Application of Oxford Nanopore MinION platform in Cannabis genomics and metagenomics: first impressions
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The recent emergence of Cannabis cultivation as a legal mainstream activity has opened up opportunities for genomic studies to establish basic information on par with other high value industrial plant crops. In particular, next generation sequencing (NGS) technologies show promise in identification of single and multi-trait Mendelian and Quantitative Trait loci as markers for selective breeding programs; in the characterization of structural and copy number variations; and through metagenomics in the discovery, identification, and characterization of associated and possibly pathogenic microorganisms including bacteria, fungi, viruses, and viroids. In contrast to more mainstream NGS platforms with high equipment and per-run costs, the Oxford Nanopore (ONT) MinION technology has potential to democratize the application of NGS technologies by providing a relatively low entry cost platform with a scale well suited for application to Cannabis. We report here on our initial experiences of application of this platform to Cannabis genomics and metagenomics. These include preliminary development of an inexpensive and technically simple but effective dried plant material DNA isolation protocol enriched for longer fragments well suited to nanopore sequencing; observations on data yield and associated costs and times downstream of this preparation method, with discussion of scalability; a consideration of our experimentally observed read length distributions in the context of potential advantages of long read technologies over short read technologies in establishing genetic scaffolds in the presence of long repeat regions; and a summary of bioinformatics challenges, resources, and possible solutions for Cannabis laboratories considering gathering NGS data. Finally, we present examples of genomic and metagenomic data we have obtained with this method.