<?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%">Alves, Sofia</style></author><author><style face="normal" font="default" size="100%">Ribeiro, Teresa</style></author><author><style face="normal" font="default" size="100%">Inácio, Vera</style></author><author><style face="normal" font="default" size="100%">Rocheta, Margarida</style></author><author><style face="normal" font="default" size="100%">Morais-Cecílio, Leonor</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genomic organization and dynamics of repetitive DNA sequences in representatives of three Fagaceae genera</style></title><secondary-title><style face="normal" font="default" size="100%">Genome</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">AFLP</style></keyword><keyword><style  face="normal" font="default" size="100%">Castanea</style></keyword><keyword><style  face="normal" font="default" size="100%">euchromatin</style></keyword><keyword><style  face="normal" font="default" size="100%">Fagaceae</style></keyword><keyword><style  face="normal" font="default" size="100%">Fagus</style></keyword><keyword><style  face="normal" font="default" size="100%">Quercus</style></keyword><keyword><style  face="normal" font="default" size="100%">retroelements</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012///</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://dx.doi.org/10.1139/g2012-020</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">55</style></volume><pages><style face="normal" font="default" size="100%">348 - 359</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Oaks, chestnuts, and beeches are economically important species of the Fagaceae. To understand the relationship between these members of this family, a deep knowledge of their genome composition and organization is needed. In this work, we have isolated and characterized several AFLP fragments obtained from Quercus rotundifolia Lam. through homology searches in available databases. Genomic polymorphisms involving some of these sequences were evaluated in two species of Quercus, one of Castanea, and one of Fagus with specific primers. Comparative FISH analysis with generated sequences was performed in interphase nuclei of the four species, and the co-immunolocalization of 5-methylcytosine was also studied. Some of the sequences isolated proved to be genus-specific, while others were present in all the genera. Retroelements, either gypsy-like of the Tat/Athila clade or copia-like, are well represented, and most are dispersed in euchromatic regions of these species with no DNA methylation associated, pointing to an interspersed arrangement of these retroelements with potential gene-rich regions. A particular gypsy-sequence is dispersed in oaks and chestnut nuclei, but its confinement to chromocenters in beech evidences genome restructuring events during evolution of Fagaceae. Several sequences generated in this study proved to be good tools to comparatively study Fagaceae genome organization.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><notes><style face="normal" font="default" size="100%">doi: 10.1139/g2012-020doi: 10.1139/g2012-020The following values have no corresponding Zotero field:&lt;br/&gt;publisher: NRC Research Press</style></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%">Almeida, Tânia</style></author><author><style face="normal" font="default" size="100%">Menéndez, Esther</style></author><author><style face="normal" font="default" size="100%">Capote, Tiago</style></author><author><style face="normal" font="default" size="100%">Ribeiro, Teresa</style></author><author><style face="normal" font="default" size="100%">Santos, Conceição</style></author><author><style face="normal" font="default" size="100%">Gonçalves, Sónia</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Molecular characterization of Quercus suber MYB1, a transcription factor up-regulated in cork tissues</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Plant Physiology</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Alternative Splicing</style></keyword><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Cork biosynthesis</style></keyword><keyword><style  face="normal" font="default" size="100%">Cork oak</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation</style></keyword><keyword><style  face="normal" font="default" size="100%">Genes</style></keyword><keyword><style  face="normal" font="default" size="100%">Lipids</style></keyword><keyword><style  face="normal" font="default" size="100%">Lipids: biosynthesis</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">phellogen</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Bark</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Bark: genetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Bark: metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Growth Regulators</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Growth Regulators: biosynthesis</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Proteins: chemistry</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Proteins: metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Quercus</style></keyword><keyword><style  face="normal" font="default" size="100%">Quercus: genetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Quercus: metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">R2R3-MYB</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription