Suchergebnisse

This research was supported by the Spanish Ministry of Science, Innovation and Universities (grants AGL2017-88702-C2-1-R and AGL2017-88702-C2-2-R). Funding was also received from the BRESOV (Breeding for resilient, efficient, and sustainable organic vegetable production) project. BRESOV was funded by the European Union's Horizon 2020 research and innovation programme under grant agreement No. 774244. We would also like to thank research facilities provided by the Campus de Excelencia Internacional Agroalimentario (CeiA3). PhD fellowships were funded by the FPU (R.F., R.Le.) Programmes of the Ministerio de Ciencia e Innovacion and the LASPAU (J.L.Q.). ; Trichomes are specialised epidermal cells developed in the aerial surface of almost every terrestrial plant. These structures form physical barriers, which combined with their capability of synthesis of complex molecules, prevent plagues from spreading and confer trichomes a key role in the defence against herbivores. In this work, the tomato gene HAIRPLUS (HAP) that controls glandular trichome density in tomato plants was characterised. HAP belongs to a group of proteins involved in histone tail modifications although some also bind methylated DNA. HAP loss of function promotes epigenomic modifications in the tomato genome reflected in numerous differentially methylated cytosines and causes transcriptomic changes in hap mutant plants. Taken together, these findings demonstrate that HAP links epigenome remodelling withmulticellular glandular trichome development and reveal that HAP is a valuable genomic tool for pest resistance in tomato breeding. ; Spanish Government AGL2017-88702-C2-1-R AGL2017-88702-C2-2-R ; European Commission 774244 ; FPU Programmes of the Ministerio de Ciencia e Innovacion ; LASPAU ; BRESOV (Breeding for resilient, efficient, and sustainable organic vegetable production) project

This work was supported by European Union [765492]; Spanish Government [AGL2017-88702-C2-2-R] to M.H.; Consejer´ıa de Econom´ıa, Conocimiento, Empresas y Universidad de la Junta de Andaluc´ıa and European Regional Development Funds (ERDF) [SOMM17-6109, UCE-PP2017-3] to J.A.M. and M.H.; Instituto de Salud Carlos III, ERDF funds [PIE16/00045] to J.A.M.; Chair 'Doctors Galera-Requena in cancer stem cell research' (to J.A.M.); Instituto de Salud Carlos III [IFI16/00041] to E.A. Funding for open access charges: Excellence Research Unit "Modelling Nature" (MNat) [SOMM17-6109]. Conflict of interest statement. None declared. ; Although miRNA-seq is extensively used in many different fields, its quality control is frequently restricted to a PhredScore-based filter. Other important quality related aspects like microRNA yield, the fraction of putative degradation products (such as rRNA fragments) or the percentage of adapter-dimers are hard to assess using absolute thresholds. Here we present mirnaQC, a webserver that relies on 34 quality parameters to assist in miRNA-seq quality control. To improve their interpretability, quality attributes are ranked using a reference distribution obtained from over 36 000 publicly availablemiRNA-seq datasets. Accepted input formats include FASTQ and SRA accessions. The results page contains several sections that deal with putative technical artefacts related to library preparation, sequencing, contamination or yield. Different visualisations, including PCA and heatmaps, are available to help users identify underlying issues. Finally, we show the usefulness of this approach by analysing two publicly available datasets and discussing the different quality issues that can be detected using mirnaQC. ; European Union (EU) 765492 ; Spanish Government AGL2017-88702-C2-2-R ; Junta de Andalucia ; European Union (EU) SOMM17-6109 UCE-PP2017-3 ; Instituto de Salud Carlos III, ERDF funds PIE16/00045 ; Instituto de Salud Carlos III IFI16/00041 ; Chair 'Doctors Galera-Requena in cancer stem cell ...

Progressive evolution, or the tendency towards increasing complexity, is a controversial issue in biology, which resolution entails a proper measurement of complexity. Genomes are the best entities to address this challenge, as they encode the historical information of a species' biotic and environmental interactions. As a case study, we have measured genome sequence complexity in the ancient phylum Cyanobacteria. To arrive at an appropriate measure of genome sequence complexity, we have chosen metrics that do not decipher biological functionality but that show strong phylogenetic signal. Using a ridge regression of those metrics against root-to-tip distance, we detected positive trends towards higher complexity in three of them. Lastly, we applied three standard tests to detect if progressive evolution is passive or driven—the minimum, ancestor– descendant, and sub-clade tests. These results provide evidence for driven progressive evolution at the genome-level in the phylum Cyanobacteria. ; Generalitat Valenciana Prometeo/2018/A/133 ; European Union (EU) ; Fulbright fellowship (Spanish Minister of Science, Innovation and Universities) ; SAF2015-65878-R ; AGL2017-88702-C2-2-R ; PGC2018-099344-B-I00

Since the original publication of sRNAtoolbox in 2015, small RNA research experienced notable advances in different directions. New protocols for small RNA sequencing have become available to address important issues such as adapter ligation bias, PCR amplification artefacts or to include internal controls such as spike-in sequences. New microRNA reference databases were developed with different foci, either prioritizing accuracy (low number of false positives) or completeness (low number of false negatives). Additionally, other small RNA molecules as well asmicroRNA sequence and length variants (isomiRs) have continued to gain importance. Finally, the number of microRNA sequencing studies deposited in GEO nearly triplicated from 2014 (280) to 2018 (764). These developments imply that fast and easy-to-use tools for expression profiling and subsequent downstream analysis of miRNAseq data are essential to many researchers. Key features in this sRNAtoolbox release include addition of all major RNA library preparation protocols to sRNAbench and improvements in sRNAde, a tool that summarizes several aspects of small RNA sequencing studies including the detection of consensus differential expression. A special emphasis was put on the user-friendliness of the tools, for instance sRNAbench now supports parallel launching of several jobs to improve reproducibility and user time efficiency. ; European Union [765492 to M.H.]; Spanish Government [AGL2017-88702-C2-2-R to M.H., J.L.O.]; Instituto de Salud Carlos III, FEDER funds [PIE16/00045 to J.A.M.]; Chair 'Doctors Galera-Requena in cancer stem cell research' to JMA and by the Ministry of Education of Spain [FPU13/05662 to R.L., IFI16/00041 to E.A.]; Strategic Research Area (SFO) program of the Swedish Research Council (to V.R.) through Stockholm University (to B.F.). Funding for open access charge: SpanishGovernment [AGL2017-88702-C2-2-R].