Cork oak (Quercus suber) is native to southwest Europe and northwest Africa where it plays a crucial environmental and economical role. To tackle the cork oak production and industrial challenges, advanced research is imperative but dependent on the availability of a sequenced genome. To address this, we produced the first draft version of the cork oak genome. We followed a de novo assembly strategy based on high-throughput sequence data, which generated a draft genome comprising 23,347 scaffolds and 953.3 Mb in size. A total of 79,752 genes and 83,814 transcripts were predicted, including 33,658 high-confidence genes. An InterPro signature assignment was detected for 69,218 transcripts, which represented 82.6% of the total. Validation studies demonstrated the genome assembly and annotation completeness and highlighted the usefulness of the draft genome for read mapping of high-throughput sequence data generated using different protocols. All data generated is available through the public databases where it was deposited, being therefore ready to use by the academic and industry communities working on cork oak and/or related species.

Plants have evolved several mechanisms in order to cope with adverse environmental conditions. The transcription factors (TFs) belonging to the DREB1/CBF subfamily have been described as major regulators of the plant responses to different abiotic stresses. This study focused on the rice gene OsDREB1B, initially described as highly and specifically induced by cold. However, here it is shown that OsDREB1B is not only induced by low temperatures, but also by drought and mechanical stress. In order to identify novel TFs that bind to its promoter, a yeast one-hybrid system was used to screen a cold-induced cDNA expression library. Thereby seven novel Zn-finger TFs were identified that bind to the promoter of OsDREB1B. Among them, there were four Zn-finger homeodomain (ZF-HD) and three C₂H₂-type Zn-finger TFs. Gene expression studies showed that these TFs are differentially regulated at transcriptional level by different abiotic stress conditions, which is illustrative of the crosstalk between stress signalling pathways. Protein–protein interaction studies revealed the formation of homo- and heterodimers among the ZF-HD TFs identified, but not for the C₂H₂-type. Using a transactivation assay in Arabidopsis protoplasts, all the TFs identified repressed the expression of the reporter gene, driven by the promoter of OsDREB1B. This assay also showed that the dimerization observed between the ZF-HD TFs may play a role on their transactivation activity. The results here presented suggest a prominent role of Zn-finger TFs in the regulation of OsDREB1B.

Plant growth and crop production are highly reduced by adverse environmental conditions and rice is particularly sensitive to abiotic stresses. Plants have developed a number of different mechanisms to respond and try to adapt to abiotic stress. Plant response to stress such as drought, cold, and high salinity, implies rapid and coordinated changes at transcriptional level of entire gene networks. During the last decade many transcription factors, belonging to different families, have been shown to act as positive or negative regulators of stress responsive genes, thus playing an extremely important role in stress signaling. More recently, epigenetic mechanisms have been also involved in the regulation of the stress responsive genes. In this review, we have performed a comprehensive analysis of the rice transcription factors reported so far as being involved in abiotic stress responses. The impact of abiotic stresses on epigenomes is also addressed. Finally, we update the connections made so far between DNA-binding transcription factors (TFs), and epigenetic mechanisms (DNA methylation and histones methylation or acetylation) emphasizing an integrative view of transcription regulation.

In temperate fruit trees, seasonal dormancy and cold acclimation have a major impact on blooming time and, consequently, fruit production. To gain insight into the still unclear molecular processes underlying blooming, expression of genes putatively involved in the cold response was studied in almond (Prunus dulcis Mill.), which is the earliest fruit tree in the family Rosaceae to bloom. The transcript levels of two C-repeat binding factor (PdCBF) genes and one of their putative targets, PdDehydrin1 (PdDHN1), were analysed in flower buds and shoot internodes during seasonal dormancy up to bud break. In parallel, expression of candidate genes related to flower development was also followed. In a 2-year study, PdCBF2 showed a progressive increase in transcript abundance during the autumn in close correlation with cold acclimation, while high transcript levels of PdCBF1 and PdDHN1 were already found by summer. After bud break, with temperatures still within the chilling range, both PdCBF genes and PdDHN1 were found to sharply reduce transcription in flower buds and internodes, suggesting damping of CBF-mediated cold signalling during growth resumption, in correlation with cold hardiness decline. Flower bud break was also followed by a decrease in the expression of PdGA20OX, a candidate gene involved in gibberellin biosynthesis, and an increase in the expression of two homeotic genes related to floral organ development, PdMADS1 and -3. These genes may also be relevant players in the regulation of anthesis in this model Rosaceae species.

C₄ photosynthesis has evolved repeatedly from the ancestral C₃ state to generate a carbon concentrating mechanism that increases photosynthetic efficiency. This specialized form of photosynthesis is particularly common in the PACMAD clade of grasses, and is used by many of the world’s most productive crops. The C₄ cycle is accomplished through cell-type-specific accumulation of enzymes but cis-elements and transcription factors controlling C₄ photosynthesis remain largely unknown. Using the NADP-Malic Enzyme (NADP-ME) gene as a model we tested whether mechanisms impacting on transcription in C₄ plants evolved from ancestral components found in C₃ species. Two basic Helix-Loop-Helix (bHLH) transcription factors, ZmbHLH128 and ZmbHLH129, were shown to bind the C₄NADP-ME promoter from maize. These proteins form heterodimers and ZmbHLH129 impairs trans-activation by ZmbHLH128. Electrophoretic mobility shift assays indicate that a pair of cis-elements separated by a seven base pair spacer synergistically bind either ZmbHLH128 or ZmbHLH129. This pair of cis-elements is found in both C₃ and C₄ Panicoid grass species of the PACMAD clade. Our analysis is consistent with this cis-element pair originating from a single motif present in the ancestral C₃ state. We conclude that C₄ photosynthesis has co-opted an ancient C₃ regulatory code built on G-box recognition by bHLH to regulate the NADP-ME gene. More broadly, our findings also contribute to the understanding of gene regulatory networks controlling C₄ photosynthesis.