Tree Lab: Portable Genomics for Early Detection of Plant Viruses and Pests in Sub-Saharan Africa
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Date
2019
Journal Title
Journal ISSN
Volume Title
Publisher
Genes
Abstract
In this case study we successfully teamed the PDQeX DNA purification technology
developed by MicroGEM, New Zealand, with the MinION and MinIT mobile sequencing devices
developed by Oxford Nanopore Technologies to produce an e ective point-of-need field diagnostic
system. The PDQeX extractsDNAusing a cocktail of thermophilic proteinases and cell wall-degrading
enzymes, thermo-responsive extractor cartridges and a temperature control unit. This closed system
delivers purified DNA with no cross-contamination. The MinIT is a newly released data processing
unit that converts MinION raw signal output into nucleotide base called data locally in real-time,
removing the need for high-specification computers and large file transfers from the field. All three
devices are battery powered with an exceptionally small footprint that facilitates transport and
setup. To evaluate and validate capability of the system for unbiased pathogen identification by
real-time sequencing in a farmer’s field setting, we analysed samples collected from cassava plants
grown by subsistence farmers in three sub-Sahara African countries (Tanzania, Uganda and Kenya).
A range of viral pathogens, all with similar symptoms, greatly reduce yield or destroy cassava
crops. Eight hundred (800) million people worldwide depend on cassava for food and yearly
income, and viral diseases are a significant constraint to its production. Early pathogen detection at
a molecular level has great potential to rescue crops within a single growing season by providing
results that inform decisions on disease management, use of appropriate virus-resistant or replacement
planting. This case study presented conditions of working in-field with limited or no access to mains
power, laboratory infrastructure, Internet connectivity and highly variable ambient temperature.
An additional challenge is that, generally, plant material contains inhibitors of downstream molecular
processes making e ective DNA purification critical. We successfully undertook real-time on-farm
genome sequencing of samples collected from cassava plants on three farms, one in each country.
Cassava mosaic begomoviruses were detected by sequencing leaf, stem, tuber and insect samples. The entire process, from arrival on farm to diagnosis, including sample collection, processing and
provisional sequencing results was complete in under 3 h. The need for accurate, rapid and on-site
diagnosis grows as globalized human activity accelerates. This technical breakthrough has applications
that are relevant to human and animal health, environmental management and conservation.
Description
Keywords
Cassava, Cassava mosaic begomovirus, Cassava mosaic disease, Bemisia tabaci, Whitefly, MinION, MinIT, PDQeX, Tanzania, Kenya, Uganda
Citation
Boykin, L. M., Sseruwagi, P., Alicai, T., Ateka, E., Mohammed, I. U., Stanton, J. A. L., ... & Ndunguru, J. (2019). Tree lab: Portable genomics for early detection of plant viruses and pests in sub-saharan africa. Genes, 10(9), 632. doi:10.3390/genes10090632