Gene activity is largely controlled by transcriptional regulation through the action of transcription factors and other regulators. QsMYB1 is a member of the R2R3-MYB transcription factor family related to secondary growth, and in particular, with the cork development process. In order to identify the putative gene targets of QsMYB1 across the cork oak genome we developed a ChIP-Seq strategy. Results provide direct evidence that QsMY1B targets genes encoding for enzymes involved in the lignin and suberin pathways as well as gene encoding for ABCG transporters and LTPs implicated in the transport of monomeric suberin units across the cellular membrane. These results highlight the role of QsMYB1 as a regulator of lignin and suberin biosynthesis, transport and assembly. To our knowledge, this work constitutes the first ChIP-Seq experiment performed in cork oak, a non-model plant species with a long-life cycle, and these results will contribute to deepen the knowledge about the molecular mechanisms of cork formation and differentiation.

Forests are essential resources on a global scale, not only for the ecological benefits, but also for economical and landscape purposes. However, in recent years, a large number of forest species have suffered a serious decline, with maritime pine being one of the most affected. In Portugal, the maritime pine forest has been devastated by the pine wood nematode (PWN), the causal agent of pine wilt disease. In this study, RNA-Seq data was used to characterize the maritime pine response to infection with PWN, by determining the differentially expressed genes and identifying the regulatory networks and pathways associated. The analyses showed clear differences between an early response that occurs immediately after inoculation and a late response that is observed seven days after inoculation. Moreover, differentially expressed genes related to secondary metabolism, oxidative stress and defense against pathogen infection were identified over different time points. These results provide new insights about the molecular mechanisms and metabolic pathways involved in the response of Pinus pinaster against PWN infection, which will be a useful resource in follow-up studies and for future breeding programs to select plants with lower susceptibility to this disease.

Pine wilt disease (PWD) caused by pine wood nematode (PWN), Bursaphelenchus xylophilus, is a serious threat to global forest populations of conifers, in particular Pinus spp. Recently, the presence of PWN was reported in dead Yunnan pine (Pinus yunnanensis) trees under natural conditions. To further understand the potential impact caused by PWN in Yunnan pine populations, a transcriptional profiling analysis was performed over different time points (0 hours (h), 6 h, 24 h, 48 h, and 7 days) after PWN inoculation. A total of 9961 differentially expressed genes were identified after inoculation, which suggested a dynamic response against the pathogen, with a more intense pattern at 48 h after inoculation. The results also highlighted a set of biological mechanisms triggered after inoculation that provide valuable information regarding the response of Yunnan pine to PWN infection. When compared with maritime pine (Pinus pinaster), the Yunnan pine response was less complex and involved a smaller number of differentially expressed genes, which may be associated with the increased degree of resistance to PWN displayed by Yunnan pine. These results revealed different strategies to cope with PWN infection by these two pine species, which display contrasting degrees of susceptibility, especially in the timely perception of the infection and response magnitude.

Motivation: Chemical named entity recognition is used to automatically identify mentions to chemical compounds in text and is the basis for more elaborate information extraction. However, only a small number of applications are freely available to identify such mentions. Particularly challenging and useful is the identification of International Union of Pure and Applied Chemistry (IUPAC) chemical compounds, which due to the complex morphology of IUPAC names requires more advanced techniques than that of brand names. Results: We present CheNER, a tool for automated identification of systematic IUPAC chemical mentions. We evaluated different systems using an established literature corpus to show that CheNER has a superior performance in identifying IUPAC names specifically, and that it makes better use of computational resources. Availability and implementation: http://metres.udl.cat/index.php/9-download/4-chener, http://chener.bioinfo.cnio.es/ Contact: miguel.vazquez@cnio.es Supplementary information: Supplementary data are available at Bioinformatics online.

Cork oak (Quercus suber L.) is an ecologically and economically important evergreen tree species native to the Mediterranean region and widespread in southwest Europe and northwest Africa. An improved genome assembly of cork oak using a combination of Illumina and PacBio sequencing is presented in this study. The assembled genome contains 2351 scaffolds longer than 1000 bp, accounting for 765.7 Mbp of genome size, L90 of 755, and a N50 of 1.0 Mbp, with 40,131 annotated genes. The repetitive sequences constitute 53.6% of the genome. The genome sequences of chloroplast and mitochondrion were determined for the first time, with a genome size of 161,179 bp and 531,858 bp, respectively. Phylogenetic analysis based on complete chloroplast genome sequence showed that Q. suber is closely related to Quercus variabilis, two cork-producing species with commercial use. All data generated are available through the public databases, being ready to be used without restrictions. This study provides an improved nuclear genome assembly together with the organelle genomes of cork oak. These resources will be useful for further breeding strategies and conservation programs and for comparative genomic studies in oak species.