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....

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Bibliographic Details
Published in:Plants (Basel) 2022-08, Vol.11 (16), p.2156
Main Authors: Mgwatyu, Yamkela, Cornelissen, Stephanie, van Heusden, Peter, Stander, Allison, Ranketse, Mary, Hesse, Uljana
Format: Article
Language:English
Subjects:
Alcohol
Aspalathus linearis
Assembly
Beans
Bioprospecting
Biosynthesis
Canu
Cold
Comparative analysis
Cost analysis
Deoxyribonucleic acid
DNA
DNA sequencing
Endemic plants
Ethanol
Flowers & plants
Gene sequencing
Genetic aspects
Genomes
Haslr
Herbal medicine
Legumes
MaSuRCA
Medicinal plants
Methods
Mimosaceae
Nitrogen
Nucleotide sequencing
Oxford Nanopore
Physiological aspects
Plant extracts
plant genome assembly
Plant species
Purification
rooibos
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Summary: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 ( ), 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.
ISSN:2223-7747
2223-7747
DOI:10.3390/plants11162156