Factors</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription Factors: chemistry</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription Factors: metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">Up-Regulation</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2012</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2012///</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/23218545http://linkinghub.elsevier.com/retrieve/pii/S0176161712004828</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">170</style></volume><pages><style face="normal" font="default" size="100%">1 - 7</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The molecular processes associated with cork development in Quercus suber L. are poorly understood. A previous molecular approach identiﬁed a list of genes potentially important for cork formation and differentiation, providing a new basis for further molecular studies. This report is the ﬁrst molecular characterization of one of these candidate genes, QsMYB1, coding for an R2R3-MYB transcription factor. The R2R3-MYB gene sub-family has been described as being involved in the phenylpropanoid and lignin pathways, both involved in cork biosynthesis. The results showed that the expression of QsMYB1 is putatively mediated by an alternative splicing (AS) mechanism that originates two different transcripts (QsMYB1.1 and QsMYB1.2), differing only in the 5 -untranslated region, due to retention of the ﬁrst intron in one of the variants. Moreover, within the retained intron, a simple sequence repeat (SSR) was identiﬁed. The upstream regulatory region of QsMYB1 was extended by a genome walking approach, which allowed the identiﬁcation of the putative gene promoter region. The relative expression pattern of QsMYB1 transcripts determined by reverse transcription quantitative polymerase chain reaction (RTqPCR) revealed that both transcripts were up-regulated in cork tissues; the detected expression was several times higher in newly formed cork harvested from trees producing virgin, second or reproduction cork when compared with wood. Moreover, the expression analysis of QsMYB1 in several Q. suber organs showed very low expression in young branches and roots, whereas in leaves, immature acorns or male ﬂowers, no expression was detected. These preliminary results suggest that QsMYB1 may be related to secondary growth and, in particular, with the cork biosynthesis process with a possible alternative splicing mechanism associated with its regulatory function.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><notes><style face="normal" font="default" size="100%">The following values have no corresponding Zotero field:&lt;br/&gt;accession-num: 23218545</style></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%">Ribeiro, Teresa</style></author><author><style face="normal" font="default" size="100%">Loureiro, João</style></author><author><style face="normal" font="default" size="100%">Santos, Conceição</style></author><author><style face="normal" font="default" size="100%">Morais-Cecílio, Leonor</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Evolution of rDNA FISH patterns in the Fagaceae</style></title><secondary-title><style face="normal" font="default" size="100%">Tree Genetics &amp; Genomes</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Castanea</style></keyword><keyword><style  face="normal" font="default" size="100%">fagaceae karyotype</style></keyword><keyword><style  face="normal" font="default" size="100%">Fagus</style></keyword><keyword><style  face="normal" font="default" size="100%">Quercus</style></keyword><keyword><style  face="normal" font="default" size="100%">rDNA</style></keyword><keyword><style  face="normal" font="default" size="100%">triploid quercus suber</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year></dates><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">1113-1122</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The Fagaceae is one of the most important plant families in European forest ecosystems, and it includes several genera distributed in the Northern hemisphere. In this work we studied the genome organization and evolution within the family, by karyotyping and physically mapping rDNA in ten European and Asian species of the genera Fagus, Quercus, and Castanea. All of the species studied had a chromosome number of 2n=2x=24, except for the first report of a single individual of Quercus suber which proved to be triploid (2n=3x=36). The rDNA physical mapping revealed several patterns: the dominant one is present in European and Asian Quercus subgenus Quercus, and in Castanea sativa and Castanea crenata, consisting of two 18S–25S rDNA loci (one subterminal major and one pericentromeric minor) and one 5S rDNA pericentromeric locus. In Fagus sylvatica and in Quercus sessilifolia, different patterns were observed: four terminal 18S–25S rDNA loci and two 5S rDNA pericentromeric loci in the former, and five 18S–25S rDNA loci (three terminal and two intercalary) and one 5S rDNA pericentromeric locus in the latter. In Castanea mollissima a distinct rDNA distribution pattern with two intercalary 18S–25S rDNA loci and two 5S rDNA was found. These findings suggest rDNA loci restructuring during Castanea evolution, and variability of 18S–25S loci between Quercus and Cyclobalanopsis subgenera.</style></abstract></record></records></xml>