Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.
Upcoming SlideShare
DNA translocation through a nanopore
Next
Download to read offline and view in fullscreen.

Share

Single-molecule real-time (SMRT) Nanopore sequencing for Plant Pathology applications

Download to read offline

A short presentation to the British Society for Plant Pathology's 'Grand Challenges in Plant Pathology' workshop on the uses of real-time DNA/RNA sequencing technology for plant health applications.

Doctoral Training Centre, University of Oxford, 14th September 2016.

Related Books

Free with a 30 day trial from Scribd

See all
  • Be the first to like this

Single-molecule real-time (SMRT) Nanopore sequencing for Plant Pathology applications

  1. 1. Single-molecule real-time (SMRT) Nanopore sequencing for Plant Pathology applications Joe Parker Early-career Research Fellow (Phylogenomics), Royal Botanic Gardens, Kew Skype, Twitter, Github: @lonelyjoeparker Email: joe.parker@kew.org
  2. 2. SMRT / Nanopore sequencing for Plant Pathology Topics: • What is it? • Unique capabilities • Current work • Plant health applications
  3. 3. What is Nanopore sequencing?
  4. 4. Unique capabilities • Portable • Real-time (~minutes) • DNA and RNA • Selective (‘read-until’) sequencing • Very long reads • Flexible / scalable
  5. 5. Real projects (i) Real-time, portable sequencing for ebolavirus (EBV) surveillance, 2015 (Guinea) Local sequencing in primary care, limitations on: • facilities, • internet bandwidth, • computation Data uploaded for further analysis worldwide Sampling-to-answer in ~days Phylogeography, demography and evolution of EBV monitored in real- time Quick et al. (2016) http://dx.doi.org/10.1038/natu re16996
  6. 6. Real projects (ii) Field-based genomics for plants: a) Unsupported sequencing and real- time identification of Arabidopsis spp. in Snowdonia  Complete leaf-to-analysis workflow in the field  Field-sequenced data comparable to lab b) Real-time identification of randomised samples  Six diverse plant species randomised and sequenced in tent at Kew Science Festival  Identification < 1hour  Minimal reference needed Papadopulos & Parker (in prep.)
  7. 7. Real projects (iii) Real-time selective sequencing on nanopore technology • Proportion of desired sequences from WGS is low • SMRT is a real-time platform, why not pick and choose individual DNA molecules? • Phage lambda regions selectively sequenced with software-based method • Any region could be selected for resequencing, and alterations to protocol made during a run Loose et al. (2016) http://dx.doi.org/10.1038/nmet h.3930
  8. 8. Real projects (iv) RNA sequencing: -RNA sequenced directly from sample -Stochiometric / quantitative -Tested on E.coli Major implications for transcriptomics, RNA virus detection Garalde et al. (submitted) http://dx.doi.org/10.1101/0688 09
  9. 9. GCPP Applications • Cryptic parasite / pathogen spp. discovery • Real-time monitoring of plant health • Import / export sequencing
  10. 10. Thanks Collaborators / funders: – Kew Foundation Pilot Study Fund – Drs. Dion Devey, Andrew Helmstetter, Alexander S.T. Papadopulos – Oxford Nanopore Technologies – Snowdonia NPA – Natural Resources Wales Contact: Skype, Twitter, Github: @lonelyjoeparker Email: joe.parker@kew.org

A short presentation to the British Society for Plant Pathology's 'Grand Challenges in Plant Pathology' workshop on the uses of real-time DNA/RNA sequencing technology for plant health applications. Doctoral Training Centre, University of Oxford, 14th September 2016.

Views

Total views

947

On Slideshare

0

From embeds

0

Number of embeds

192

Actions

Downloads

22

Shares

0

Comments

0

Likes

0

×