Crop disease outbreaks are often associated with clonal expansions of single pathogenic lineages. To determine whether similar boom-and-bust scenarios hold for wild pathosystems, we carried out a multi-year, multi-site survey Pseudomonas in its natural host Arabidopsis thaliana. The most common lineage corresponded to ubiquitous clade. Sequencing 1,524 genomes revealed this have diversified approximately 300,000 years ago, containing dozens genetically identifiable sublineages. There is...

Given the negative fitness effects that pathogens impose on their hosts, benefits of resistance should be universal. However, there is marked variation across plant species in number nucleotide-binding leucine-rich repeat receptors, which form a cornerstone defense. The growth-defense trade-off hypothesis predicts costs associated with defense investment to generate these traits. Our analysis comparing features intracellular immune-receptor repertoires trait data 187 shows wild plants, size...

A high-quality genome sequence of any model organism is an essential starting point for genetic and other studies. Older clone-based methods are slow expensive, whereas faster, cheaper short-read-only assemblies can be incomplete highly fragmented, which minimizes their usefulness. The last few years have seen the introduction many new technologies assembly. These associated algorithms typically benchmarked on microbial genomes or, if they scale appropriately, larger (e.g., human) genomes....

All species shed DNA during life or in death, providing an opportunity to monitor biodiversity via environmental (eDNA). In recent years, combining eDNA, high-throughput sequencing technologies, bioinformatics, and increasingly complete sequence databases has promised a non-invasive non-destructive monitoring tool. Modern agricultural systems are often large monocultures so highly vulnerable disease outbreaks. Pest pathogen ecosystems is key for efficient early prevention, lower pesticide...

The Oxford Nanopore Technologies MinION™ sequencer is a small, portable, low cost device that accessible to labs of all sizes and attractive for in-the-field sequencing experiments. Selective breeding crops has led reduction in genetic diversity, wild relatives are key source new resistance pathogens, usually via NLR immune receptor-encoding genes. Recent studies have demonstrated how crop repertoires can be targeted on Illumina or PacBio (RenSeq) the specific gene conveying pathogen...

Targeted capture provides an efficient and sensitive means for sequencing specific genomic regions in a high-throughput manner. To date, this method has mostly been used to exons from the genome (the exome) using short insert libraries short-read technology, enabling identification of genetic variants or new members large gene families. Sequencing larger molecules results whole genes, including intronic intergenic sequences that are typically more polymorphic allow resolution structure...

Thorough understanding of complex model systems requires the characterisation processes in different cell types an organism. This can be achieved with high-throughput spatial transcriptomics at a large scale. However, for plant this is still challenging as suitable methods are sparsely available. Here we present GaST-seq (Grid-assisted, Spatial Transcriptome sequencing), easy to adopt, micro-scale spatial-transcriptomics workflow that allows study expression profiles across small areas...

Soil salinity is a major stress limiting agricultural productivity worldwide. To counteract the adverse effects of salinity, plants from coastal habitats may engage in positive interaction with microbial partners. We recently discovered inland and populations Brassica fruticulosa contrasting tolerance. Here we characterize microbiomes salt-tolerant (PST) salt-sensitive (PSS) populations, analyzing diversity abundance bacteria fungi taxa bulk soil, rhizosphere, roots, leaves eight...

Common bottlenecks in environmental and crop microbiome studies are the consumable personnel costs necessary for genomic DNA extraction sequencing library construction. This is harder challenging samples such as soil, which rich Polymerase Chain Reaction (PCR) inhibitors. To address this, we have established a low-cost method soil samples. We also present an Illumina-compatible 16S ITS rRNA gene amplicon preparation workflow that uses common laboratory equipment. evaluated performance of our...

Abstract The requirement for large amounts of purified DNA limits many sequencing experiments, especially when seeking to avoid pre-amplification or using third generation technology sequence molecules directly. We wanted test the current nanopore input requirements and devised a set experiments evaluate extraction library preparation approaches low inputs. found an optimised bead beating approach combined with magnetic protocol, rather than traditional spin columns extraction, improved both...

Assessing the response of pancreatic islet cells to glucose stimulation is important for understanding β-cell function. Zebrafish are a promising model studies metabolism in general, including stimulus-secretion coupling pancreas. We used transgenic zebrafish embryos expressing genetically-encoded Ca2+ sensor β-cells monitor key step induced insulin secretion; elevations intracellular [Ca2+]i. In vivo and ex analyses [Ca2+]i demonstrate that responsiveness well established late embryogenesis...

A high quality genome sequence of your model organism is an essential starting point for many studies. Old clone based methods are slow and expensive, whereas faster, cheaper short read only assemblies can be incomplete highly fragmented, which minimises their usefulness. The last few years have seen the introduction new technologies assembly. These algorithms typically benchmarked on microbial genomes or, if they scale appropriately, human. However, plant much more repetitive larger than...

All species shed DNA into their environment during life or in death providing an opportunity to monitor biodiversity via its environmental DNA. Biodiversity monitoring using based technologies has become important tool understanding ecosystems. In recent years promising progress for non-invasive and, more importantly, non-destructive been made by combining the retrieval of information transmitted released with high-throughput sequencing technologies. Important ecosystems under continuous...

Abstract Background All species shed DNA into their environment during life or in death providing an opportunity to monitor biodiversity via its environmental DNA. Biodiversity monitoring using based technologies has become important tool understanding ecosystems. In recent years promising progress for non-invasive and, more importantly, non-destructive been made by combining the retrieval of information transmitted released with high-throughput sequencing technologies. Important ecosystems...

Abstract Background Oxford Nanopore Technologies’ MinION sequencer is a compact, USB-powered device that has been available since 2014. Since the release of earliest model, throughput and error rate platform have improved dramatically it become possible to consider sequencing assembly eukaryotic organisms using single nanopore flow cell. Here, we present sequence data, methylation analysis for Columbia (Col-0) accession model plant Arabidopsis thaliana . Further, demonstrate effect recent...

Summary Crop disease outbreaks are often associated with clonal expansions of single pathogenic lineages. To determine whether similar boom-and-bust scenarios hold for wild plant pathogens, we carried out a multi-year multi-site survey Pseudomonas in the natural host Arabidopsis thaliana. The most common lineage corresponded to clade present all sites. Sequencing 1,524 genomes revealed this have diversified approximately 300,000 years ago, containing dozens genetically distinct sublineages....

Abstract Background Thorough understanding of complex model systems requires the characterisation processes in different cell types an organism. This can be achieved with high-throughput spatial transcriptomics at a large scale. However, for plant this is still challenging as suitable methods are sparsely available. Here we present Grid-seq, easy to adopt, micro-scale spatial-transcriptomics workflow that allows study expression profiles across small areas tissue fraction cost existing...

Abstract Background Common bottlenecks in environmental microbiome studies are the consumable and personnel costs necessary for genomic DNA extraction sequencing library construction. This is harder challenging samples such as soil, which rich PCR inhibitors. To address this, we have established a low-cost method inhibitor alongside an Illumina-compatible 16S ITS rRNA gene amplicon preparation workflow that uses common laboratory equipment. We evaluated performance of our against two leading...