New molecular methods to assess biodiversity. Potentials and pitfalls of DNA metabarcoding: a workshop report

This report presents the outcome of the joint work of PhD students and senior researchers working with DNA-based biodiversity assessment approaches with the goal to facilitate others the access to definitions and explanations about novel DNA-based methods. The work was performed during a PhD course (SLU PNS0169) at the Swedish University of Agricultural Sciences (SLU) in Uppsala, Sweden. The course was co-organized by the EU COST research network DNAqua-Net and the SLU Research Schools Focus on Soils and Water (FoSW) and Ecology - basics and applications. DNAqua-Net (COST Action CA15219, 2016-2020) is a network connecting researchers, water managers, politicians and other stakeholders with the aim to develop new genetic tools for bioassessment of aquatic ecosystems in Europe and beyond. The PhD course offered a comprehensive overview of the paradigm shift from traditional morphology-based species identification to novel identification approaches based on molecular markers. We covered the use of molecular tools in both basic research and applied use with a focus on aquatic ecosystem assessment, from species collection to the use of diversity in environmental legislation. The focus of the course was on DNA (meta)barcoding and aquatic organisms. The knowledge gained was shared with the general public by creating Wikipedia pages and through this collaborative Open Access publication, co-authored by all course participants

DNA-based monitoring for assessing the effect of invasive species on aquatic communities in the Amazon basin of Ecuador

Ecuador is well-known as one of the most biodiverse countries, but this species richness is being threatened by invasive alien species. The early detection of these invasive species is crucial for their fast and successful eradication and for limiting their effects on aquatic communities. Therefore, a Belgian VLIR-UOS project was started that aims at the development of a fast detection method to monitor the Ecuadorian Amazon river basin for the presence of invasive fishes, macroinvertebrates and amphibians. An (e)DNA field lab, equipped with miniaturized and portable DNA-processing equipment, such as centrifuges, thermal cyclers, and electrophoresis equipment (MiniPCR), was developed. In the next phase, the Nanopore Next-Generation sequencing (NGS) technique (MinION) will be optimized to enable the eDNA-based biomonitoring of tropical aquatic environments in the field. The fast detection of invasive species may help to prevent their further spread and perhaps even facilitate their eradication, and will promote more effective actions for the conservation of aquatic ecosystems. Furthermore, new DNA-sequences of amphibians, macroinvertebrates, and fishes are being incorporated into the newly developed Ecuadorian DNA database. We also focus on building and strengthening the capacities of staff and students (Ecuadorian as well as Belgian) through theses, practical courses, field work, trainings and internships

High degree of polyclonality hinders somatic mutation calling in lung brush samples of COPD cases and controls

International audienceChronic obstructive pulmonary disease (COPD) is induced by cigarette smoking and characterized by inflammation of airway tissue. Since smokers with COPD have a higher risk of developing lung cancer than those without, we hypothesized that they carry more mutations in affected tissue. We called somatic mutations in airway brush samples from medium-coverage whole genome sequencing data from healthy never and ex-smokers (n = 8), as well as from ex-smokers with variable degrees of COPD (n = 4). Owing to the limited concordance of resulting calls between the applied tools we built a consensus, a strategy that was validated with high accuracy for cancer data. However, consensus calls showed little promise of representing true positives due to low mappability of corresponding sequence reads and high overlap with positions harbouring known genetic polymorphisms. A targeted re-sequencing approach suggested that only few mutations would survive stringent verification testing and that our data did not allow the inference of any difference in the mutational load of bronchial brush samples between former smoking COPD cases and controls. High polyclonality in airway brush samples renders medium-depth sequencing insufficient to provide the resolution to detect somatic mutations. Deep sequencing data of airway biopsies are needed to tackle the question