<?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></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><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%">Almeida, Tânia</style></author><author><style face="normal" font="default" size="100%">Pinto, Glória</style></author><author><style face="normal" font="default" size="100%">Correia, Barbara</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%">QsMYB1 expression is modulated in response to heat and drought stresses and during plant recovery in Quercus suber</style></title><secondary-title><style face="normal" font="default" size="100%">Plant Physiology and Biochemistry</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Abiotic stress</style></keyword><keyword><style  face="normal" font="default" size="100%">Adaptation</style></keyword><keyword><style  face="normal" font="default" size="100%">Cork oak</style></keyword><keyword><style  face="normal" font="default" size="100%">Droughts</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene expression</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%">Hot Temperature</style></keyword><keyword><style  face="normal" font="default" size="100%">Physiological</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 Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Plant Proteins: genetics</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%">Recovery</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA Splicing</style></keyword><keyword><style  face="normal" font="default" size="100%">Stress</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription Factors</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription Factors: genetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription Factors: metabolism</style></keyword><keyword><style  face="normal" font="default" size="100%">water</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013///</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/24161757http://www.sciencedirect.com/science/article/pii/S0981942813003537</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">73</style></volume><pages><style face="normal" font="default" size="100%">274 - 281</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Abstract Cork oak is an economically important forest species showing a great tolerance to high temperatures and shortage of water. However, the mechanisms underlying this plasticity are still poorly understood. Among the stress regulators, transcription factors (TFs) are especially important since they can control a wide range of stress-inducible genes, which make them powerful targets for genetic engineering of stress tolerance. Here we evaluated the influence of increasing temperatures (up to 55 °C) or drought (18% field capacity, FC) on the expression profile of an R2R3-MYB transcription factor of cork oak, the QsMYB1. QsMYB1 was previously identified as being preferentially expressed in cork tissues and as having an associated alternative splicing mechanism, which results in two different transcripts (QsMYB1.1 and QsMYB1.2). Expression analysis by reverse transcription quantitative PCR (RT-qPCR) revealed that increasing temperatures led to a gradual down-regulation of QsMYB1 transcripts with more effect on QsMYB1.1 abundance. On the other hand, under drought condition, expression of QsMYB1 variants, mainly the QsMYB1.2, was transiently up-regulated shortly after the stress imposition. Recovery from each stress has also resulted in a differential response by both QsMYB1 transcripts. Several physiological and biochemical parameters (plant water status, chlorophyll fluorescence, lipid peroxidation and proline content) were determined in order to monitor the plant performance under stress and recovery. In conclusion, this report provides the first evidence that QsMYB1 TF may have a putative function in the regulatory network of cork oak response to heat and drought stresses and during plant recovery.</style></abstract><notes><style face="normal" font="default" size="100%">From Duplicate 1 (QsMYB1 expression is modulated in response to heat and drought stresses and during plant recovery in Quercus suber - Almeida, Tânia; Pinto, Glória; Correia, Barbara; Santos, Conceição; Gonçalves, Sónia)From Duplicate 1 (QsMYB1 expression is modulated in response to heat and drought stresses and during plant recovery in Quercus suber - Almeida, Tânia; Pinto, Glória; Correia, Barbara; Santos, Conceição; Gonçalves, Sónia)The following values have no corresponding Zotero field:&lt;br/&gt;publisher: Elsevier Masson SAS&lt;br/&gt;accession-num: 24161757</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></records></xml>