A workflow for practical training in plant genomics using Oxford Nanopore long‐read sequencing

Societal Impacts Statement Advances in DNA sequencing technologies are revolutionising all areas of plant genomic research. In response to the current deficit of educational resources in modern plant genomic methods, we have developed a comprehensive genomics training course for sequencing and analysing non‐model plant species. This course effectively equips students in all stages of a genomic workflow, enabling them to produce partial nuclear and complete plastid genomes with long‐read sequencing data. Such an approach significantly enhances science education by empowering students with the skills necessary for generating and analysing contemporary plant genomic data. Summary Long‐read sequencing technologies continue to grow in popularity and provide an effective way to resolve large and complex genomic variants. However, uptake of these technologies for teaching and training is hampered by the complexity of high molecular weight DNA extraction protocols, the time required for library preparation and the costs for sequencing, as well as challenges with downstream data analyses. We present a long‐read workflow for teaching, that covers each stage from DNA extraction, to library preparation and sequencing, to data QC and genome assembly and characterisation, which can be completed in under two weeks. We use a case study of plant identification, where students generate sequence data and assemble genomes to help identify an unlabelled plant sample. Long‐read genome skimming of wild‐collected plant species extracted with a modified kit‐based approach produced an average of 8Gb of Oxford Nanopore data, enabling the complete assembly of plastid genomes, and partial assembly of nuclear genomes. All students were able to complete the protocol, and to correctly identify their sample based on sequence matches of barcoding loci extracted from the plastid genome, coupled with phylogenetic analyses of whole plastid genomes. Our comprehensive and easy‐to‐follow workflow will enable training in the use of long‐read sequencing for plant genomic analysis in a range of teaching settings.