Next-generation sequencing technologies have aided molecular detection and diagnosis of plant pathogens. Short read sequencing technologies can be expensive, time consuming, and lack portability. The Oxford Nanopore Technologies (ONT) MinION sequencer offers plant diagnosticians an alternative for whole-genome and transcriptome sequencing with the advantages of portability, rapid results and access to sequences generated, and relatively low cost. Although this company offers multiple sequencing products, most previous articles focused on comparing this technology with other sequencing technology (Sanger, Illumina) and not comparing ONT product performance. In this project, we explored the potential of using ONT’s kits without modifications for the sequencing of plant pathogens. We compared the performance of DNA library preparation protocols (1D versus 1D2 versus Rapid) and RNA library preparation protocols (cDNA PCR Sequencing versus Direct RNA) on the MinION sequencer and examined different data analysis approaches for two well-characterized plant pathogens of agricultural concern, Ralstonia solanacearum and plum pox virus. For bacterial DNA sequencing, the Rapid Sequencing kit had the lowest throughput but offered the shortest sample-to-sequence turnaround time. The cDNA PCR Sequencing kit was better suited for plant RNA viruses than the Direct RNA. Whole-genome assemblies using all tested kits provided accurate identification of the target pathogen when pure cultures or infected plant material was used. This technology offers a shorter sample-to-sequence timeline than previous technologies for both DNA and RNA samples. Data analysis can still be time- and resource-consuming, but we found that 1 h of data generation was sufficient for accurate identification of the target pathogens, which can alleviate computing resources because a full 48-h run of sequencing data is not required. With the decreasing costs of flow cells, MinION is now an additional tool to be considered by plant diagnosticians for whole-genome and transcriptome-based diagnostics.

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● Quantifying the mechanisms underlying hybrid zone formation requires an evaluation of both neutral and nonneutral evolutionary processes. Population demographic changes, alongside landscape heterogeneity and climate adaptation, can influence the timing, stability, and extent of introgression where species hybridize. Thus, quantifying interactions across diverged lineages, and the relative contributions of interspecific genetic exchange and selection to divergence at the genome-wide level is needed. ● We quantified the contributions of climate and geography to the genetic structure across replicate contact zones betweenPopulus trichocarpaandP. balsamifera, evaluating the demographic context of hybridization and the role of genetic connectivity over time. ● We found genomic structure differed among the seven latitudinally arrayed transects. While ancestry was strongly structured by climate, geography appears to have restricted gene flow in certain regions of the hybrid zone. The best fitting demographic model indicated high rates of gene flow alongside selection have likely influenced the establishment and maintenance of the hybrid zone. ● Our results point towards the importance of climate in structuring the contact zones betweenP. trichocarpaandP. balsamiferaand emphasize the value of sampling replicated zones of contact to understand how neutral and non-neutral processes influence hybrid zone formation across space and time.