CorkOakDB-The Cork Oak Genome Database Portal

Research on the Molecular Mechanisms and Key Gene Discovery in Quercus variabilis Root Pruning Based on Transcriptomics and Hormone Profiling

Quercus variabilis (Q. variabilis), a significant broadleaf species used in afforestation across high, sandy, and mountainous regions, presents unique challenges for transplantation. This species is characterized by its slow above-ground growth and rapid taproot development, which suppresses the proliferation of lateral and fibrous roots, negatively impacting post-transplant survival. Research indicates that targeted root pruning-specifically, the removal of one-third of the roots-promotes the development of lateral roots in these seedlings. This study involved pruning the root systems of Q. variabilis and assessing the subsequent root development in comparison to an unpruned control group. Our analysis, which included transcriptome sequencing and plant hormone metabolism assays conducted at 2, 12, and 25 days post-pruning, yielded 126.02 Gb of clean data and identified 7662 differentially expressed genes (DEGs). These genes were primarily enriched in the plant hormone signal transduction pathway. Further investigation of this pathway, along with hormone content measurements, elucidated the mechanisms that contribute to enhanced root growth following pruning. Additionally, through a weighted correlation network analysis (WGCNA), we identified 20 key genes that are instrumental in promoting root development in Q. variabilis saplings. This research advances the theoretical framework for forestry seedling production and afforestation, laying the groundwork for scientifically informed vegetation restoration techniques.

OpenGenomeBrowser: a versatile, dataset-independent and scalable web platform for genome data management and comparative genomics

BACKGROUND

As the amount of genomic data continues to grow, there is an increasing need for systematic ways to organize, explore, compare, analyze and share this data. Despite this, there is a lack of suitable platforms to meet this need.

RESULTS

OpenGenomeBrowser is a self-hostable, open-source platform to manage access to genomic data and drastically simplifying comparative genomics analyses. It enables users to interactively generate phylogenetic trees, compare gene loci, browse biochemical pathways, perform gene trait matching, create dot plots, execute BLAST searches, and access the data. It features a flexible user management system, and its modular folder structure enables the organization of genomic data and metadata, and to automate analyses. We tested OpenGenomeBrowser with bacterial, archaeal and yeast genomes. We provide a docker container to make installation and hosting simple. The source code, documentation, tutorials for OpenGenomeBrowser are available at opengenomebrowser.github.io and a demo server is freely accessible at opengenomebrowser.bioinformatics.unibe.ch .

CONCLUSIONS

To our knowledge, OpenGenomeBrowser is the first self-hostable, database-independent comparative genome browser. It drastically simplifies commonly used bioinformatics workflows and enables convenient as well as fast data exploration.

OakRootRNADB-a consolidated RNA-seq database for coding and noncoding RNA in roots of pedunculate oak (Quercus robur)

The degree to which roots elongate is determined by the expression of genes that regulate root growth in each developmental zone of a root. Most studies have, however, focused on the molecular factors that regulate primary root growth in annual plants. In contrast, the relationship between gene expression and a specific pattern of taproot development and growth in trees is poorly understood. However, the presence of a deeply located taproot, with branching lateral roots, can especially mitigate the effect of insufficient water availability in long-lived trees, such as pedunculated oak. In the present article, we integrated the ribonucleic acid (RNA) sequencing data on roots of oak trees into a single comprehensive database, named OakRootRNADB that contains information on both coding and noncoding RNAs. The sequences in the database also enclose information pertaining to transcription factors, transcriptional regulators and chromatin regulators, as well as a prediction of the cellular localization of a transcript. OakRootRNADB has a user-friendly interface and functional tools that increase access to genomic information. Integrated knowledge of molecular patterns of expression, specifically occurring within and between root zones and within root types, can elucidate the molecular mechanisms regulating taproot growth and enhanced root soil exploration. Database URL https://oakrootrnadb.idpan.poznan.pl/.

Genome-wide identification, phylogeny, and gene duplication of the epigenetic regulators in Fagaceae

Epigenetic regulators are proteins involved in controlling gene expression. Information about the epigenetic regulators within the Fagaceae, a relevant family of trees and shrubs of the northern hemisphere ecosystems, is scarce. With the intent to characterize these proteins in Fagaceae, we searched for orthologs of DNA methyltransferases (DNMTs) and demethylases (DDMEs) and Histone modifiers involved in acetylation (HATs), deacetylation (HDACs), methylation (HMTs), and demethylation (HDMTs) in Fagus, Quercus, and Castanea genera. Blast searches were performed in the available genomes, and freely available RNA-seq data were used to de novo assemble transcriptomes. We identified homologs of seven DNMTs, three DDMEs, six HATs, 11 HDACs, 32 HMTs, and 21 HDMTs proteins. Protein analysis showed that most of them have the putative characteristic domains found in these protein families, which suggests their conserved function. Additionally, to elucidate the evolutionary history of these genes within Fagaceae, paralogs were identified, and phylogenetic analyses were performed with DNA and histone modifiers. We detected duplication events in all species analyzed with higher frequency in Quercus and Castanea and discuss the evidence of transposable elements adjacent to paralogs and their involvement in gene duplication. The knowledge gathered from this work is a steppingstone to upcoming studies concerning epigenetic regulation in this economically important family of Fagaceae.

Making European performance and impact assessment frameworks glocal

Sustainability of research infrastructures (RIs) is a big challenge for funders, stakeholders and operators, and the development and adoption of adequate management tools is a major concern, namely tools for monitoring and evaluating their performance and impact. BioData.pt is the Portuguese Infrastructure of Biological and Portuguese node of the European Strategy Forum on Research Infrastructures "Landmark" ELIXIR. The foundations of this national research infrastructure were laid under the "Building BioData.pt" project, for four years. During this period, performance and impact indicators were collected and analysed under the light of international guidelines for assessing the performance and impact of European research infrastructures produced by the European Strategy Forum on Research Infrastructures, the Organisation for Economic Co-operation and Development and the EU-funded RI-PATHS project. The exercise shared herein showed that these frameworks can be adopted by national RIs, with the necessary adaptations, namely to reflect the national landscape and specificity of activities, and can be powerful tools in supporting the management of RIs. "Not everything that counts can be counted, and not everything that can be counted, counts". Albert Einstein, Theoretical physicist and Nobel Prize winner.

Making European performance and impact assessment frameworks for research infrastructures glocal

Sustainability of research infrastructures (RIs) is a big challenge for funders, stakeholders and operators, and the development and adoption of adequate management tools is a major concern, namely tools for monitoring and evaluating their performance and impact. BioData.pt is the Portuguese Infrastructure of Biological data and the Portuguese node of the European Strategy Forum on Research Infrastructures "Landmark" ELIXIR. The foundations of this national research infrastructure were laid under the "Building BioData.pt" project, for four years. During this period, performance and impact indicators were collected and analysed under the light of international guidelines for assessing the performance and impact of European research infrastructures produced by the European Strategy Forum on Research Infrastructures, the Organisation for Economic Co-operation and Development and the EU-funded RI-PATHS project. The exercise shared herein showed that these frameworks can be adopted by national RIs, with the necessary adaptations, namely to reflect the national landscape and specificity of activities, and can be powerful tools in supporting the management of RIs. "Not everything that counts can be counted, and not everything that can be counted, counts". (Attributed to William Bruce Cameron).