Tree Lab: Portable Genomics for Early Detection of Plant Viruses and Pests in Sub-Saharan Africa

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dc.contributor.authorBoykin, Laura M.
dc.contributor.authorSseruwagi, Peter
dc.contributor.authorAlicai, Titus
dc.contributor.authorAteka, Elijah
dc.contributor.authorUmar Mohammed, Ibrahim
dc.contributor.authorStanton, Jo-Ann L.
dc.contributor.authorKayuki, Charles
dc.contributor.authorMark, Deogratius
dc.contributor.authorFute, Tarcisius
dc.contributor.authorErasto, Joel
dc.contributor.authorBachwenkizi, Hilda
dc.contributor.authorMuga, Brenda
dc.contributor.authorMumo, Naomi
dc.contributor.authorMwangi, Jenniffer
dc.contributor.authorAbidrabo, Phillip
dc.contributor.authorOkao-Okuja, Geofrey
dc.contributor.authorOmuut, Geresemu
dc.contributor.authorAkol, Jacinta
dc.contributor.authorApio, Hellen B.
dc.contributor.authorOsingada, Francis
dc.contributor.authorKehoe, Monica A.
dc.contributor.authorEccles, David
dc.contributor.authorSavill, Anders
dc.contributor.authorLamb, Stephen
dc.contributor.authorKinene, Tonny
dc.contributor.authorRawle, Christopher B.
dc.contributor.authorMuralidhar, Abishek
dc.contributor.authorMayall, Kirsty
dc.contributor.authorTairo, Fred
dc.contributor.authorNdunguru, Joseph
dc.date.accessioned2022-02-16T05:31:41Z
dc.date.available2022-02-16T05:31:41Z
dc.date.issued2019
dc.description.abstractIn 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.en_US
dc.identifier.citationBoykin, 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/genes10090632en_US
dc.identifier.other10.3390/genes10090632
dc.identifier.urihttps://nru.uncst.go.ug/xmlui/handle/123456789/2171
dc.language.isoenen_US
dc.publisherGenesen_US
dc.subjectCassavaen_US
dc.subjectCassava mosaic begomovirusen_US
dc.subjectCassava mosaic diseaseen_US
dc.subjectBemisia tabacien_US
dc.subjectWhiteflyen_US
dc.subjectMinIONen_US
dc.subjectMinITen_US
dc.subjectPDQeXen_US
dc.subjectTanzaniaen_US
dc.subjectKenyaen_US
dc.subjectUgandaen_US
dc.titleTree Lab: Portable Genomics for Early Detection of Plant Viruses and Pests in Sub-Saharan Africaen_US
dc.typeArticleen_US
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