are particularly difficult to investigate due to high phenolic, resin, and tannin contents and laborious sample preparation. In particular, protein isolation from woody plants for two-dimensional gel electrophoresis (2-DE) is challenging as secondary metabolites negatively interfere with protein extraction and separation. In this study, three protein extraction protocols, using TCA, phenol and ethanol as precipitation or extraction agents, were tested in order to select the more efficient for woody recalcitrant plant gel-based proteomics. Grapevine leaves, pine needles and cork oak ectomycorrhizal roots were used to represent woody plant species and tissues. The phenol protocol produced higher quality 2-DE gels, with increased number of resolved spots, better spot focusing and representation of all molecular mass and isoelectric point ranges tested. In order to test the compatibility of the phenol extracted proteomes with protein identification several spots were excised from the phenol gels and analyzed by mass spectrometry (MALDI-TOF/TOF). Regardless the incomplete genome/protein databases for the plant species under analysis, 49 proteins were identified by Peptide Mass Fingerprint (PMF). Proteomic data have been deposited to the ProteomeXchange with identifier PXD000224. Our results demonstrate the complexity of protein extraction from woody plant tissues and the suitability of the phenol protocol for obtaining high quality protein extracts for efficient 2-DE separation and downstream applications such as protein identification by mass spectrometry.</style></abstract><accession-num><style face="normal" font="default" size="100%">23724367</style></accession-num></record></records></xml>