Research at the interface of evolution, informatics, and ecology
This is a tale of two small flowers. Arabidopsis thaliana and Arabidopsis lyrata ssp. petraea are small, flowering plants from the same genus. In many respects they're hard to tell apart - appearence, flowering times, location... like many, many other plant and fungal species across the world which need rapid, accurate identification to fight wildlife crime, discover new drugs and fight crop diseases.
It's not always easy to work out which species a plant belongs to just by looking at it. In fact few people could correctly identify all the species in their own gardens!
Being able to quickly identify species is critical for scientific research, conservation of biodiversity and fighting wildlife crime, for example. By sequencing an individuals genome (i.e., reading their DNA sequence) it's possible to determine which species it belongs.
Until now sequencing whole genomes has been slow, expensive and needed a laboratory with lots of specialised equipment.
In this film a team of scientists from the Royal Botanic Gardens, Kew travelled to Snowdonia National Park to try and sequence plant genomes in a tent. They took a MinION DNA sequencer which fits in a pocket and is made by UK-based Oxford Nanopore Technologies. To our knowledge this was the first time genomic sequencing of higher eukaryotes has been performed in the field.
Can the team, fighting against the weather, use minimal equipment and this exciting new technology to identify plants from their DNA alone?
Rapid - even instant - analyses of genetic material could overturn medicine, rare species discovery and export control. The coming ubiquity of both portable DNA sequencers and cloud computation mean scenarios formerly found in sci-fi films (instant DNA analysis) are coming, soon. We're developing methods to streamline DNA sequence analysis using cloud computation and other novel techniques.
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Often, waiting to get the sample from the field to the lab isn't practical. Some specimens decay too quickly, or can't be moved for legal reasons. DNA-based evidence might be needed on-site, to direct further research or arrest or release poachers. Finally, the best argument for developing portable sequencers is that more people, from more countries, can do more sequencing...
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The next wave of DNA sequencers, like the MinION, will be highly portable, compared to lab-bound models of the last decade. Even if we only attained comparable throughputs to current devices - certain to improve - the total volume of data generated will explode as the number of experimenters with easy access to sequencing leaps from thousands to millions; spanning academics, rangers, students, farmers, businesses and citizen scientists. Absorbing this data and putting it to work will be the defining challenge of the next decade in biology.
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A normal lab has thousands of pounds-worth of sophisticated machines, calibrated and installed in climate-controlled conditions and with plentiful power and chemicals. What happens when you try to shrink that into a tent? What can you omit, what compromises do you have to make?
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There's a big difference between a toy and a workhorse. How, in detail, would these sequencers perform compared to lab-based alternatives? We collected operational and performance data on both field-based MinION sequencers running R7.3 and brand-new R9 chemisty, versus MiSeq, using replicate split aliquots of field-collected and field-extracted DNA.
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Just collecting DNA letters on a screen wasn't good enough. We sequenced congeneric (closely-related) species with completed reference genomes to allow us to investigate the statistical performance of the field-based sequence ID in detail: true/false positive rates, power, etc.
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See Google Scholar for the most recent...We've just released our manuscript to bioarXiv:
Pipelines and analyses for this project are documented & versioned on GitHub.
Sequencing / basecalling
Data wrangling / mapping / ID
As much of our work as possible, including data, will soon be available in the public realm. We're a public-funded scientists and advocates of Open Data and Reproducible Research. If you want workflow scripts and software please email and we'll try to help where we can.
At present one machine image is available, from the pilot 'lightweight bioinformatics' project. Search AWS AMIs for 'ami-90296be7'.
We are currently employed in the Biodiversity Informatics & Spatial Analysis, and Conservation Biology departments of the Science Directorate at the Royal Botanic Gardens, Kew in London.
Current collaborators include:
So the site you see is generated simply from a (largely) static HTML file with a couple of bits of PHP pulling in Wordpress posts to populate the blog and publications. Parallax effects use Aen Tan's Parallax-Scroll code and I figured out the integration with Bootstrap (actually pretty simple) with a lot of help from this tutorial. The whole site probably took less than 20 hours to put together including design, parsing WP, and deployment and testing - I think that's pretty good, on balance.
Tag this project with #realtimephylogenomics! More about us, too - members:
I currently hold an Early-Career Research Fellowship in Phylogenomics at the Royal Botanic Gardens, Kew. This post allows me wide freedom pursue my research into real-time phylogenomics, field-based DNA sequencing for turbotaxonomy and metagenomics, and integrated alignment & phylogeny models of molecular evolution.
I also lead the Informatics workpackage for the Plant & Fungal Trees Of Life project, a Kew-led initiative to reconstruct a genus-level supertree for 80% of all plant and fungal genera by 2020.
My role is to use genetic techniques to understand and conserve plant diversity. My research combines population genetics/genomics with ecological analyses and experiments to study adaptation and speciation. I am interested in how organisms adapt to their environment, the influence this can have on the evolution of reproductive isolation and the extent to which this can be a predictable and repeatable process. I am particularly interested in the evolution and conservation of island plants and divergence in the face of continuing gene flow.
I use a variety of approaches and study groups to understand the evolutionary origins of diversity. My research typically revolves around phylogenetics, population genetics and genomics but also delves into modelling species distributions and examining patterns of growth and development.
I am responsible for managing the RBG Kew molecular biology and genetics laboratory facilities. We undertake a range of highly-specialised techniques, including DNA extraction, plant and fungal Sanger sequencing, next generation sequencing (MiSeq) and population-genetics (DNA micro-satellites and Amplified Fragment Length Polymorphisms). We train and supervise staff, students and visiting researchers, and support Royal Botanic Gardens Kew science projects, by providing experimental design, project management, troubleshooting and costing for grant submissions. I also work closely with the Kew Innovation Unit to undertake ethical commercial activities and am leading the development of novel techniques to further expand Kew’s fundraising capabilities.