We are gearing up for the trip! Before Laura heads to Tanzania and Uganda (1-13 September 2017) the team at UWA is testing kits and protocols. In addition, Anders has been working very hard to get all the necessary software installed on the MacPro at MARI in Tanzania and Laura’s laptop- which might be used in Uganda. The teams in Tanzania and Uganda are also preparing the labs to ensure we have everything we need to trial the technology.
The plan for our nanopore expedition: Visit smallholder farmers in Tanzania and Uganda and identify the cassava diseases and cassava whitefly devastating their production (near real-time!) Why? The quicker we can tell farmers the fields/material are infected (with the added bonus of genomic data to characterize diversity and fine scale changes in the viruses), the quicker farmers can take action. For example, the farmer might be advised to clear infected cassava and plant replacement clean cassava (virus-free) provided by MARI or NaCRRI- this quick replacement ensures food security. To do this, we are going to test material that is showing symptoms of infection by collecting both suspected CMD infected leaf tissue and the whiteflies feeding on infected plants, take samples back to the lab and do DNA extractions then 1) metagenomic run on nanopore and 2) PCR of CMD & mtCOI of whiteflies and run PCR products on nanopore.
The kits we are planning to use: Rapid Barcoding Sequencing (SQK-RBK001) and Rapid Low Input by PCR Barcoding (SQK-RLB001).
The software we are planing to use: MinKNOW, (MinION software) Albacore (local basecalling) and Geneious. We have reference datasets for the whitefly mtCOI and also CMD strains. Update: we are going to try and use minimap2 because Geneious is not good at mapping nanopore data.
Shipping: Huge shout-out to the entire team at Oxford Nanopore for working tirelessly to have ALL the supplies we need for this upcoming trip sent directly to Charles and Fred at MARI in Tanzania. Also, NEB & Inqaba huge shout out to you all too! Enzymes being sent straight to MARI in TZ. Our goal is to not hand carry things – we want this to be a sustainable solution for the teams in East Africa.