London Calling: Live first-time sequencing of the Fever Tree - the plant that some say has saved millions of lives from malaria
Today, the annual London Calling conference starts. 600 attendees from all over the world have converged on Old Billingsgate to discuss all things nanopore, to hear 87 speakers and read 81 posters – as well as great food and music. You can follow the action here on twitter and check back at nanoporetech.com/news for writeups and videos of the talks.
Each year, the Live Lounge at London Calling showcases Oxford Nanopore technology with live demos and hands-on workshops.
Live, real-time, first-time sequencing of the Fever Tree, with the Royal Botanic Gardens, Kew and collaborators
This year the PromethION 48 will be used to live-sequence the Fever Tree, Cinchona pubescens. The PromethION will sequence several hundred-fold depth of coverage of the genome, which is estimated to be 1.1Gb in size. The team will be generating several datasets and aiming for read N50s of 48kb. These long reads - that are uniquely provided at ultra-high yields by PromethION - will support the first assembly of this high-impact genome by The Cinchona genome project team (see below).
The Fever Tree (Cinchona) was discovered by native Americans in South America in the 16th century. The tree produces quinine, which was the only effective medicine against malaria used globally for several centuries and still remains an important anti-malarial drug today. Quinine and related alkaloids are known to be produced by many species in the genus Cinchona and its relatives in the Cinchoneae tribe of the coffee family Rubiaceae.
Considering this group’s high species diversity and wide distribution, the researchers want to settle one of the long standing questions in the use of traditional plant knowledge:
“Did the historical plant collectors succeed in locating the species with the highest concentrations of quinine, or are there still species to be discovered that produce more quinine or perhaps different alkaloids that are even more effective in treating malaria?”
More specifically, the researchers aim to use the sequence to:
- understand how the different species of Cinchona are related to each other, to aid the search for the best quinine-producing species
- discover the genes involved in the quinine biosynthetic pathway, to help researchers understand how the production of quinine and related alkaloids is regulated within and between species.
This project will revisit and settle one of the most compelling stories in the use of traditional plant knowledge and potentially provide new solutions to combat the malaria parasites’ resistance against current drugs.
The Cinchona genome project team includes:
- Royal Botanic Gardens, Kew
- Royal Holloway, University of London
- Natural History Museum of Denmark, University of Copenhagen
- Department of Pharmacy, University of Copenhagen
- National Herbarium of Bolivia
- University of Gothenburg