Establishing MinION Sequencing and Genome Assembly Procedures for the Analysis of the Rooibos (Aspalathus linearis) Genome

While plant genome analysis is gaining speed worldwide, few plant genomes have been sequenced and analyzed on the African continent. Yet, this information holds the potential to transform diverse industries as it unlocks medicinally and industrially relevant biosynthesis pathways for bioprospecting. Considering that South Africa is home to the highly diverse Cape Floristic Region, local establishment of methods for plant genome analysis is essential. Long-read sequencing is becoming standard procedure for plant genome research, as these reads can span repetitive regions of the DNA, substantially facilitating reassembly of a contiguous genome. With the MinION, Oxford Nanopore offers a cost-efficient sequencing method to generate long reads; however, DNA purification protocols must be adapted for each plant species to generate ultra-pure DNA, essential for these analyses. Here, we describe a cost-effective procedure for the extraction and purification of plant DNA and evaluate diverse genome assembly approaches for the reconstruction of the genome of rooibos (Aspalathus linearis), an endemic South African medicinal plant widely used for tea production. We discuss the pros and cons of nine tested assembly programs, specifically Redbean and NextDenovo, which generated the most contiguous assemblies, and Flye, which produced an assembly closest to the predicted genome size.

Automated summary

While plant genome analysis is progressing globally, there is still limited research on plant genomes in Africa. However, the study of African plant genomes holds great potential for medical and industrial applications. Establishing local methods for plant genome analysis in South Africa is crucial due to the region's rich biodiversity. Long-read sequencing has become a standard procedure for plant genome research, but DNA purification protocols need to be adjusted for each plant species to obtain high-quality DNA.