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Real time portable genome sequencing for global food security

View ORCID ProfileLaura M. Boykin, Ammar Ghalab, Bruno Rossitto De Marchi, Anders Savill, James M Wainaina, Tonny Kinene, Stephen Lamb, Myriam Rodrigues, Monica A. Kehoe, Joseph Ndunguru, Fred Tairo, Peter Sseruwagi, Charles Kayuki, Deogratius Mark, Joel Erasto, Hilda Bachwenkizi, Titus Alicai, Geoffrey Okao-Okuja, Phillip Abidrabo, John Francis Osingada, Jimmy Akono, Elijah Ateka, Brenda Muga, Samuel Kiarie
doi: https://doi.org/10.1101/314526
Laura M. Boykin
1School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA 6009 Australia
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  • ORCID record for Laura M. Boykin
  • For correspondence: laura.boykin@uwa.edu.au
Ammar Ghalab
1School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA 6009 Australia
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Bruno Rossitto De Marchi
1School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA 6009 Australia
2São Paulo State University (UNESP), School of Agriculture, Dept. of Plant Protection, CEP 18610-307, Botucatu (SP), Brazil
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Anders Savill
1School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA 6009 Australia
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James M Wainaina
1School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA 6009 Australia
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Tonny Kinene
1School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA 6009 Australia
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Stephen Lamb
1School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA 6009 Australia
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Myriam Rodrigues
1School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, WA 6009 Australia
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Monica A. Kehoe
3Crop Protection Branch, Department of Agriculture and Food Western Australia, South Perth, WA 6151, Australia
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Joseph Ndunguru
4Mikocheni Agricultural Research Institute (MARI), P.O. Box 6226, Dar es Salaam, Tanzania
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Fred Tairo
4Mikocheni Agricultural Research Institute (MARI), P.O. Box 6226, Dar es Salaam, Tanzania
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Peter Sseruwagi
4Mikocheni Agricultural Research Institute (MARI), P.O. Box 6226, Dar es Salaam, Tanzania
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Charles Kayuki
4Mikocheni Agricultural Research Institute (MARI), P.O. Box 6226, Dar es Salaam, Tanzania
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Deogratius Mark
4Mikocheni Agricultural Research Institute (MARI), P.O. Box 6226, Dar es Salaam, Tanzania
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Joel Erasto
4Mikocheni Agricultural Research Institute (MARI), P.O. Box 6226, Dar es Salaam, Tanzania
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Hilda Bachwenkizi
4Mikocheni Agricultural Research Institute (MARI), P.O. Box 6226, Dar es Salaam, Tanzania
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Titus Alicai
5National Crops Resources Research Institute (NaCRRI), P.O. Box 7084, Kampala, Uganda
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Geoffrey Okao-Okuja
5National Crops Resources Research Institute (NaCRRI), P.O. Box 7084, Kampala, Uganda
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Phillip Abidrabo
5National Crops Resources Research Institute (NaCRRI), P.O. Box 7084, Kampala, Uganda
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John Francis Osingada
5National Crops Resources Research Institute (NaCRRI), P.O. Box 7084, Kampala, Uganda
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Jimmy Akono
5National Crops Resources Research Institute (NaCRRI), P.O. Box 7084, Kampala, Uganda
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Elijah Ateka
6Jomo Kenyatta University of Agriculture and Technology (JKUAT), P.O. Box 62000 - 00200, Nairobi, Kenya
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Brenda Muga
6Jomo Kenyatta University of Agriculture and Technology (JKUAT), P.O. Box 62000 - 00200, Nairobi, Kenya
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Samuel Kiarie
6Jomo Kenyatta University of Agriculture and Technology (JKUAT), P.O. Box 62000 - 00200, Nairobi, Kenya
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Abstract

The United Nations has listed Zero Hunger as one of the 17 global sustainable development goals to end extreme poverty by 2030. Plant viruses are a major constraint to crop production globally causing an estimated $30 billion in damage 1 leaving millions of people food insecure 2. In Africa, agriculture employs up to 50% of the workforce, yet only contributes 15% to the GDP on average 3, suggesting that there is low productivity and limited value addition. This can be addressed through continued innovation in the fields of science and technology as suggested in the Science Agenda for Agriculture in Africa (S3A) 4. Sustainable management of plant viruses and their associated vectors must include efficient diagnostics for surveillance, detection and identification to inform disease management, including the development and strategic deployment of virus resistant varieties. To date, researchers have been utilizing conventional methods such as include; PCR, qPCR, high throughput sequencing (RNA-Seq, DNA-Seq) and Sanger sequencing for pathogen identification. However, these methods are both costly and time consuming, delaying timely control actions. The emergence of new tools for real-time diagnostics, such as the Oxford Nanopore MinION, have recently proven useful for early detection of Ebola 6 and Zika 7,8, even in low resourced laboratories. For the first time globally, the MinION portable pocket DNA sequencer was used to sequence whole plant virus genomes. We used this technology to identify the begomoviruses causing the devastating CMD which is ravaging smallholder farmers’ crops in sub-Saharan Africa. Cassava, a carbohydrate crop from which tapioca originates, is a major source of calories for over eight hundred (800) million people worldwide. With this technology, farmers struggling with diseased crops can take immediate, restorative action to improve their livelihoods based on information about the health of their plants, generated using a portable, real-time DNA sequencing device.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted May 04, 2018.
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Real time portable genome sequencing for global food security
Laura M. Boykin, Ammar Ghalab, Bruno Rossitto De Marchi, Anders Savill, James M Wainaina, Tonny Kinene, Stephen Lamb, Myriam Rodrigues, Monica A. Kehoe, Joseph Ndunguru, Fred Tairo, Peter Sseruwagi, Charles Kayuki, Deogratius Mark, Joel Erasto, Hilda Bachwenkizi, Titus Alicai, Geoffrey Okao-Okuja, Phillip Abidrabo, John Francis Osingada, Jimmy Akono, Elijah Ateka, Brenda Muga, Samuel Kiarie
bioRxiv 314526; doi: https://doi.org/10.1101/314526
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Real time portable genome sequencing for global food security
Laura M. Boykin, Ammar Ghalab, Bruno Rossitto De Marchi, Anders Savill, James M Wainaina, Tonny Kinene, Stephen Lamb, Myriam Rodrigues, Monica A. Kehoe, Joseph Ndunguru, Fred Tairo, Peter Sseruwagi, Charles Kayuki, Deogratius Mark, Joel Erasto, Hilda Bachwenkizi, Titus Alicai, Geoffrey Okao-Okuja, Phillip Abidrabo, John Francis Osingada, Jimmy Akono, Elijah Ateka, Brenda Muga, Samuel Kiarie
bioRxiv 314526; doi: https://doi.org/10.1101/314526

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