Real time portable genome sequencing for global food security

Abstract

Crop losses due to viral diseases and pests are major constraints on food security and income for millions of households in sub-Saharan Africa (SSA). Such losses can be reduced if plant diseases and pests are correctly diagnosed and identified early. Currently, accurate diagnosis for definitive identification of plant viruses and their vectors in SSA mostly relies on standard PCR and next generation sequencing technologies (NGS). However, it can take up to 6 months before results generated using these approaches are available. The long time taken to detect or identify viruses impedes quick, within-season decision-making necessary for early action, crop protection advice and disease control measures by farmers. This ultimately compounds the magnitude of crop losses and food shortages suffered by farmers. The MinION portable pocket DNA sequencer was used, to our knowledge globally for the first time, to sequence whole plant virus genomes. We used this technology to identify the begomoviruses causing the devastating cassava mosaic virus, which is ravaging smallholder farmers’ crops in sub-Saharan Africa.

Pathogen Detection and Microbiome Analysis of Infected Wheat Using a Portable DNA Sequencer

“…Nanopore metagenomics has great potential for quick diagnosis of suddenly emerging crop disease and large-scale disease monitoring at centralized agricultural institutions. As shown from other sequencing studies performed in a more extreme environment (Johnson et al 2017; Boykin et al 2018), all processes including DNA extraction and purification, library preparation and sequencing can be completed within a few hours. A tailored database can be created for each crop species containing the genomes of pathogens known to cause diseases to minimise processing time.…”

“…Because the MinION is a mobile technology independent of large sequencing facilities, it has been useful for on-site sample sequencing in extreme environments such as microbial paleo mats in the Antarctic (Johnson et al 2017). For rapid pathogen identification, studies have shown a turnaround time of six hours for bacterial from clinical samples with MinION (Charalampous et al 2018), and from seconds to up to four hours for detecting cassava virus in Africa (Boykin et al 2018) - both unachievable with previous technologies. For antibiotic resistance, Brinda et al (2018) reported their identification of known resistant bacterial strain within five minutes from real time MinION data.…”

A lab in the field: applications of real-time, in situ metagenomic sequencing

“…Co-occurrences between fungal and bacterial genera were also detected. Viral infectious diseases could be in situ monitored by using this technology, allowing rapid and improved response to outbreaks [ 66 ]. Other successful applications of ONT in the food industry included the characterization of the microbiome of a salmon ectoparasite ( Caligus rogercresseyi ), revealing its potential role as a reservoir for fish pathogens [ 67 ]; and the determination of the fish species present in complex mixtures, which would help to prevent—and rapidly detect—food fraud [ 68 ].…”

Draft genome assemblies using sequencing reads from Oxford Nanopore Technology and Illumina platforms for four species of North American killifish from the Fundulus genus

“…Small genomes from bacteria and viruses appear to be ideal for sequencing on the ONT MinION platform [12]. The portable nature of the technology makes it appealing as a resource for teaching [14,15], working in remote locations [16–18] and for investigating viral outbreak public health emergencies [19–21]. However, despite the demonstrated ability to achieve yields >6.5 Gb per flow cell [22], the MinION platform can be prohibitively expensive for sequencing larger eukaryotic genomes.…”