Cargando…

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

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 usin...

Descripción completa

Detalles Bibliográficos
Autores principales: Boykin, Laura M., Sseruwagi, Peter, Alicai, Titus, Ateka, Elijah, Mohammed, Ibrahim Umar, Stanton, Jo-Ann L., Kayuki, Charles, Mark, Deogratius, Fute, Tarcisius, Erasto, Joel, Bachwenkizi, Hilda, Muga, Brenda, Mumo, Naomi, Mwangi, Jenniffer, Abidrabo, Phillip, Okao-Okuja, Geoffrey, Omuut, Geresemu, Akol, Jacinta, Apio, Hellen B., Osingada, Francis, Kehoe, Monica A., Eccles, David, Savill, Anders, Lamb, Stephen, Kinene, Tonny, Rawle, Christopher B., Muralidhar, Abishek, Mayall, Kirsty, Tairo, Fred, Ndunguru, Joseph
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6769854/
https://www.ncbi.nlm.nih.gov/pubmed/31438604
http://dx.doi.org/10.3390/genes10090632
_version_ 1783455334520586240
author Boykin, Laura M.
Sseruwagi, Peter
Alicai, Titus
Ateka, Elijah
Mohammed, Ibrahim Umar
Stanton, Jo-Ann L.
Kayuki, Charles
Mark, Deogratius
Fute, Tarcisius
Erasto, Joel
Bachwenkizi, Hilda
Muga, Brenda
Mumo, Naomi
Mwangi, Jenniffer
Abidrabo, Phillip
Okao-Okuja, Geoffrey
Omuut, Geresemu
Akol, Jacinta
Apio, Hellen B.
Osingada, Francis
Kehoe, Monica A.
Eccles, David
Savill, Anders
Lamb, Stephen
Kinene, Tonny
Rawle, Christopher B.
Muralidhar, Abishek
Mayall, Kirsty
Tairo, Fred
Ndunguru, Joseph
author_facet Boykin, Laura M.
Sseruwagi, Peter
Alicai, Titus
Ateka, Elijah
Mohammed, Ibrahim Umar
Stanton, Jo-Ann L.
Kayuki, Charles
Mark, Deogratius
Fute, Tarcisius
Erasto, Joel
Bachwenkizi, Hilda
Muga, Brenda
Mumo, Naomi
Mwangi, Jenniffer
Abidrabo, Phillip
Okao-Okuja, Geoffrey
Omuut, Geresemu
Akol, Jacinta
Apio, Hellen B.
Osingada, Francis
Kehoe, Monica A.
Eccles, David
Savill, Anders
Lamb, Stephen
Kinene, Tonny
Rawle, Christopher B.
Muralidhar, Abishek
Mayall, Kirsty
Tairo, Fred
Ndunguru, Joseph
author_sort Boykin, Laura M.
collection PubMed
description 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.
format Online
Article
Text
id pubmed-6769854
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-67698542019-10-30 Tree Lab: Portable Genomics for Early Detection of Plant Viruses and Pests in Sub-Saharan Africa Boykin, Laura M. Sseruwagi, Peter Alicai, Titus Ateka, Elijah Mohammed, Ibrahim Umar Stanton, Jo-Ann L. Kayuki, Charles Mark, Deogratius Fute, Tarcisius Erasto, Joel Bachwenkizi, Hilda Muga, Brenda Mumo, Naomi Mwangi, Jenniffer Abidrabo, Phillip Okao-Okuja, Geoffrey Omuut, Geresemu Akol, Jacinta Apio, Hellen B. Osingada, Francis Kehoe, Monica A. Eccles, David Savill, Anders Lamb, Stephen Kinene, Tonny Rawle, Christopher B. Muralidhar, Abishek Mayall, Kirsty Tairo, Fred Ndunguru, Joseph Genes (Basel) Article 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. MDPI 2019-08-21 /pmc/articles/PMC6769854/ /pubmed/31438604 http://dx.doi.org/10.3390/genes10090632 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Boykin, Laura M.
Sseruwagi, Peter
Alicai, Titus
Ateka, Elijah
Mohammed, Ibrahim Umar
Stanton, Jo-Ann L.
Kayuki, Charles
Mark, Deogratius
Fute, Tarcisius
Erasto, Joel
Bachwenkizi, Hilda
Muga, Brenda
Mumo, Naomi
Mwangi, Jenniffer
Abidrabo, Phillip
Okao-Okuja, Geoffrey
Omuut, Geresemu
Akol, Jacinta
Apio, Hellen B.
Osingada, Francis
Kehoe, Monica A.
Eccles, David
Savill, Anders
Lamb, Stephen
Kinene, Tonny
Rawle, Christopher B.
Muralidhar, Abishek
Mayall, Kirsty
Tairo, Fred
Ndunguru, Joseph
Tree Lab: Portable Genomics for Early Detection of Plant Viruses and Pests in Sub-Saharan Africa
title Tree Lab: Portable Genomics for Early Detection of Plant Viruses and Pests in Sub-Saharan Africa
title_full Tree Lab: Portable Genomics for Early Detection of Plant Viruses and Pests in Sub-Saharan Africa
title_fullStr Tree Lab: Portable Genomics for Early Detection of Plant Viruses and Pests in Sub-Saharan Africa
title_full_unstemmed Tree Lab: Portable Genomics for Early Detection of Plant Viruses and Pests in Sub-Saharan Africa
title_short Tree Lab: Portable Genomics for Early Detection of Plant Viruses and Pests in Sub-Saharan Africa
title_sort tree lab: portable genomics for early detection of plant viruses and pests in sub-saharan africa
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6769854/
https://www.ncbi.nlm.nih.gov/pubmed/31438604
http://dx.doi.org/10.3390/genes10090632
work_keys_str_mv AT boykinlauram treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT sseruwagipeter treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT alicaititus treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT atekaelijah treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT mohammedibrahimumar treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT stantonjoannl treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT kayukicharles treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT markdeogratius treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT futetarcisius treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT erastojoel treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT bachwenkizihilda treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT mugabrenda treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT mumonaomi treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT mwangijenniffer treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT abidrabophillip treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT okaookujageoffrey treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT omuutgeresemu treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT akoljacinta treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT apiohellenb treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT osingadafrancis treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT kehoemonicaa treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT ecclesdavid treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT savillanders treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT lambstephen treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT kinenetonny treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT rawlechristopherb treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT muralidharabishek treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT mayallkirsty treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT tairofred treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica
AT ndungurujoseph treelabportablegenomicsforearlydetectionofplantvirusesandpestsinsubsaharanafrica