Job offersmore »

Tweeting Growers

Top 5 - yesterday

Top 5 - last week

Top 5 - last month

Exchange ratesmore »

New record in lettuce nanopore sequencing

This week KeyGene researchers generated 76 gigabases of DNA sequence of a lettuce (Lactuca sativa) genome with a single Oxford Nanopore Technologies (ONT) PromethION flow cell. This is a new record in the plant genome sequencing area for long reads. As the PromethION has the capacity to run 48 such flow cells, large-scale de novo whole genome sequencing will soon be feasible. KeyGene expects that PromethION’s long reads and low costs per base will disrupt the current sequencing field, accelerating crop innovation.

The nanopore sequencing of the lettuce genome was completed for KeyGene’s partners Rijk Zwaan, Enza Zaden, Limagrain Vegetable Seeds and Takii & Co, which use the genome sequence to support the development of new varieties. Lettuce is an important vegetable crop with a complex genome of approximately 2.7 gigabase pairs (Gbp). The output of 76 gigabases generated by KeyGene with a single PromethION flow cell thus represents approximately 30-fold genome coverage. The N50 reads lengths were 29 kb with a fair amount of reads longer than 100 kb. With these very long DNA sequences the assembly of complex genomes becomes much easier.

Since its introduction in 2014, KeyGene used ONT’s MinION to sequence plant pathogens, BACs and amplicons. PromethION and GridION now open up the way to large scale whole genome sequencing of complex crops like lettuce and others.

Michiel van Eijk, Chief Scientific Officer of KeyGene states: “The record sequence output is due to recent improvements from Oxford Nanopore Technologies, as well as advances made by KeyGene in high-molecular weight DNA isolation and sample preparation. We are excited about our ability to sequence truly complex plant genomes with ONT’s platforms in just a few days. De novo whole genome sequencing will be the standard going forward.”

Clive G. Brown, Chief Technology Officer of Oxford Nanopore adds: “Congratulations to KeyGene for achieving this result on a single PromethION Flow Cell, and the work that KeyGene has been doing on plant DNA extraction and preparation to enable these results.  Internally we have recently been achieving more than 150Gb per PromethION Flow Cell, so we are excited about the pathway to even more nanopore data for our customers.”

For more information:
KeyGene Netherlands
Agro Business Park 90
6708 PW Wageningen
The Netherlands

P.O. Box 216
6700 AE Wageningen
The Netherlands
T +31 (0)317 466 866
F +31 (0)317 424 939

Publication date: 2/23/2018



Other news in this sector:

3/20/2018 Italy: Three new basil varieties
3/19/2018 US (WA): Plant researcher’s work helps lucrative spinach seed industry
3/16/2018 France: Innovations in seeds production
3/16/2018 US (PA): Penn State-bred grape tomato becomes commercially available
3/15/2018 New Zealand: Māori-owned company to breed unique berries
3/15/2018 International breeders learn latest watermelon grafting techniques
3/14/2018 Interesting hybrids
3/13/2018 "Stronger partnerships can catalyze African vegetable markets"
3/12/2018 Tanzania: hybridizing the vegetable farming sector
3/9/2018 Labour costs of concern to Spanish growers
3/9/2018 Seeding a sustainable future for American agriculture
3/9/2018 "Protecting genetic diversity essential for future of food security"
3/7/2018 The impact of genetic changes on healthy food development
3/6/2018 US (IA): How birds help to produce rare wild chili peppers
3/6/2018 India: CIOPORA puts forward “different-rules-for-different-crops” proposal
3/6/2018 South Africa: Margaret Roberts honored with seed bank
3/5/2018 Pink vegetables are new Social Media hype
3/5/2018 US: Regulatory barriers to biotechnology development
3/2/2018 "National Plant Germplasm System critical for plant breeding"
3/1/2018 Brazil: Genome editing capabilities to modernize crop improvement