A workflow for practical training in plant ecological genomics using Oxford Nanopore long-read sequencing
Long-read single molecule sequencing technologies continue to grow in popularity for genome assembly 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. Here, we present a full long-read workflow optimised for teaching, that covers each stage from DNA extraction, to library preparation and sequencing, to data QC and genome assembly and characterisation, that can be completed over 6 days. We use a specific application of plant identification, where students identify an anonymous plant sample from analyses of newly generated genomic data. In testing, nine wild-collected plant species extracted with a modified kit based approach produced an average of 8Gb of Oxford Nanopore long read data, enabling the complete assembly of plastid genomes, and partial assembly of nuclear genomes (average contig N50 of 32 Kb, representing c. 33% genome span). Nearly all students were able to correctly identify their plant samples based on BOLD searches of barcoding loci coupled with phylogenetic analyses of whole plastid genomes. We supply all the learning material and raw data allowing this to be adapted to a range of teaching settings.