Tree Lab: Portable Genomics for Early Detection of Plant Viruses and Pests in Sub-Saharan Africa
School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA 6009, Australia
Mikocheni Agricultural Research Institute (MARI), Dar es Salaam P.O. Box 6226, Tanzania
National Crops Resources Research Institute (NaCRRI), Kampala P.O. Box 7084, Uganda
Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi P.O. Box 62000-00200, Kenya
Department of Crop Science, Faculty of Agriculture, Kebbi State University of Science and Technology, Aliero P.O. Box 1144, Nigeria
Department of Anatomy, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
Department of Primary Industries and Regional Development Diagnostic Laboratory Services, Plant Pathology, South Perth, WA 6151, Australia
Malaghan Institute of Medical Research, P.O. Box 7060, Newtown, Wellington 6242, New Zealand
MicroGEM Ltd., 9 Melody Ln, Ruakura, Hamilton 3216, New Zealand
Author to whom correspondence should be addressed.
Genes 2019, 10(9), 632; https://doi.org/10.3390/genes10090632
Received: 26 July 2019 / Revised: 16 August 2019 / Accepted: 19 August 2019 / Published: 21 August 2019
(This article belongs to the Special Issue MetaGenomics Sequencing In Situ)
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 effective point-of-need field diagnostic system. The PDQeX extracts DNA using 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 effective 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.